[ase-users] Building nanoparticles

[Albert Bruix Fusté]

Dear Sepideh,

I'm not sure I fully understand your questions.


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)
««««««««


Keep in mind that you can add atoms objects to one another with the line:

atoms1 += atoms2

which would add atoms2 to atoms1, keeping the cell and periodicity of atoms1 (if any).


-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?


It is hard to understand what you are asking here, especially if you do not mention the type of calculation you are trying to carry out and why. The requirement for a simulation box or cell depends on the calculator that you want to use. I guess you are doing some tddft calculation with GPAW, but that is still not enough information to be able to help you out. GPAW calculations require defining a simulation cell and it's periodicity. Anyways, I would first try to reproduce some of the many examples from the GPAW website and perhaps contact their mailing list if you need help with that code.


Best wishes,
Albert


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