Messages

1

General Questions and Answers / Opening a ATK script in vnl

« on: August 1, 2011, 03:04 »

I tried to open a ATK script in vnl to modify the calculation. However, when I opened in with scriptor, only the left electrode shows up.

Also is it possible to import a calculation from the .nc file with vnl?

thanks,
Zhiyong

2

General Questions and Answers / import ATK commnad

« on: July 25, 2011, 05:45 »

I got the following error and the first few lines of the py script is as follows. How do I define the path correctly so that atk finds the ATK module?

Thanks,
Zhiyong

import ATK
from ATK.KohnSham import *

# Define the unit cell
unit_cell = [
        [ 8.6514     ,   0.,  0.        ],
        [ 4.3257     ,   7.4922,   0.        ],
        [  0.        ,   0.        ,  59.39]
              ]*Angstrom

elementList = []
coordinatesList = []

+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 11.2.1 [Build 3053]                                        |
|                                                                              |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File "xyztovnl.py", line 1, in <module>
    import ATK
ImportError: No module named ATK

3

General Questions and Answers / Re: structure in 111 plane

« on: April 8, 2011, 23:48 »

Hello,

With the 11.2.1 version of vnl, when I tried to cleave an electrode in the 1,1,1 direction, I go the following error message: "Only cubic lattices may be cleaved".

How do I cleave a metal with the 11.2.1 version of VNL?

Thanks,
Zhiyong

4

General Questions and Answers / Re: spin orbit interaction

« on: October 8, 2009, 03:28 »

Thanks! Does the non-collinear spin dependent calculations take into spin-orbit effects? If not are there any plans to implement it in the future?

Zhiyong

5

General Questions and Answers / spin orbit interaction

« on: October 8, 2009, 01:56 »

Hello All,

Is it possible to do a calculation of a bulk structure with spin-orbit interaction with ATK?

Thanks,
Zhiyong

6

General Questions and Answers / Re: LDOS as a function of both energy and momentum

« on: October 8, 2009, 01:55 »

Anders,

Thanks for the information. I have used this function before. I want project the DOS to, say a layer of atoms, for a given E and k. Actually I did something quite similar before but forgot the location of the scripts. If there is already a standard function or script that allows us to project the DOS to a layer of atoms or even a specific atom, it would be great.

Best,
Zhiyong 

Hi Zhiyong,

there is a bit of an ambiguity when it comes to LDOS, so I just want to make sure I understand the question right. Do you mean the DOS, projected onto real space (hence, "local"), for a given E and k? In that case, this is already a standard function (http://quantumwise.com/documents/manuals/ATK-2008.10/ref.calculatelocaldensityofstates.html).

7

General Questions and Answers / LDOS as a function of both energy and momentum

« on: October 7, 2009, 03:13 »

Dear All,

I'd like to calculate the LDOS of a system as a function of both energy and momentum (k-points). Is there a script available for this already?

Thanks,
Zhiyong

8

General Questions and Answers / Re: Where is the equlibrium fermi level ?

« on: July 8, 2009, 08:49 »

It seems to me that there are three Fermi levels or reference energies we can speak of: Fermi energy of the electrodes only, Fermi level of the equivalent bulk, and Fermi level of the two-probe system. Since physically the equivalent bulk and the two-probe system are different, all the three quantities are different.

For a two probe calculation without bias, there reports a Fermi energy, which is common to both electrodes and the scattering region. This Fermi level is different form that of the Fermi level for the electrode only. I guess one way to see the difference is to calculate the charges in the electrode region, in cases of the isolated electrode and also in the case when the electrode is actually treated as part of the two probe system, up to the Fermi level. The charges thus obtained should be different. 

When calculating the transmission spectra, I guess the bias is relative to the Fermi level obtained in the two probe calculation with ZERO bias, neither the Fermi level in the electrode calculation nor the Fermi level in the equivalent bulk calculation. 

Could somebody correct me if I am missing something here?

9

General Questions and Answers / Re: total charge question

« on: July 8, 2009, 08:11 »

For these charges referred below, the calculation is done with zero applied voltage.  When you refer to the equilibrium and non-equilibrium cases, do you mean with and without applied potential?

Supposedly both charges are calculated from the coefficients of the scattering states. During the iteration steps of the two probe calculation, are the Mulliken charges calculated from the scattering state coefficients only, as opposed to the charge, supposedly calculated with the Fermi distribution function, in the properties section?

Could some body please clarify how these charges are calculated in more detail?

Thanks,
Zhiyong

10

Installation and License Questions / ATK-semi library

« on: July 6, 2009, 23:53 »

Hello,

When running the ATK-semi, I go the following error: /home/zzhang/ATK/atk-2009.06/nlpython/bin/nlpython_exec: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by /home/zzhang/ATK/atk-2009.06/nlpython/bin/../lib/libpython2.6.so.1.0).

When I tried to look for GLIBC_2.4 I found the following link:
http://gbgames.com/blog/2008/04/linux-game-development-glibc_24-errors-solved/

There it was mentioned that GLIBC_2.4 is not needed when the correct compiler flags export CFLAGS="-fno-stack-protector" are used. If by mistake the flag -fno-stack-protector is used in building the libraries, it requires GLIBC_2.4.

Could somebody explain if this the case for the ATK-semi? Or is it necessary to install GLIBC_2.4?

Thanks,
Zhiyong

11

General Questions and Answers / importing VNL files into VNL on Linux

« on: January 20, 2009, 19:19 »

Hello,

I am running VNL with Linux and I am trying to import a vnl file to the lab space. Under the file menu, only an exit option is given. How do I import a vnl to the lab space in this case?  I am using the 2008.10 release.

Thanks,
Zhiyong