pymatgen创建不同终端的表面

from pymatgen.core.surface import generate_all_slabs
from pymatgen.core.structure import Structure
from pymatgen.io.vasp import Poscar
structure = Structure.from_file('CONTCAR')   # 读取文件
slabs = generate_all_slabs(structure, 2, 1, 0.1, max_normal_search=2)  # 输入结构，最大miller_index，min_slab_size ，min_vacuum_size
index = 0
for slab in slabs:
    print(slab.miller_index)
    poscar = Poscar(slab, comment=str(slab.miller_index))
    poscar.write_file(str(index)+str(slab.miller_index)+'.vasp', direct=False)
    index += 1

pymatgen与ASE结构转换

from pymatgen.io.ase import AseAtomsAdaptor
structure = Structure.from_file('CONTCAR')
atoms = adaptor.get_atoms(slab)
structure = read('CONTCAR')

ASE创建不对称表面

structure = read('CONTCAR')
slab = surface(structure, [1, 1, 1], 1, vacuum=2)
vaccum = 15
slab.cell[2, 2] = slab.cell[2, 2] + vaccum - 2*2
# print(slab.get_positions())
coords = slab.get_positions()
z = np.around(coords[:, 2], 5)
unique_z = np.unique(z, axis=0)
tags_list = []
index = 1
for j in range(len(z)):
    for i in range(len(unique_z)):
        if z[j] == unique_z[i]:
            tags_list.append(i+1)
slab.set_tags(tags_list)
layers_num = len(unique_z)
print(layers_num)
write('POSCAR', slab)