Messages

1

General Questions and Answers / Re: Inconsistency in CalculateCurrent for different number of integration points

« on: March 19, 2009, 23:25 »

Nordland,

You've been a tremendous help. I will keep you posted on some of the results I get with added screening layers and new spectrums, etc. I'll also look into using version 10.

Best Regards,

Chris

2

General Questions and Answers / Re: Inconsistency in CalculateCurrent for different number of integration points

« on: March 19, 2009, 21:53 »

Nordland,

My overall objective is to find qualitative differences in the tunneling current for different types of DNA molecules placed above the GNR. I agree the current is small at 10-9 A but this is significantly larger than the current across the GNR without a molecule, 10^-14. Some ways I could increase the current further (keeping bias constant)  are to move the molecule closer to the ribbon and also to place the molecule over the edge since this is where the conduction in the ribbon occurs.

In the present system, regarding calculations at higher voltages. I'm guessing my choice of higher voltage should depend on the peaks and profile in the Transmission Spectrum. For example, if I see a peak at energy 4.1 eV, I'm guessing I should I run a calculation at bias 4.1V?

Regarding electrodes and screening layers: I'll follow your advice and recalculate at low bias and high bias to see if I can find any differences. I don't have version .10 yet, but I'll  see if I can get it installed on our cluster.

Thanks again and I appreciate your helpful comments.

chris

3

General Questions and Answers / Re: Inconsistency in CalculateCurrent for different number of integration points

« on: March 19, 2009, 17:09 »

Nordland,

Thanks for your comments regarding resolution and integration of T(E) to get the current. Before it seemed like guesswork. Now I have a systematic way to approach the subject. Having said that, I integrated the current at .9V using 9000 points and unfortuanately the order of magnitude did not change. At 1000 points, I = 2.2E-10. At 9000 points, I=5.9E-10.

The current for this system starts to saturate near .3V but is pretty monotonic and at least of the same order of magnitude through .8V. But at .9V and 1.0V, there is a huge drop in current. You mentioned the possibility of artificial scattering at higher bias. Can this be fixed by increasing the size of the electrode cell and/or increasing the screening layers in the central region or are things sufficient as is? I'd like to avoid adding atoms which as you know will increase calculation time.

Also, you mentioned the high bias Transmission spectrum should be no different than the low bias Transmission spectrum. I will look at the spectrums at higher bias and compare with the same at lower bias. If there are noticeable differences, which might explain the huge drop in current at .9V and 1.0V, could I assume that such differences are due to artificial scattering?

Chris

4

General Questions and Answers / Re: Inconsistency in CalculateCurrent for different number of integration points

« on: March 19, 2009, 00:48 »

Great!

To respond to Nordland's comments on the number of points and resolution of the transmission spectrum:

The two transmission plots contain 200 points between -.5eV and .5 eV and again 200 points between -5 eV and 5eV. I'll recalculated using the prescribed rules for resolution and integration at various bias.

Thanks,

chris

5

General Questions and Answers / Re: Inconsistency in CalculateCurrent for different number of integration points

« on: March 18, 2009, 23:49 »

Great! Thanks. All images are in .png format.

Attached are configuration files and one bias transmission spectrums.
The configuration consists of two zigzag edge GNR electrodes with a 5 angstrom vacuum gap in the middle. About 2.3 angstroms above the plane of the ribbon is a DNA molecule. I should mention that without the molecule, the current across the gap is on the order of 10^-14...which is much smaller than the previously reported currents with the molecule.

Hopefully this clears up some of previously raised issues..

Thanks again for your input,

Chris

6

General Questions and Answers / Inconsistency in CalculateCurrent for different number of integration points

« on: March 18, 2009, 18:07 »

Hi,

I'm calculating current for a two probe system with graphene nano-ribbon electrodes.

I have converged sc files at .1V,.2V,.3V,.4V,.5V,.6V,.7V,.8V,.9V,1.0V.

At each bias, I have been calculating current using a different number of integration points over the energy. The default number of points is 100 and I also calculated current for 200, 400, 600, 800, and 1000 points as a check for consistency.

At lower bias, there is consistency across current calculations for different number of energy points. At higher bias, I'm getting some inconsistency. For example, at .8V I'm getting the following currents for different number of energy points:

100 Points
2.70322906734e-08 A

200 Points
6.15809652354e-09 A

400 Points
2.0376602094e-08 A

600 Points
2.67889424829e-08 A

800 Points
1.86633465855e-08 A

1000 Points
1.57990714177e-08 A


Furthermore, at a bias of .9V the currents have dropped a whole two orders of magnitude compared to .8V as seen from this data below:

100 Points
3.93849284671e-11 A

200 Points
3.90495735902e-10 A

400 Points
1.24586672635e-10 A

600 Points
2.48097024468e-10 A

800 Points
1.6369171909e-10 A

1000 Points
2.21587823888e-10 A

For lower bias up until a bias of .5V the I-V curve was monotonic increasing and there was more consistency in currents at a single bias. Clearly, at .9V the currents have dropped and are also inconsistent with the number of points.

Is there some explanation for this behavior? In another post, I recall reading that artificial scattering could occur if the electrode cell is not long enough in the z direction. Could artificial scattering be happening here at higher bias levels and not at lower bias levels? Note that, my electrode cells are 4 atoms thick (4.9 angstroms) and I have included this same number of atoms (thickness) for the screening layers on each electrode.

Any comments are appreciated,

Chris

7

General Questions and Answers / Re: Internal Error Message: viewing Transmission Eigenstates in VNL Nanoscope

« on: March 13, 2009, 22:22 »

Hi Anders,

It's a little reassuring to know that I've approached this problem as you've stated. In a single VNL file I have included only the two probe configuration and only the first transmission eigenstate. As mentioned before, this file is about 20 MB and I'm still having the same problem. I also tried reinstalling VNL but to no avail, the error still exists.

thanks again,

chris

8

General Questions and Answers / Re: Internal Error Message: viewing Transmission Eigenstates in VNL Nanoscope

« on: March 13, 2009, 03:33 »

as an addition to my last post...I should mention that the scattering region and both electrodes of my two probe system contain 177 atoms in all... this is a large system which could pose a memory problem for visualizing both the atoms and transmission eigenstates together...I forgot to mention that I am able to visualize in nanoscope both transmission eigenstates and atoms together for smaller systems of 150 atoms...any comments are appreciated.

chris

9

General Questions and Answers / Re: Internal Error Message: viewing Transmission Eigenstates in VNL Nanoscope

« on: March 13, 2009, 02:59 »

Hi Nordland,

I'm using version VNL 2008.07.
My machine is only a week old and has 2.0 GB of RAM which should be plenty considering I also made sure to close all other applications before retrying.

I should note that I was getting the same error message on my old machine. I transferred the same version of VNL from the old machine to the new machine but I doubt there would be a problem with both PCs. There could be something wrong with my version of VNL?

chris

10

General Questions and Answers / Re: Internal Error Message: viewing Transmission Eigenstates in VNL Nanoscope

« on: March 12, 2009, 22:12 »

this is an addition to the previous post:

I should note that nanoscope opens the file and displays the configuration of the atoms with no problem...the trouble is when i try to insert a plot of the transmission eigenstates...

11

General Questions and Answers / Re: Internal Error Message: viewing Transmission Eigenstates in VNL Nanoscope

« on: March 12, 2009, 22:08 »

Hi,

The VNL file is about 20 MB. It contains  both the atoms of the two-probe configuration as well as the transmission eigenstates output. I guess I could eliminate the atoms from the VNL file to make it smaller, but then I wouldn't be able to see the superposition of the eigenstates on the atoms which is sort of the point.

thanks again,

chris

12

General Questions and Answers / Internal Error Message: viewing Transmission Eigenstates in VNL Nanoscope

« on: March 12, 2009, 19:47 »

Hello,

I'm consistently getting the following error messages when trying to view an isosurface plot of the Transmission Eigenstates for a two-probe system in VNL Nanoscope:


An internal error occured

exceptions. MemoryError:
can't allocate memory for array

....

I should mention that I do not get the same error message for other isosurface plots such as LDOS.
Is there anything I can do to avoid the error...I'm running VNL on a new PC with lots of memory so I don't think it's due to any limitation of the PC.

Thanks,

chris

13

General Questions and Answers / monkhorst paramaters and periodicity for the scattering region

« on: January 29, 2009, 19:22 »

Hi,

When I define the brillioun zone monkhorst parameters in the VNL NanoLanguage Tool, the resulting script returns these parameters for both the left and right electrodes. In the same resulting script, however, there are no brillioun zone parameters defined for the central (or scattering) region. I am curious how ATK performs the brillioun zone integration for the scattering region during the scf calculation and whether the scattering region is treated as periodic like the electrodes or as non-periodic during the scf calculation. Any insight is appreciated.

Thank You,

Chris