Messages

1

General Questions and Answers / Re: can a charge located near a molecule modifies its conductivity?

« on: October 31, 2010, 16:22 »

what i tried to mean was...
is there a way to build a system made of a molecule and a ion directly on VNL and  subsequently to study its I-V curve...
I said that because i find VNL quite hard to use but gaussian is even more complicated..

2

General Questions and Answers / can a charge located near a molecule modifies its conductivity?

« on: October 26, 2010, 18:29 »

I swear this is the last question (for this month )
I got a particular job:
to try to found out if a charge located near the molecule can change its habit to conduct.
With gaussian i made a moecule and i put a charge in a well known position.
can i
1) export the new configuration with the charge in VNL?
2) to study the conduction with the molecular junction system?

if it is possible,i'd finally like to know if i can use directly with vnl without using gaussian or other software...

i hope someone could solve this problem so i'll finally be able to finish my reserch

3

General Questions and Answers / Re: I-V courve for benzene set

« on: October 26, 2010, 16:40 »

in your opinion is it possible to put a terthiophene-tiolatated instead of the graphene?

4

General Questions and Answers / I-V courve for benzene set

« on: October 26, 2010, 01:14 »

 i'd like to know if it is possible to trace an iv courve of a fet starting with the benzene set profile (for example) or starting everything from the beginning....thanks

5

General Questions and Answers / Re: Putting a molecule between two electrods

« on: October 19, 2010, 18:00 »

Thank you so much you've been very helpfull now i got the right i-v courve...i said that 4 uA was insane because in an important paper aboud conduction of tiolated thiophene and i read a compleatly different value.
 for a Au-3TT-Au for a 2 volt bias we would reach about 12 uA.
I inserted a wrong adsorbation number and i 've inserted a wrong bonding angle now I set everything in a proper manner and all works

6

General Questions and Answers / Re: Putting a molecule between two electrods

« on: October 19, 2010, 08:54 »

Thanks it works very well but when i try to plot the i-v curve i get a wrong one courrent is in fact about 4 uA with 2 V applied...how could i try to understand if the molecule is bounded to the electrods in the right way? And an other question if i put my molecule in the builder i see it as balls but where informations about the bonding between its atoms is stored?....what i mean is how can i be sure that those i see are sp3 sp2 sp C thanks

7

General Questions and Answers / Putting a molecule between two electrods

« on: October 18, 2010, 01:17 »

Hi i'm new with atk and i'd like to know how i can put a molecule into a two-probe system...
i've got atk 2008 and 2010 too i 've just finished to build the Au electrods and i've a terthiophene molecule ready to be studied but i can't put it properly...
how can i do?

8

General Questions and Answers / Re: Import other file formats in VNL?

« on: October 17, 2010, 23:15 »

First of all thanks for the fast answare
I'm sorry but i've been using the 2008 version of the program...have you any other suggestion?

9

General Questions and Answers / Re: Import other file formats in VNL?

« on: October 17, 2010, 13:03 »

Well, at least in NanoLanguage you can use the small script provided in the examples directory. It is called import_xyz.py and it's quite straight-forward to use; in fact, and example (import_xyz-test.py) is also included in the same directory.

For convenience, I copy the example here:

Code

from ATK.KohnSham import *

# Import XYZ file 
from import_xyz import *
(elements,positions) = importXYZFile ('3-octanol.xyz')

# Create NanoLanguage molecule
molecule = MoleculeConfiguration(elements, positions*Angstrom)

# Save in VNL file    
vnlfile = VNLFile('3-octanol.vnl')
vnlfile.addToSample(new_vnl_molecule,'3-octanol')

Just remember to copy the file import_xyz.py to the same directory as your script, or add these lines at the top:

Code

import sys
sys.path.append('c:/Program Files/Atomistix/ATK 2008.02/examples')

(Yeah, I run ATK on Windows! the performance is actually not much worse, except there is no MPI parallelization of course...)

Hi I'm new with VNL and so i find it preatty hard to use.
My job is to optimize a number of thiophene molecules with a crescent number of elements with gaussian than to put those molecules in a two-probe system and so calculate an I-V courve...i tried to use the two methods listed above but neither one or the other worked....
i just copy and paste the script in the job manager but it crash everytime and it report an error.
it is the code wrong? should i add the entire file path?
could anyone help me to convert .xyz file in vnl?
i apologize for my bad english and hope i'll recive an answare....please help me