def test_detect_bonds_water_exceptions():
system = get_system_water32()
# create system without bonds
system = System(system.numbers, system.pos)
# Add bonds between hydrogen atoms (unrealistic but useful for testing)
system.detect_bonds({(1, 1): 2.0 * angstrom})
assert system.nbond >= 96
def test_detect_bonds_water_exceptions():
system = get_system_water32()
# create system without bonds
system = System(system.numbers, system.pos)
# Add bonds between hydrogen atoms (unrealistic but useful for testing)
system.detect_bonds({(1,1): 2.0*angstrom})
assert system.nbond >= 96
def test_xyz():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_xyz')
try:
system0.to_file('%s/tmp.xyz' % dirname)
system1 = System.from_file('%s/tmp.xyz' % dirname, rvecs=system0.cell.rvecs, ffatypes=system0.ffatypes, ffatype_ids=system0.ffatype_ids)
compare_water32(system0, system1, 1e-10, xyz=True)
finally:
shutil.rmtree(dirname)
def test_chk():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_chk')
try:
system0.to_file('%s/tmp.chk' % dirname)
system1 = System.from_file('%s/tmp.chk' % dirname)
compare_water32(system0, system1, 1e-10)
finally:
shutil.rmtree(dirname)
def test_chk():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_chk')
try:
system0.to_file('%s/tmp.chk' % dirname)
system1 = System.from_file('%s/tmp.chk' % dirname)
compare_water32(system0, system1, 1e-10)
finally:
shutil.rmtree(dirname)
def test_xyz():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_xyz')
try:
system0.to_file('%s/tmp.xyz' % dirname)
system1 = System.from_file('%s/tmp.xyz' % dirname, rvecs=system0.cell.rvecs, ffatypes=system0.ffatypes, ffatype_ids=system0.ffatype_ids)
compare_water32(system0, system1, 1e-10, xyz=True)
finally:
shutil.rmtree(dirname)
def test_hdf5():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_hdf5')
try:
fn = '%s/tmp.h5' % dirname
system0.to_file(fn)
with h5.File(fn) as f:
assert 'system' in f
system1 = System.from_file(fn)
compare_water32(system0, system1)
finally:
shutil.rmtree(dirname)
def test_hdf5():
system0 = get_system_water32()
dirname = tempfile.mkdtemp('yaff', 'test_hdf5')
try:
fn = '%s/tmp.h5' % dirname
system0.to_file(fn)
with h5.File(fn) as f:
assert 'system' in f
system1 = System.from_file(fn)
compare_water32(system0, system1)
finally:
shutil.rmtree(dirname)
def test_ffatypes():
system = get_system_water32()
assert (system.ffatypes == ['O', 'H']).all()
assert (system.ffatype_ids[system.numbers==8] == 0).all()
assert (system.ffatype_ids[system.numbers==1] == 1).all()
def test_detect_bonds_water32():
system = get_system_water32()
assert system.nbond == 64
check_detect_bonds(system)
def test_ffatypes():
system = get_system_water32()
assert (system.ffatypes == ['O', 'H']).all()
assert (system.ffatype_ids[system.numbers == 8] == 0).all()
assert (system.ffatype_ids[system.numbers == 1] == 1).all()
def test_detect_bonds_water32():
system = get_system_water32()
assert system.nbond == 64
check_detect_bonds(system)
def test_iter_matches_water4_nonoverlapping():
system = get_system_water32().subsystem(range(12))
water = system.subsystem([0, 1, 2])
assert len(list(system.iter_matches(water))) == 8
assert len(list(system.iter_matches(water, overlapping=False))) == 4
