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
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
|
"""Test suit for the CP2K ASE calulator.
http://www.cp2k.org
Author: Ole Schuett <ole.schuett@mat.ethz.ch>
"""
import subprocess
import numpy as np
import pytest
from ase.build import molecule
from ase import io
from ase.io.cp2k import iread_cp2k_dcd
from ase.calculators.calculator import compare_atoms
inp = """\
&MOTION
&PRINT
&TRAJECTORY SILENT
FORMAT DCD_ALIGNED_CELL
&END TRAJECTORY
&END PRINT
&MD
STEPS 5
&END MD
&END MOTION
&GLOBAL
RUN_TYPE MD
&END GLOBAL
"""
@pytest.mark.calculator_lite
@pytest.mark.calculator('cp2k')
def test_dcd(factory, factories):
# (Should the cp2k_main executable live on the cp2k factory?)
exes = factories.executables
cp2k_main = exes.get('cp2k_main')
if cp2k_main is None:
pytest.skip('Please define "cp2k_main" in testing executables. '
'It should point to the main cp2k executable '
'(not the shell)')
calc = factory.calc(label='test_dcd', max_scf=1, inp=inp)
h2 = molecule('H2', calculator=calc)
h2.center(vacuum=2.0)
h2.set_pbc(True)
energy = h2.get_potential_energy()
assert energy is not None
subprocess.check_call([cp2k_main, '-i', 'test_dcd.inp', '-o',
'test_dcd.out'])
h2_end = io.read('test_dcd-pos-1.dcd')
assert (h2_end.symbols == 'X').all()
traj = io.read('test_dcd-pos-1.dcd', ref_atoms=h2,
index=slice(0, None), aligned=True)
ioITraj = io.iread('test_dcd-pos-1.dcd', ref_atoms=h2,
index=slice(0, None), aligned=True)
with open('test_dcd-pos-1.dcd', 'rb') as fd:
itraj = iread_cp2k_dcd(fd, indices=slice(0, None),
ref_atoms=h2, aligned=True)
for i, iMol in enumerate(itraj):
ioIMol = next(ioITraj)
assert compare_atoms(iMol, traj[i]) == []
assert compare_atoms(iMol, ioIMol) == []
assert iMol.get_pbc().all()
traj = io.read('test_dcd-pos-1.dcd', ref_atoms=h2, index=slice(0, None))
pbc = [mol.get_pbc() for mol in traj]
assert not np.any(pbc)
|
