ASE快速上手

参考
Modules
- ATOMS
- 读写vasp
组合操作示例
- 平移POSCAR中原子到中心

参考

Modules

https://wiki.fysik.dtu.dk/ase/ase/ase.html

ATOMS

建结构

>>> atoms = Atoms('H2',
...               positions=[(0, 0, 0),
...                          (0, 0, d)],
...               cell=(a, a, a))

平移原子

atoms.center()

读取位置

>>> atoms.get_positions()
array([[3.  , 3.  , 2.63],
       [3.  , 3.  , 3.37]])

>>> atoms.get_chemical_formula()
'H2'
>>> atoms.get_chemical_symbols()
['H', 'H']

下面的需要计算获得，计算完第一个后，后续如果不需要重复计算可直接显示结果，修改calc后会重新计算

>>> atoms.get_magnetic_moment()
0.0
>>> atoms.get_total_energy()
-6.627349275455906

读写vasp

from ase import Atoms
from ase.io import read, write
molecule = read("center.frac.car.roat.8883.vasp",format="vasp")
#write(molecule,"out.vasp",format="vasp")#这行报错???
molecule.write("out.vasp")#保存到out.vasp

读取后就是Atoms类型

>>> molecule
Atoms(symbols='C10H16', pbc=True, cell=[15.0, 15.0, 15.0])

不过写出的结构,缺少原子标注，如10 16的上一行缺少 C H

 C  H 
0000000000000000
0000000000000000    0.0000000000000000    0.0000000000000000
0000000000000000   15.0000000000000000    0.0000000000000000
0000000000000000    0.0000000000000000   15.0000000000000000
16
Cartesian
9822077500000006  7.5817357500000018  6.7195537500000002
8290642500000001  6.2047867500000002  6.7125397500000004
5578482500000010  7.4264887500000007  8.8350322500000011

组合操作示例

平移POSCAR中原子到中心

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
 
@author: cndaqiang 2020-
POSCAR中的原子坐标平移到中心
"""
import sys
import os
#-----Input File
if len(sys.argv) > 1:
    inputfile = str(sys.argv[1])
else:
    inputfile = "POSCAR"
if os.path.exists(inputfile):
    print("read from",inputfile)
else:
    print(inputfile+" not exists")
    exit()
from ase import Atoms
from ase.io import read,write
atoms = read(inputfile,format="vasp")
atoms.center()
atoms.write("center."+inputfile,format="vasp")
print("Save center POSCAR to "+"center."+inputfile)

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