Messages

1

General Questions and Answers / Re: Geometry optimization of two probe system

« on: December 9, 2010, 19:39 »

I use VNL 2008.1. The initial distance in each side is 1.9 ang.  I know from literature that the normal distance between S-atom and gold electrode is between 1.9 to 2.4 ang.

Regards,
Sayed

2

General Questions and Answers / Geometry optimization of two probe system

« on: December 9, 2010, 06:30 »

Dear ATK community,

 I have preformed optimization for two-probe system where the molecule is donor-acceptor system ended by sulfur linkers ie: electrode-S-Donor-Acceptor-S-electrode.

After the optimization I found that the distance between S-atom of acceptor part and the left electrode is 2.32 ang. while the distance between S-atom of the donor part and the right electrode is 1.38 ang
I have some doubt about the last distance. Please let me know your opinion.

Thanks beforehand,
Regards,
Sayed

3

General Questions and Answers / Re: Which is better for calculating MPSH ....?

« on: November 16, 2010, 23:56 »

Another question related:  I saw in the beginning of the output the index of atoms start from zero If the projected atoms were only all molecule's atoms, should the projected atoms include one atom before and one atom after the atomic list of molecule's atoms. For example: Suppose if you have a molecule of 10 atoms in between two electrodes: The index start from zero to 54, and the included list of molecule's atoms start from 18 to 27. Therefore the projected atoms will be 18,19,20,21,22,23,24,25,26,27 or 17,18,19,20,21,22,23,24,25,26,27,28?

Thanks in advance;
Sayed

4

General Questions and Answers / Question in the output?

« on: November 16, 2010, 19:40 »

Dear All,
I found this part of the output:

# Homogeneous Two Probe Configuration
# -----------------------------------------------------------------------------
# Electrode                0      1
Equivalent Atoms      (0, 0) (2, 71)
Electrode Repetitions (3, 3) (3, 3)

Could you please explain me what does mean by "

# Electrode                0      1
Equivalent Atoms      (0, 0) (2, 71)

Regards,
Sayed M

5

General Questions and Answers / Which is better for calculating MPSH ....?

« on: November 16, 2010, 14:16 »

Dear Quantumwise community:

I would like to calculate MPSH for two probe system. Which give better description: choosing only the atoms of molecule or the whole central region as projected atoms (molecule + surface gold atoms)?

Regards,
Sayed M

6

General Questions and Answers / Conversion postscript to ASCII file

« on: November 11, 2010, 20:07 »

Dear All,
Do you know free program to convert Postscript to ASCII? I need it because when I plot the transmission spectrum, I can save it only as png, eps or ps file in VNL 2008.1. After I close the log file I cannot retrieve the XY data again. 

Regards,
Morad

7

General Questions and Answers / dipole moment + specify HOMO and LUMO on transmission spectrum

« on: November 11, 2010, 09:57 »

Dear All,

I am VNL 2008.1 user under windows XP. I have four questions:

1- Can I calculate the dipole moment of an isolated molecule using VNL?
2- I see in many papers that the Frontier MOs are shown on the transmission spectrum as small vertical lines around the Fermi energy level (zero eV). Which one can specified on transmission spectrum, molecular spectrum (of isolated molecule) or projected Hamiltonian energy spectrum (two probe system)?

3-In the context, what does mean by "energy bias" or "windows bias"? And how can I calculate it? Please give me an example for clarification.

4- In case of calculation of MPSH ( projected Hamiltonian energy spectrum), there are three points to for setting up:
(i) projected atoms (ii) include molecule atoms (iii) include surface atoms
My case: organic molecule has 32 atoms in two probe system. When I specify (ii) and leave (i) empty I found that the number of projected atoms in the script is 72 atoms and I found also the list start with zero. When I add in (i) list from 0 to 20,I found it excatly in the script. Could you please clarify this point.
Regards,
Sayed

8

General Questions and Answers / Clarification how to calculate the current

« on: November 4, 2010, 16:17 »

Dear All,
I use VNL 2008.1 windows and I have not much experience with it.Although I have read the tutorial but still some point are ambiguous to me. I want to calculate the current at 0.5, 1 and 1.5 volt for two probe system in separate jobs. What I do is the following:

1- Firstly I calculate the transmission spectrum (range: -3 to 3 eV) at zero voltage and save it as checkpoint file, for example "Trans.nc". By the way, I choose only Transmission spectrum in the "ANALYSIS" section, Am I right?
2-After the first step finished, I restore "Trans.nc" then set the voltage of left electrode= 0.5 volt and the right electrode=zero volt to make bias=0.5 volt. Then I choose only "Current" in the ANALYSIS section.
And so on.
1-My question is this scenario valid?
2- Should I recalculate the transmission spectrum at 0.5 volt to calculate the current at the same value?   
Thanks in advance
Sayed