sofiasanz
commented
2 years ago Hi! Yes, we removed that function since it doesn't actually belong to this package. I don't know if sisl has a function to add H atoms, @zerothi ?
In any case I can leave you here the function that we had for adding H atoms to sp2 carbon-like nanostructures, hope is useful:
import numpy as np
import sisl
def add_Hatoms(geom, d=1.1, sp3=[]):
''' Function to saturate edge C atoms with Hydrogen
Parameters
----------
geom : sisl.Geometry instance
geometry of the system that is going to be saturated with H-atoms
d : float, optional
distance from the saturated C-atom to the H-atom
sp3 : array_like, optional
atomic indices where an sp3 configuration is desired
Returns
-------
sisl.Geometry object of the system saturated with H-atoms
'''
Hxyz = []
for ia in geom:
idx = geom.close(ia, R=(0.1, 1.6))
if len(idx[1]) == 2:
a, b = idx[1]
v1 = geom.axyz(a) - geom.xyz[ia, :]
v2 = geom.axyz(b) - geom.xyz[ia, :]
p = -1*(v1 + v2)
p = p * d / ((p**2).sum())**0.5
Hxyz.append(p+geom.xyz[ia, :])
if ia in sp3:
Hxyz[-1][2] -= 1.5
p = Hxyz[-1]-geom.xyz[ia, :]
p = p * d / ((p**2).sum())**0.5
Hxyz[-1] = p + geom.xyz[ia, :]
Hxyz.append(Hxyz[-1]*1.0)
Hxyz[-1][2] -= 2*Hxyz[-1][2]
Hgeom = sisl.Geometry(Hxyz, sisl.Atom(Z=1, R=d), sc=geom.sc)
return geom.add(Hgeom)
zerothi
tfrederiksen
mlorenznano
Hello,
I wanted to add H-Atoms to one edge of an AGNR-structure using the command
geom.add_Hatomsbut I found that this comment was removed during one update (probably because the geometry module used currently is the one from sisl and not the one from the Hubbard code itself).Is there another way of adding H-Atoms except creating a new .xyz file?
Thank you very much! Lorenz