[ase-users] Building nanoparticles

[Sepide Araban]

Dear Albert,
Thank you very much for your advices. Especially for atoms1+=atoms2. I will
try them and connect with gpaw users about the other issues as you said.

Best regards
Sepideh

On Fri, 23 Apr 2021, 00:03 Albert Bruix Fusté, <abruix at ub.edu> wrote:

> 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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