Messages

76

Scripts, Tutorials and Applications / sp3-passivation with H for bare Si nanorod

« on: August 25, 2010, 04:31 »

Dear Everyone,

I made a script for passivating dangling bonds of bare Si nanorod with Hydrogen and share it with you.
(passivate_sp3.py)
The usage is as follows:
1. Open Custom Builder and drop "passivate_sp3.py" onto the Custom Builder window.
2. make a structure of bare Si nanorod like "sinr110_bare.py" using Builder, Database, and Custom Builder.
3. drop the script of bare Si nanorod onto "Drop unpassivated system here" in the Custom Builder window.

After step 3, you can obtain sp3-passivated Si nanorod like "sinr110_passivated.png".

This script is still prototype and any kinds of feedback is appreciated

77

General Questions and Answers / Re: some questions about the pseudopotential

« on: June 24, 2010, 03:45 »

I re-calculated a spin polarization of Cr with ATK 10.8b and obtaind [tex]\pm 0.82  \mu_{\rm B}[/tex] at each Cr, which is very reasonable result.
I don't know why but ATK 10.8b is more accurate than ATK 2008.10

78

General Questions and Answers / Re: some questions about the pseudopotential

« on: June 2, 2010, 04:10 »

It's difficult to answer your question assertively　but I feel the pseudopotential of VASP is better than one of ATK at least for Cr.
As you know, The ground state of Cr crystal is anti-ferromagnetic.
In my calculation with ATK, each Cr element in unit-cell has 4 [tex]\mu_{\rm B}[/tex] or -4 [tex]\mu_{\rm B}[/tex] magnetic moment, that is unphysical result.
On the other hand, in the calculation with VASP, each Cr element in unit-cell has 1 [tex]\mu_{\rm B}[/tex] or -1 [tex]\mu_{\rm B}[/tex] magnetic moment, that is reasonable result.

79

Gallery / Re: Voltage drop calculated with ATK-SE 2010.02

« on: May 16, 2010, 12:41 »

Thank you for your comment 

I used VNL 2010.02 for the left side of the pictures and Excel for the right side of the pictures.

80

Gallery / Re: Voltage drop calculated with ATK-SE 2010.02

« on: April 26, 2010, 02:15 »

Another one is here.
Besides it, you can find the beautiful voltage drop at http://arxiv.org/abs/1004.2812.

81

Gallery / Voltage drop calculated with ATK-SE 2010.02

« on: April 26, 2010, 02:14 »

I give the examples of voltage drop calculated with ATK-SE 2010.02 in this thread.
As you know, how to calculate Hartree potential is changed in new ATK (since 2009.06),
where Hartree potential is calculated against only central region, while in ATK 2008.10 it is calculated against whole system(left electrode + central region + right electrode).

This change bring mainly two benefits as follows:
1. New method makes SCF convergence more stable,
2. more reliable voltage drop can be obtained.

"more reliable" means that voltage drop mainly occurs around high resistance region like molecule, insulator, interface, and so-on, and is smoothly connected to reservoirs.

82

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

« on: April 23, 2010, 03:02 »

I regard your voltage drop as qualitatively the same as mine.
Perhaps the quantitative difference comes from k-point sampling.
I couldn't find out the script used for the calculation in my hard disc, so that I'm not sure precise k-point sampling in my calculation.
However, it would probably not be (10,10,10) but like (6,6,100).
  

83

General Questions and Answers / Re: what's happen when I compute the voltage drop?

« on: April 20, 2010, 08:15 »

Please note that it is very difficult to judge whether a calculated voltage drop is CORRECT.
But I feel your latest one is the most reasonable because there is no dip at the interface between central region and right electrode and no dipole-like potential is induced.

I guess any more improvement can't be achieved with 2008.10 unless the bias voltage is decreased.
Possibly the new algorithm of 2010.02 can make it better.

84

General Questions and Answers / Re: what's happen when I compute the voltage drop?

« on: April 17, 2010, 17:38 »

Another possible reason is that you choose multi-grid solver.
If my memory is right, strange voltage drop is obtained with multi-grid solver of 2008.10 in some 2probe systems.

Could you try the scripts attached in this post?
With these scripts, calculations with "ElectrodeConstraints.DensityMatrix" and FFT solver are executed.

85

General Questions and Answers / Re: what's happen when I compute the voltage drop?

« on: April 17, 2010, 17:19 »

and I am so sorry that I can't find the best choice you said " "ElectrodeConstraints.DensityMatrix"

You can't select "ElectrodeConstraints.DensityMatrix" in NanoLanguage Scripter and you have to modify the script by hand.

86

General Questions and Answers / Re: what's happen when I compute the voltage drop?

« on: April 17, 2010, 17:01 »

The bug is fixed in 2008.10 so you should always use 2008.10.
But unfortunately, "VNL2008.10.png" is also strange because voltage drop should occur mainly around H2...
Have you changed the ElectrodeConstraint?
It seems that "ElectrodeConstraints.RealSpaceDensity" is still selected in "VNL2008.10.png"...

87

General Questions and Answers / Re: what's happen when I compute the voltage drop?

« on: April 17, 2010, 16:01 »

The above are all performed in VNL 2008.10, and I also test the same script above ( lisufficen1v.py lisufficen0v.py) in VNL 2008.02

and I get the difference image and output as below!?

There is the bug in VNL 2008.02 which some physical properties such as Effective potential don't be calculated properly when you use a density matrix stored in NetCDF file.

As regards your latest example, the electrode size is too small as Anders mentioned above and you have to use the electrode that includes more than 4 atoms in the unit cell.
Besides it, if you use "ElectrodeConstraints.RealSpaceDensity", the coordinates of electrodes should be centered.

I guess that "ElectrodeConstraints.DensityMatrix" is the best choice for you system and recommend you to try it.

88

Scripts, Tutorials and Applications / Re: error with plot the I-V

« on: April 14, 2010, 09:41 »

Have you investigated the transmission spectra at each bias?
I guess some negative transmission coefficients are included in integral range of current calculation.

89

General Questions and Answers / Re: Possible Bug in the code: dips in the transmittance

« on: April 2, 2010, 02:12 »

I did transmission calculation of (5,5) CNT with "55cnt_l14_2_dzp_rsd.py" and there is no dip in my transmission spectrum.
So I guess ATK 2008.10 is able to treat (5,5) CNT properly and your calculation is something wrong.
(I'm not sure the exact reason why such dips appear in your calculation though...)

If you get the correct answer about this issue, you should give us the NanoLanguage script used for the calculation.

90

Scripts, Tutorials and Applications / Re: An Error for calculating the current of LiH2 chain

« on: March 28, 2010, 12:10 »

The space key between "Transmission" and "Spectrum" isn't needed.
So, you should write "transmission_spectrum = nlread("LiH2.nc",TransmissionSpectrum)[0]".

bad: transmission_spectrum = nlread("LiH2.nc",Transmission Spectrum)[0]
right: transmission_spectrum = nlread("LiH2.nc",TransmissionSpectrum)[0]