1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
|
from ase import Atoms
from ase.build import fcc111
from ase.calculators.emt import EMT
from ase.db import connect
db1 = connect('bulk.db')
db2 = connect('ads.db')
def run(symb, a, n):
atoms = fcc111(symb, (1, 1, n), a=a)
atoms.calc = EMT()
atoms.get_forces()
return atoms
# Clean slabs:
for row in db1.select():
a = row.cell[0, 1] * 2
symb = row.symbols[0]
for n in [1, 2, 3]:
id = db2.reserve(layers=n, surf=symb, ads='clean')
if id is not None:
atoms = run(symb, a, n)
db2.write(atoms, id=id, layers=n, surf=symb, ads='clean')
# Atoms:
for ads in 'CNO':
a = Atoms(ads)
a.calc = EMT()
a.get_potential_energy()
db2.write(a)
|
