QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: cinda on May 22, 2012, 04:23

Title: The results of pathway?
Post by: cinda on May 22, 2012, 04:23

Dear all,
In my attach figure, you can see the above of the NO2 have two arrows, why does the arrow point to NO2 from somewhere there is not any atom? Where did the current from?

Thank you!

Title: Re: The results of pathway?
Post by: Anders Blom on May 22, 2012, 09:51

Hard to say without a clearer picture of the structure. I could imagine the unit cell in X/Y is too small, so there is actually a coupling from the lower part of the nanotube to the molecule due to the periodic boundary conditions in X/Y.

Title: Re: The results of pathway?
Post by: cinda on May 22, 2012, 11:27

I used the py file from ATK2008.10, is that affect the size of unit cell?
And I attach the other clearer figure, there is same situation like the above one, but the arrow is under the tube.

Title: Re: The results of pathway?
Post by: Anders Blom on May 22, 2012, 11:30

Yes, the cell is a bit too small.

Title: Re: The results of pathway?
Post by: cinda on May 22, 2012, 12:21

Thank you very much for your answer.I have the other question, in the output of pathway.
Like this


   +----------------------------------------------------------+
   | Transmission Pathways Report                             |
   | -------------------------------------------------------- |
   | Relative Energy             =  0.000000e+00              |
   | Energy zero                 = -4.610666e+00              |
   | Left electrode Fermi level  = -4.610666e+00              |
   | Right electrode Fermi level = -4.610666e+00              |
   | Units = eV                                               |
   +----------------------------------------------------------+
   Pathways for Spin = Up
   
     0 ->  2 (-1,-1, 0) : 3.251415e-03
     0 ->  9 (-1,-1, 0) : -7.054556e-04
     0 -> 12 (-1,-1, 0) : -1.141724e-02
     0 -> 15 (-1,-1, 0) : -2.408455e-06
     0 -> 16 (-1,-1, 0) : 1.173300e-03
     0 -> 18 (-1,-1, 0) : 2.683015e-03
     0 -> 19 (-1,-1, 0) : -2.185313e-02
     0 -> 20 (-1,-1, 0) : 1.057683e-01
     0 -> 21 (-1,-1, 0) : -2.677941e-05
     0 -> 30 (-1,-1, 0) : 1.052997e-08
     0 -> 31 (-1,-1, 0) : 1.120160e-06
     0 -> 32 (-1,-1, 0) : 1.345200e-05
     0 -> 35 (-1,-1, 0) : -1.891534e-05
     0 -> 38 (-1,-1, 0) : -2.171946e-03
     0 -> 49 (-1,-1, 0) : -9.780147e-04
     0 -> 50 (-1,-1, 0) : -2.530531e-06
     0 -> 52 (-1,-1, 0) : 1.709798e-05
     0 ->  1 (-1, 0, 0) : 1.330517e-03
     0 ->  3 (-1, 0, 0) : -3.196077e-03
     0 ->  5 (-1, 0, 0) : 1.919671e-02
            ............
            .............


Is the number corresponding to the coordinates of py file? Is there a easier way to identify each line corresponding to which atom? And what these values represent?

Title: Re: The results of pathway?
Post by: Anders Blom on May 22, 2012, 13:23

Yes, the indices are atom numbers, and the three numbers like (-1,-1,0) indicates which cell the second atom belongs to. So, in the case

Quote

0 ->  2 (-1,-1, 0)

we have a bond from atom 0 to atom 2 placed in the "left" neighbor cell in X and Y.

If you see pathways which are not to atoms in (0,0,0), your cell is possibly too small in XY (if the transmission values are not very small) - unless of course the system is intended to be periodic in X and Y.

Title: Re: The results of pathway?
Post by: cinda on May 23, 2012, 05:13

I have one more question.
In the output
0 ->  2 (-1,-1, 0) : 3.251415e-03

What the values 3.251415e-03 represents? Does it represent the magnitude of current?

Title: Re: The results of pathway?
Post by: Anders Blom on May 23, 2012, 08:07

See http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.transmissionpathways.html (end of the page).
Also http://www.nature.com/nchem/journal/v2/n3/full/nchem.546.html