Messages

106

General Questions and Answers / Can a numerical data of transmission spectrum in a VNL file be extracted?

« on: July 6, 2009, 06:11 »

Dear Everyone,

I'd like to know whether or not a numerical data of transmission spectrum in a VNL file can be extracted with NanoLanguage.
In other words, Can one also access data stored in VNL file other than "atomic configuration" with NanoLanguage?
I tried to do it, but I couldn't.
Can anybody help me?

Thanks in advance.

107

General Questions and Answers / Re: how to get the table?

« on: June 19, 2009, 08:33 »

Dear yangzw1985,

>In order to understand the table, I have try to calculate the transmission eigenstates and
>transmission eigenvalues of my two probe model,

You're right.
"Eigenchannel" in the paper is equivalent to "transmission eigenstates" in ATK.
Also, the value of channel X in the table 2 is equivalent to "transmission eigenvalue" in ATK.
For instance, the coefficient of 1st channel of <100> at Fermi energy is 0.01*0.76= 0.0076.


>but the results are not like this.

What do you mean about it?
Have you tried to calculate completely the same system as one in the paper ?
Or have you done similar calculation but not for the same system in the paper?


>In table 2, they also calculate the percentage probability of transmission, in my opinion, one channel should have a value,
>the wire should have lots of channels, so we can calculate the percentage. I don't know what I have said is right or not?

You're right.
Maybe more correctly, the 2probe system has several transmission channels at each energies,
so we can calculate the percentage of each channels against total transmission(= sum of transmission eigenvalue) at some energy.


>Can anyone tell me  how to distinguish the channel 1, channel 2 and channel 3.......?
>In other words, if I want to obtain the table, what should I do?

You should do the calculation of transmission eigenvalues at Fermi energy.
http://www.quantumwise.com/documents/manuals/ATK-2008.10/ref.calculatetransmissioneigenvalues.html

108

General Questions and Answers / Re: why?

« on: June 4, 2009, 11:20 »

Was SCF calculation converged at reasonable state?
It seems that electrons in central region disappear...

109

General Questions and Answers / Re: Reflection coefficient

« on: May 13, 2009, 10:07 »

I'm not sure but if the electrodes are homogeneous, Γ_L = Γ_R is approved.
It means that obviously reflection coefficient is NOT Tr(Γ_L*G^R*Γ_L*G^A).

110

General Questions and Answers / Re: What's the physical insight of the variation of HOMO and LUMO with bias voltage?

« on: May 13, 2009, 09:39 »

Dear fan0221,

One of the main reason is the potential shift due to applied bias voltage.
However, there is another factor to get MPSH spectrum changed, which is non-equilibrium density matrix.

In your case from Vb = 0V to Vb = 1V, HOMO and LUMO shift are almost the same because only the potential shift seem to affect the spectrum shift.
But above Vb = 1V, the electric structure gets drastically changed because LUMO is included in non-equilibrium density matrix,
 so that the spectrum shift get more complex.

It is the general suggestion, so the detailed analysis for your specific system is needed to understand more precisely why the spectrum get such a change under finite bias.

I'd be happy if my advice can help you.

111

Scripts, Tutorials and Applications / Re: Script for calculating the voltage drop.

« on: April 15, 2009, 02:30 »

Yes, the Li-H2-Li is symmetric, and so should the voltage drop be, but it is a matter of convergence, if the tolerance is low!

It seems there is no need for this system to have the symmetric voltage drop under finite bias.
Because the non-equilibrium part of the electron density exists.

I'll give you the example with attached, which is the voltage drop of au111_vacuum_au111 system.
The structure has symmetry but the voltage drop does not.
You can understand that It's reasonable with the following reasons:

# As regards left electrode part, any incident electron can't be transmitted from right to left due to vacuum region, so that the electric structure does not change compared with equilibrium and the potential gets flat-shift.
# As regards right electrode part, all incident electrons are perfectly reflected , so that the electric structure changes compared with equilibrium and the potential gets more complex.

That's why the voltage drop Norland offered has no matter.

112

General Questions and Answers / Re: Questions about conductance of nanowire

« on: March 26, 2009, 10:24 »

Dear chp,

The electric structure you got is apparently unphysical because there are excessively 33 electrons in central region and the transmission is not ballistic.

I calculated SCF and the transmission with some different parameters you had and the reasonable result was obtained.
Please check attached.

113

General Questions and Answers / Re: Error about runtime_parameters

« on: March 17, 2009, 09:14 »

Dear phylyh,

I might be able to help you because I'd studied almost the same system as you with ATK.
(please see "fig.pdf", I feel it's miracle!)

When I tried the calculation for such a system, I encounterd the same trouble as you.
Judging from a conclusion, the solution is not to use "DobuleZeta" or "DobuleZetaPolarized" basis.
I don't know why, but when I used DZ or DZP in this system, SCF convergence got suddenly worse.
On the other hand, when I used SZP for both "C" and "Fe", the calculation was normally completed
(Parhaps SZ for both "C" and "Fe" is also good).

In addition, "Initial scaled spin" you designate is not good because (5,5)CNT is not spin-polarized.
("Initial scaled spin" is relevant to SCF convegence in some cases)
It seems natural that "Initial scaled spin" for Fe is 1 and "Initial scaled spin" for C is 0.

I attach the modified version of script(input2.py).
I only changed the "Initial scaled spin" for both central region and electrode in "input2.py".
I recommend the further modifications as follows:
1. k-point sampling for C-direction: from 500 to 100,
2. basis set for Fe: from DZP to SZP or SZ,
3. initial_density_type: from InitialDensityType.NeutralAtom to InitialDensityType.EquivalentBulk,
and if you're interested in finite-bias calculation,
4. electrode_constraint: from electrodeConstraints.Off to electrodeConstraints.RealSpaceDensity or electrodeConstraints.DensityMatrix.

I hope your calculations are done well!

114

Scripts, Tutorials and Applications / Re: Script for making data files to plot k-resolved transmission with gnuplot

« on: March 10, 2009, 04:18 »

Dear M.Albert,

It might not be easy to take advantage of k-resolved transmission in order to investigate physical(transport) properties in the system,
but in some cases it's useful.

The system "fe/mgo/fe" is a perfect example.
If spin-configuration between electrodes is parallel, k-resolved transmission at fermi-level is like "fe_mgo_fe.png".
In "fe_mgo_fe.png", you can understand following things:
1. The nature of majority transmission is "Tunneling", because maximum value exists at gamma-point and transmission gets monotone decreasing when (kx, ky) gets larger.
(As Nordland mentioned above)
2. The nature of minority transmission is "Resonant Scattering" through interface state(s) between Fe and MgO, because there are some sharp peak away from gamma-point.

In addition, the nature of majority/minority transmission at fermi-level in the case of anti-parallel spin-configuration  is also "Resonant Scattering".
(Please see "femgo_antipara_trans_up.png" offerd by Anders)

These facts are very important for understanding TMR properties in the system "fe/mgo/fe".
For instance, if some adittional layers are inserted between Fe and MgO interface, It is expected that TMR ratio gets better.
Because interface states that contribute to "minority transmission in parallel" and "majority/minority transmission in anti-parallel" are broken by inserting addional layers, the conductances get dramatically decreasing while "majority transmission in parallel" gets little influence.
(Please refer to "Phys. Rev. B 72, 140404 (2005)" for more information)

115

General Questions and Answers / Re: the error about the IterationControlParameters.DensityMatrix

« on: March 6, 2009, 03:25 »

Dear anyipeng,

Please fix the input of parameter "quantity" from "IterationControl.DensityMatrix" to "IterationMixing.DensityMatrix".
Then, Probably you can execute the script normally.

116

General Questions and Answers / Re: Is ZnO nanowire a metal?

« on: February 24, 2009, 03:28 »

Hi Nordland,

I appreciate your proffesional advice!
It really helps me a lot!!

Size dependence of ZnO nanowire seems very interesting.
I'll go ahead further calculation for ZnO nanowire

117

General Questions and Answers / Is ZnO nanowire a metal?

« on: February 23, 2009, 07:54 »

Dear everyone,

I've tried the calculations of ZnO nanowire as bulk system and obtained the results that ZnO nanowire is a metal(zno_nanowire_7_band.vnl).

As you know, ZnO crystal  is a semi-conductor, so I suspect that my calculation might be wrong.
("zno_nanowire_7.py" is the script used for the calculation and  "zno_nanowire_7.out" is the log.)

My questions are as follows:
1. which property should ZnO nanowire has, metal or semi-conductor?
2. If the latter is right, that means my calculation is wrong, which part of it is wrong?(input structure?, parameter setting?)

I'd be happy to get any comments about it.
Thanks in advance!

118

Scripts, Tutorials and Applications / Re: Script for calculating the voltage drop.

« on: February 10, 2009, 01:40 »

I offer some calculation examples of voltage drop.
All calculations were done with the algorithm "ElectrodeConstraints.DensityMatrix".

As Nordland mentioned above, "ElectrodeConstraints.DensityMatrix" instead of "ElectrodeConstraints.Off" should be used when you calculate the voltage drop.
But in some cases such as "Au-DTB-Au", you might get less convergence of SCF with "ElectrodeConstraints.DensityMatrix" (More correctly, the electronic structure that seems to be strange is obtained).
Then, you had better use "ElectrodeConstraints.RealSpaceDensity" instead of "ElectrodeConstraints.DensityMatrix".

119

Scripts, Tutorials and Applications / Re: Script for making data files to plot k-resolved transmission with gnuplot

« on: February 5, 2009, 01:04 »

Hi ugglebot,

"pm3d" is used to plot "fe_mgo_fe_parallel_0eV.GIF".
So, If you get the error after executing command "set pm3d", please install the latest version of Gnuplot.

In the following, I show the commands:
gnuplot> set pm3d
gnuplot> set ticslevel 0
gnuplot> splot ‘xxxx.dat’ w pm3d

If you want 2D plot like "2d_plot.GIF", please input the commands as follows:
gnuplot> set pm3d map
gnuplot> set size square
gnuplot> splot ‘xxxx.dat’

120

Scripts, Tutorials and Applications / Script for making data files to plot k-resolved transmission with gnuplot

« on: February 4, 2009, 07:51 »

Dear all,

I'd like to share the script for calculating k-resolved transmission coefficients and making data files to plot them with gnuplot.

Converged 2probe NetCDF file is needed in order to use it.
In addition, you have to set three parameters in the script:
-line 16, NetCDF file name
-line 20, the number of k points
-line 23, the energy for which the transmission coefficients are to be calculated

Usage:
1. execute SCF calculation for your interesting system and save the result in NetCDF file
2. store "k_resolved_transmission.py" and the ncfile in the same directory
3. set-up three parameters mentioned above
4. execute "k_resolved_transmission.py"

After the task 4, you can get "xxxx.dat" for plotting.
(If the system is spin-polarized, "xxxx_up.dat" and "xxxx_dn.dat" are output.)

If you apply "k_resolved_transmission.py" to the system fe/mgo/fe (fe_mgo_fe.png),
you can obtain the picture like "fe_mgo_fe_parallel_0eV.GIF".