Topics

1

General Questions and Answers / Dynamical Matrix of a Tiny Graphene Nanoribbon takes hours x hours

« on: October 6, 2015, 15:07 »

Hi
I tried the inelastic spectrum tutorial of the silicon pn junction and the calculation of the dynamical matrix takes around  a min. However when I try to calculate the dynamical matrix of a tiny graphene nanoribbon as attached it takes ages. I'm sure I'm making an error in the parameters of the dynamical matrix calculation.

I checked the ATK manual and it says that the number of repetitions should be given as the repetitions of the structure.

1. As I understand if I build an 6-atoms wide GNR and repeat it 3 times in C direction, I have to set the repetitions in the calculation of the dynamical matrix as (1,1,3), is it right? But when I do this, it takes ages to calculate hours and hours. (attachment 1)

2. And another problem is that when I build a GNR device as attached (attachment 2), the settings for the z-repetitions in the dynamical matrix in VNL seems disabled however the structure is 1-D and I have to set it as the number of repetitions of the unit sell in z-direction? Is it right? When I set the repetitions as (1,1,4) in the Editor, this calculation (attachment 2) also takes hours and hours.

I'd be very glad if you could  tell me the trick about calcultaing the dynamical matrix in a min as in the Si pn junction tutorial, otherwise I cannot set it up and takes ages to calculate (and probably wrong).  Couldn't manage to work this for a few days. Thanks.

2

General Questions and Answers / atkpython stopped working error...

« on: September 25, 2015, 14:09 »

Dear friends, I installed the 2015 rc2 version and it constantly gives the following error in any simulation:

Code

Calculating Density Matrix : 
** Back Engine Exception : LU factorization failed
** Location of Exception : linearsystems.cpp:663

There's no problem when I run a simulation on my laptop but the above error is given on my desktop pc which has 16gb ram and a better processor. I uninstalled rc1 and installed rc2 and tried a lot but couldn't overcome this problem. I'd be glad if you could help. Best regards. Heinz.

3

General Questions and Answers / netcdf file open

« on: July 28, 2015, 05:39 »

Dear friends,

Is there a program to open nc files generated in ATK for looking at the I-V curve data calculated?

Best

4

General Questions and Answers / Export to MATLAB or Scilab

« on: February 20, 2015, 15:47 »

Hi,

I need to export electron density to MATLAB or Scilab. I searched the forum and found a relevant post: http://quantumwise.com/forum/index.php?topic=39.0
However the code given there doesn't work with ATK 2014 version. How can I do that?

Note: I tried to export as CUBE file and then into MATLAB but MATLAB shows NaN (not a number) errors for that. I attached the beginning of the  CUBE file got from the electron density in ATK.

Best
Heinz

5

General Questions and Answers / ThermoloXCalculator

« on: January 19, 2015, 08:59 »

Hi
In the tutorial for the Si atoms, StillingerWeber_Si_1985() potential set is used for the ThermoloxCalculator. Could you please tell which potential set(s) to use in the ThermoloXCalculator for a structure in which C, Si and H atoms present?
Hope can get a reply. Thanks.

6

General Questions and Answers / GNR p and n doping how???

« on: December 15, 2014, 15:03 »

I replicated the pn junction of silicon tutorial, it's awesome thanks.

Then I tried to do the similar p-n junction simulation of the attached GNR section. Please could you help how I can dope the attached GNR as p-n junction?

Best regards,
Heinz

7

General Questions and Answers / About the phosphorene tutorial

« on: November 17, 2014, 09:46 »

Hi,

I set up 2D phosphorene per the tutorial: http://quantumwise.com/publications/tutorials/item/516-how-to-create-a-crystal-structure-with-the-crystal-builder

However I cannot follow the bandstructure route as the key S is not allowed.  How was the bandstructure route set for this tutorial? Could you please send the input .py file for this tutorial?

Best,

8

General Questions and Answers / Dielectric tensor and susceptibility tensor mismatch in optical spectrum

« on: November 15, 2014, 13:43 »

Dear all,

I performed a simple optical spectrum analyses of a GNR sample and got the dielectric and susceptibility data as attached. In the ATK manual page it says that Er=1+X where Er is the relative dielectric constant and X is the susceptibility. However as you can see from the data below there is no such a relation. Is the dielectric or susceptibility data correct? I'm using ATK 2014.1. Thanks in advance.

9

General Questions and Answers / Simple question: broadening in optical spectrum

« on: September 18, 2014, 14:29 »

Hi,

What does this broadening model in ATK? Does it correspond to the the electrochemical potential of the structure?

Thanks a lot.

10

General Questions and Answers / Optical conductivity

« on: August 29, 2014, 20:54 »

Hi,

In the manual here: http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.opticalspectrum.html it is said that the optical conductivity can be calculated from the susceptibility. However, when I calculate optical conductivity from the formula in this part of the manual, the obtained values are so low that it can only correspond to the 2D conductivity. Is the formula in the manual


          \sigma(\omega)  =  - i \omega \epsilon_0 \chi(\omega).
       

show 2D or 3D conductivity?

Thanks in advance.

11

General Questions and Answers / Optical spectrum-bug???

« on: August 15, 2014, 15:33 »

Hi,

I followed the optical spectrum tutorial of silicon. However when we plot, it shows the calculated values as the dielectric constant but when we export as text file, the optical values are labelled as susceptibility. Are the calculated values the "dielectric constant" or "susceptibility" of the material?

Thanks.

12

General Questions and Answers / Optical spectrum question

« on: August 2, 2014, 14:17 »

Hi,

I plotted the optical spectrum of silicon following the tutorial. How can I plot the Re(eps) and Im(eps) versus frequency not the energy?

Best regards

13

General Questions and Answers / The relation of transmission eigenstates and the transmission probability

« on: July 10, 2014, 20:47 »

Hello,

We can obtain the 3-D isosurface plot of the transmission eigenstate of a device in ATK. However what's the relation of "the shape and localization of transmission eigenstates" and the transmission probability (hence the transmission spectrum)? Because it is written in some papers that delocalized MPSH states imply a high transmission probability. Is there a similar argument for the transmission eigenstates and the transmission spectrum?

Thanks in advance.

14

General Questions and Answers / iso value for plotting eigenstate in 3D

« on: June 23, 2014, 22:33 »

Hi,

I'm trying to plot eigenstate (MPSH) for a molecule. However, after doing the eigenstate calculation, when I plot in 3D I'm confused to select the isovalue in the viewer-properties. According to what shall I select the isovalue because changing the isovalue changes the plotted eigenstate to be very different (localized, delocalized etc...)?

15

General Questions and Answers / Relationship of MPSH eigenstate and transmission eigenstate

« on: June 18, 2014, 17:48 »

Hi,

What's the mathematical relationship of the "eigenstate" and the "transmission eigenstate" calculated by ATK? As mush as I know eigenstate is the eigenfunction of the Hamiltonian and the transmission eigenstate is the eigenfunction of the transmission matrix. But what's the formal or conceptual relation?

Moreover, when plotting eigenstates as isosurface, which iso value has to be used? Since changing the isovalue also changes the shape of the eigenstate plotted?

Hope to have some answers. Thanks in advance.