ASEによる表面モデルの作成方法
fcc111など、典型的な表面の作成
from ase.build import fcc111
surf = fcc111("Cu", size=[3,3,5], a=3.2, vacuum=10.0)
- fcc100, fcc110, bcc100, bcc110, bcc111, fcc111, hcp0001が使える
一般的な表面の作成
from ase.build import bulk, surface
bulk = bulk("Cu", "fcc", a=3.2)
surf = surface(bulk, (1,1,1), 5, vacuum=10.0) # lattice, Miller indices, layers
surf = surf*[3, 3, 1] # if you want to replicate
surf = surf.translate([0, 0, -10]) # if you want to shift
CIF/POSCARをロードして表面を作る例
from ase import Atoms, Atom
from ase.build import surface
from ase.visualize import view
from ase.io import read
from ase.io import write
bulk = read("1000053.cif") # or read("oldPOSCAR")
surf = surface(lattice=bulk, indices=(1,1,1), layers=5, vacuum=10.0)
surf.translate([0,0,-10.0+0.1]) # shift slightly for easier to view
view(surf*[5,5,1])
write("POSCAR", surf)
原子・分子を表面に吸着させる
- add_adsorbateを使う
from ase import Atoms
from ase.build import fcc111, add_adsorbate
surf = fcc111("Cu", size=[3,3,6], vacuum=10.0)
mol = Atoms("CO", [(0,0,0),(0,0,1.2)])
add_adsorbate(surf, mol, 1.6, position="ontop")
# slab, adsorbate, height, position=(0,0), offset=None, mol_index=0)
-
offsetはfloatでよい(e.g.offset=(1, 1),offset=(0.5, 0))。unit cellのfractional coordinateになっている - メジャーなsurfaceに対してはstringでの吸着位置がある
| surface | available adsorption sites |
|---|---|
| fcc100 | ontop, hollow, bridge |
| fcc110 | ontop, hollow, longbridge, shortbridge |
| bcc100 | ontop, hollow, bridge |
| fcc111 | ontop, bridge, fcc, hcp |
| hcp0001 | ontop, bridge, fcc, hcp |
| bcc110 | ontop, shortbridge, longbridge, hollow |
| bcc111 | ontop, hollow |