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import filecmp
import pytest
from ase.build import molecule
from ase.io import read, write
from ase.calculators.calculator import compare_atoms
from ase.calculators.emt import EMT
def atoms_equal(atoms1, atoms2):
# Check that the tolerance is compatible with the writer's precision
return compare_atoms(atoms1, atoms2, tol=1e-8) == []
def test_single_write_and_read():
# Test that `format='extxyz', plain=True` writes a standard xyz file
# like the `format='xyz'`
atoms = molecule('H2O')
write('1.xyz', atoms, format='extxyz', plain=True)
write('2.xyz', atoms, format='xyz', fmt='%16.8f')
assert filecmp.cmp('1.xyz', '2.xyz', shallow=False), 'Files differ'
# Test reading
atoms1 = read('1.xyz', format='xyz')
assert atoms_equal(atoms, atoms1), 'Read failed'
def test_single_write_with_forces():
# Create atoms with forces and test that
# those aren't written to the file
atoms = molecule('CO')
atoms.calc = EMT()
atoms.get_forces()
write('1.xyz', atoms, format='extxyz', plain=True)
write('2.xyz', atoms, format='xyz', fmt='%16.8f')
write('3.xyz', molecule('CO'), format='xyz', fmt='%16.8f')
assert filecmp.cmp('1.xyz', '2.xyz', shallow=False), 'Files differ'
assert filecmp.cmp('1.xyz', '3.xyz', shallow=False), 'Files differ'
def test_single_write_and_read_with_comment():
# Test writing
atoms = molecule('C6H6')
comment = 'my comment'
write('1.xyz', atoms, format='extxyz', plain=True, comment=comment)
write('2.xyz', atoms, format='xyz', fmt='%16.8f', comment=comment)
assert filecmp.cmp('1.xyz', '2.xyz', shallow=False), 'Files differ'
# Test reading
atoms1 = read('1.xyz', format='xyz')
assert atoms_equal(atoms, atoms1), 'Read failed'
@pytest.mark.parametrize('format', ['xyz', 'extxyz'])
def test_single_write_with_newline_comment(format):
# Test writing
atoms = molecule('C6H6')
comment = 'my comment\nnext line'
try:
write('atoms.xyz', atoms, format=format, comment=comment)
except ValueError as e:
assert 'comment line' in str(e).lower()
else:
raise RuntimeError('Write should fail for newlines in comment.')
def test_multiple_write_and_read():
images = []
for name in ['C6H6', 'H2O', 'CO']:
images.append(molecule(name))
write('1.xyz', images, format='extxyz', plain=True)
write('2.xyz', images, format='xyz', fmt='%16.8f')
assert filecmp.cmp('1.xyz', '2.xyz', shallow=False), 'Files differ'
# Test reading
images1 = read('1.xyz', format='xyz', index=':')
assert len(images) == len(images1)
for atoms, atoms1 in zip(images, images1):
assert atoms_equal(atoms, atoms1), 'Read failed'
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