[ase-users] Building nanoparticles

[Sepide Araban]

Dear ASE users,

I have a question about building nanoparticles, if you answer that  I wouId
appreciate. I want to have two nanoparticles (or more) at a distance 'd'
from each other.
1 First I creat one nanoparticle and optimize it
2 I creat another one, optimize it and shift it by d.
3 I make one  position dict of all positions
4 I creat a new Atoms with the new positions dict of 2 nanoparticles and a
new vacuum in order to cover all atoms.
5 without new optimization  I run ground state and ...

Here is an example script:

«««««««««
from ase import Atoms, io, optimize
from gpaw import GPAW, FermiDirac
from gpaw.cluster import Cluster
from gpaw.lrtddft import LrTDDFT
from ase.cluster.cubic import BodyCenteredCubic
from ase.visualize import view
import numpy as np
a0=.53#.053nm
n=20
d = n*a0 # starting distance
#Na particle
surfaces = [(1, 0, 0), (1, 1, 0), (1, 1, 1)]
layers = [1, 5, 5]
lc = 4.28#0.428nm
atoms1 = BodyCenteredCubic('Na', surfaces, layers, latticeconstant=lc)
view(atoms1)
positions1=atoms1.get_positions()
positions2=positions1
positions2[:,2]=positions2[:,2]+d
positions1=atoms1.get_positions()
atoms2=Atoms('Na9',positions2)
view(atoms2)
positions3=np.vstack((positions1,positions2))
c=Atoms('Na18',positions3)
cp=c.get_positions()
view(c)
#s = Cluster(symbols='Na18',positions=cp)
#s.minimal_box(box,h=h)
#view(s)
««««««««

-Is that correct (physical and simulation) to consider the transition
electrons between two nanoparticles or tunnelling for example? or there is
some other task to do?
-Is it necessary to define a cluster of nanoparticles or a simulation box ?
_ s.minimal_box(box,h=h)
or atoms and vacuum or even unitcell are enough?
_Is there a more simple scripts?

The version of the installed ASE is 3.18.1

I am really sorry for taking your time. I would appreciate if you answer my
questions.

With Best regards
Sepideh Araban
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