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
|
# fmt: off
import pytest
import ase.units as units
from ase.calculators.qmmm import EIQMMM, LJInteractions, SimpleQMMM
from ase.calculators.tip3p import TIP3P, angleHOH, epsilon0, rOH, sigma0
from ase.constraints import FixBondLengths
from ase.data.s22 import create_s22_system as s22
from ase.md.verlet import VelocityVerlet
@pytest.mark.slow()
def test_rattle(testdir):
i = LJInteractions({('O', 'O'): (epsilon0, sigma0)})
for calc in [TIP3P(),
SimpleQMMM([0, 1, 2], TIP3P(), TIP3P(), TIP3P()),
EIQMMM([0, 1, 2], TIP3P(), TIP3P(), i)]:
dimer = s22('Water_dimer')
for m in [0, 3]:
dimer.set_angle(m + 1, m, m + 2, angleHOH)
dimer.set_distance(m, m + 1, rOH, fix=0)
dimer.set_distance(m, m + 2, rOH, fix=0)
fixOH1 = [(3 * i, 3 * i + 1) for i in range(2)]
fixOH2 = [(3 * i, 3 * i + 2) for i in range(2)]
fixHH = [(3 * i + 1, 3 * i + 2) for i in range(2)]
dimer.set_constraint(FixBondLengths(fixOH1 + fixOH2 + fixHH))
dimer.calc = calc
e = dimer.get_potential_energy()
with VelocityVerlet(dimer, 8.0 * units.fs,
trajectory=calc.name + '.traj',
logfile=calc.name + '.log',
loginterval=5) as md:
md.run(25)
de = dimer.get_potential_energy() - e
assert abs(de - -0.028) < 0.001
|
