Blue and Green lines of transmission path-not known

[Sabyasachi Sen]

Kindly help me in identifying the meaning of Blue and Green lines of transmission path attached as .jpeg file with this query. Please also note in the output only spin up data is presented (see output and .py file) for spinpolarized calculation. Please help me in getting data of both spin up and down. Also illustrate the meaning of various terms in the outpt file.

[Umberto Martinez]

The color is coded accordingly to the direction of the arrow, see  usage examples in the Reference Manual. http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.transmissionpathways.html
in 2014 a color bar has been introduced.
see also http://quantumwise.com/documents/tutorials/latest/VNLTutorial/index.html/chap.gnr.html#sect2.gnr.results.transmission_pathway

Unfortunately, even in 2014 it is still not possible to plot transmission pathways for up and down components.
This will be possible in  VNL 2015 coming out very soon.

In the output file the following is printed, for example:
  0 ->  4 (-1,-1, 0) : 1.214424e-02
which means:

• 0->4 indices of atoms from and to the pathway is calculated, i.e. arrow is drawn.
• (-1,-1,0) indicates the cell where the second atom should be connected. This is a little tricky:
  Compare the line above with this:
    0 ->  4 ( 0, 0, 0) : 3.177780e-01
  In the first case, the pathway is from atom 0 and the periodic repetition of atom 4 placed in -x and -y.
  In the second case, the pathway is from atom 0 to atom 4 in the same cell.
  NOTE: this is relevant for a periodic systems. For a 1D system this will always give you (0,0,0)
  
• 1.214424e-02 is the relative contribution to the transmission as explained in the reference manual