
 How to plot the potential profile for a junction
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We here give an example of how to plot the potential 
profile of a junction.

This can provide detailed information about the coupling
to electrodes and which part of a junction has the most
importance for the transport constriction.

A potential profile shows how an applied bias voltage
drop will be placed in a junction.

To calculate the potential profile you need several calculations, 
 1) The electrodes
 2) A transiesta calculation at 0 V
 3) A transiesta calculation at finite V
 4) Calculation of the potential profile by
    subtracting 2) from 3).

Notice the flags provided in the fdf file. We need to save
the electrostatic potential from the calculations to be 
able to extract the needed quantities.

We have prepared an input which can be used together with the grid2cube
program. (see vh2cube.inp)

We have prepared an executable which can subtract two cube files from each other.

You can call it in two different ways:
 cubediff <first cube> <second cube> <saved name cube>
 cubediff -xy <first cube> <second cube> <saved name data>

the former will calculate the difference in each grid-point, 
the latter will take the mean of the potential profile in the x-y plane 
and save it for each z (only a single line), we can call this a projected 
potential profile to the transport direction. In this case it is a very crude
projection, yet for other systems this might be very useful.
