The results of pathway?

[cinda]

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!

[Anders Blom]

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.

[cinda]

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.

[Anders Blom]

Yes, the cell is a bit too small.

[cinda]

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?

[Anders Blom]

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

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.

[cinda]

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?

[Anders Blom]

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