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
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
|
from ase.build import niggli_reduce
from ase.calculators.singlepoint import SinglePointCalculator
from ase.constraints import ExpCellFilter
from ase.ga import set_raw_score
from ase.optimize import FIRE
try:
from asap3 import EMT
except ImportError:
from ase.calculators.emt import EMT
def finalize(atoms, energy=None, forces=None, stress=None):
# Finalizes the atoms by attaching a SinglePointCalculator
# and setting the raw score as the negative of the total energy
atoms.wrap()
calc = SinglePointCalculator(
atoms, energy=energy, forces=forces, stress=stress
)
atoms.calc = calc
raw_score = -atoms.get_potential_energy()
set_raw_score(atoms, raw_score)
def relax(atoms, cellbounds=None):
# Performs a variable-cell relaxation of the structure
calc = EMT()
atoms.calc = calc
converged = False
niter = 0
while not converged and niter < 10:
if cellbounds is not None:
cell = atoms.get_cell()
if not cellbounds.is_within_bounds(cell):
niggli_reduce(atoms)
cell = atoms.get_cell()
if not cellbounds.is_within_bounds(cell):
# Niggli reduction did not bring the unit cell
# within the specified bounds; this candidate should
# be discarded so we set an absurdly high energy
finalize(atoms, 1e9)
return
ecf = ExpCellFilter(atoms)
dyn = FIRE(ecf, maxmove=0.2, logfile=None, trajectory=None)
dyn.run(fmax=1e-3, steps=100)
converged = dyn.converged()
niter += 1
dyn = FIRE(atoms, maxmove=0.2, logfile=None, trajectory=None)
dyn.run(fmax=1e-2, steps=100)
e = atoms.get_potential_energy()
f = atoms.get_forces()
s = atoms.get_stress()
finalize(atoms, energy=e, forces=f, stress=s)
|
