def adsorb(self,
mol,
loc=[0.5, 0.5, 0.5],
spec_z=False,
theta=[0, 0, 0],
v=[0, 0, 0],
distance=2,
ifpca=True,
frac=True):
from sklearn.decomposition import PCA
if ifpca:
pca = PCA(n_components=3)
pca.fit(mol.cart_coords)
new_coords = pca.transform(mol.cart_coords)
newmol = Molecule(coords=new_coords, species=mol.species)
else:
newmol = mol
newmol.rotate_sites(axis=[1, 0, 0], theta=theta[0] / 180 * math.pi)
newmol.rotate_sites(axis=[0, 1, 0], theta=theta[1] / 180 * math.pi)
newmol.rotate_sites(axis=[0, 0, 1], theta=theta[2] / 180 * math.pi)
if not spec_z:
if frac:
ztop = np.max(self.poscar.structure.frac_coords[:, 2], axis=0)
zz = ztop + distance / self.poscar.structure.lattice.c
loc = [loc[0] + v[0], loc[1] + v[1], zz + v[2]]
else:
ztop = np.max(self.poscar.structure.cart_coords, axis=0)[2]
loc[2] = distance + ztop
else:
loc = [loc[0] + v[0], loc[1] + v[1], loc[2] + v[2]]
if frac:
loc = self.f_to_c(loc)
sufsite = AdsorbateSiteFinder(self.poscar.structure)
ads_struct = sufsite.add_adsorbate(newmol,
loc,
reorient=True,
translate=False)
return ads_struct
