I have the cif file database for machine learning. I want to get soap diors

Hi! This is certainly possible. You can use the <a href="https://wik

How to get soap from cif file? about soaplite HOT 1 CLOSED

hori1537 commented on July 17, 2024

How to get soap from cif file?

from soaplite.

Comments (1)

lauri-codes commented on July 17, 2024

Hi!

This is certainly possible. You can use the ase-library to load many kinds of atomic structures into SOAPLite. This can be done e.g. like this:

import soaplite
import ase.io

structure = ase.io.read("hydrogen.cif")
pos = [[0, 0, 0]]
rcut = 4
nmax = 6
alphas, betas = soaplite.genBasis.getBasisFunc(rcut, nmax)
out = soaplite.get_soap_locals(
    structure,
    pos,
    alp=alphas,
    bet=betas,
    rCut=rcut,
    nMax=nmax,
    Lmax=6,
    eta=1/(2*0.4**2),
    all_atomtypes=[1]
)

If you wish, you can also take a look at the DScribe-library that internally uses SOAPLite, but offers maybe a bit easier interface. The same calculation with DScribe could be done with:

from dscribe.descriptors import SOAP
import ase.io

structure = ase.io.read("hydrogen.cif")
pos = [[0, 0, 0]]
desc = SOAP(
   species=["H"],
   rcut=4.0,
   nmax=6,
   lmax=6,
   rbf="gto",
   sigma=0.4,
   sparse=False,
   periodic=False
)
out = desc.create(structure, positions=pos)