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import warnings
import pytest
import numpy as np
from ase import Atoms
from ase.io import write, read, iread
from ase.io.formats import all_formats, ioformats
from ase.calculators.singlepoint import SinglePointCalculator
try:
import matplotlib
except ImportError:
matplotlib = 0
try:
import netCDF4
except ImportError:
netCDF4 = 0
@pytest.fixture
def atoms():
a = 5.0
d = 1.9
c = a / 2
atoms = Atoms('AuH',
positions=[(0, c, c), (d, c, c)],
cell=(2 * d, a, a),
pbc=(1, 0, 0))
extra = np.array([2.3, 4.2])
atoms.set_array('extra', extra)
atoms *= (2, 1, 1)
# attach some results to the Atoms.
# These are serialised by the extxyz writer.
spc = SinglePointCalculator(atoms,
energy=-1.0,
stress=[1.0, 2.0, 3.0, 4.0, 5.0, 6.0],
forces=-1.0 * atoms.positions)
atoms.calc = spc
return atoms
def check(a, ref_atoms, format):
assert abs(a.positions - ref_atoms.positions).max() < 1e-6, \
(a.positions - ref_atoms.positions)
if format in ['traj', 'cube', 'cfg', 'struct', 'gen', 'extxyz',
'db', 'json', 'trj']:
assert abs(a.cell - ref_atoms.cell).max() < 1e-6
if format in ['cfg', 'extxyz']:
assert abs(a.get_array('extra') -
ref_atoms.get_array('extra')).max() < 1e-6
if format in ['extxyz', 'traj', 'trj', 'db', 'json']:
assert (a.pbc == ref_atoms.pbc).all()
assert a.get_potential_energy() == ref_atoms.get_potential_energy()
assert (a.get_stress() == ref_atoms.get_stress()).all()
assert abs(a.get_forces() - ref_atoms.get_forces()).max() < 1e-12
@pytest.fixture
def catch_warnings():
with warnings.catch_warnings():
yield
def all_tested_formats():
skip = []
# Someone should do something ...
skip += ['dftb', 'eon', 'lammps-data']
# Standalone test used as not compatible with 1D periodicity
skip += ['v-sim', 'mustem', 'prismatic']
# We have a standalone dmol test
skip += ['dmol-arc', 'dmol-car', 'dmol-incoor']
# Complex dependencies; see animate.py test
skip += ['gif', 'mp4']
# Let's not worry about these.
skip += ['postgresql', 'trj', 'vti', 'vtu', 'mysql']
if not matplotlib:
skip += ['eps', 'png']
if not netCDF4:
skip += ['netcdftrajectory']
return sorted(set(all_formats) - set(skip))
@pytest.mark.parametrize('format', all_tested_formats())
def test_ioformat(format, atoms, catch_warnings):
if format in ['proteindatabank', 'netcdftrajectory']:
warnings.simplefilter('ignore', UserWarning)
# netCDF4 uses np.bool which may cause warnings in new numpy.
warnings.simplefilter('ignore', DeprecationWarning)
if format == 'dlp4':
atoms.pbc = (1, 1, 0)
images = [atoms, atoms]
io = ioformats[format]
print('{0:20}{1}{2}{3}{4}'.format(format,
' R'[io.can_read],
' W'[io.can_write],
'+1'[io.single],
'SF'[io.acceptsfd]))
fname1 = 'io-test.1.{}'.format(format)
fname2 = 'io-test.2.{}'.format(format)
if io.can_write:
write(fname1, atoms, format=format)
if not io.single:
write(fname2, images, format=format)
if io.can_read:
for a in [read(fname1, format=format), read(fname1)]:
check(a, atoms, format)
if not io.single:
if format in ['json', 'db']:
aa = read(fname2, index='id=1') + read(fname2, index='id=2')
else:
aa = [read(fname2), read(fname2, 0)]
aa += read(fname2, ':')
for a in iread(fname2, format=format):
aa.append(a)
assert len(aa) == 6, aa
for a in aa:
check(a, atoms, format)
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