Dear SIESTA developers and users,

I recently read Papior et al. 's article on Phys. Chem. Chem. Phys. entitled 
"Manipulating the voltage drop in graphene nanojunctions using a gate potential 
(DOI: 10.1039/C5CP04613K)". I am very interested in the method of adding gate 
voltage to a system in this article and try to learn how to use it. However, I 
have encountered some difficulties in the process, and I'm really looking 
forward to some help. 

1. When I use the square (Bounded plane) option in Gate, I need to set the 
starting point of the square and two spanning vectors. As shown below (copied 
from the SIESTA 4.1-b4 manual).

%block Geometry.Hartree

square 1. eV          # The lifting potential on the geometry

gauss 1. 2. Ang      # the std. and the cut-off length

1.0  1.0  1.0  Ang  # The starting point of the square

2.0  0.5  0.2  Ang  # The first spanning vector

0.0  2.5  0.2  Ang  # The second spanning vector

%endblock Geometry.Hartree

But we all know that two points define a vector, so do the coordinates that 
define the spanning vector in the example above represent the end point of the 
vector? If so, what is the starting point of this spanning vector? Is the 
spanning vector starting at the origin (0  0  0) or at the starting point of 
the square (1.0  1.0  1.0) defined in the example above?

I have the same question about plane (Infinite plane, a vector) and Box (three 
vectors) in Gate.

2. Whether a shorter vacuum layer in the direction of adding Gate makes 
self-consistency difficult to converge. How to determine the appropriate length 
of vacuum layer?

I'm really looking forward to some help.

Thank you very much!


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