def test_md(factory):
# XXX ugly hack
ver = factory.factory.version()
if tokenize_version(ver) < tokenize_version('3.8'):
pytest.skip('No stress tensor until openmx 3.8+')
bud = Atoms('CH4',
np.array([[0.000000, 0.000000, 0.100000],
[0.682793, 0.682793, 0.682793],
[-0.682793, -0.682793, 0.68279],
[-0.682793, 0.682793, -0.682793],
[0.682793, -0.682793, -0.682793]]),
cell=[10, 10, 10])
calc = factory.calc(
label='ch4',
xc='GGA',
energy_cutoff=300 * Ry,
convergence=1e-4 * Ha,
# Use 'C_PBE19' and 'H_PBE19' for version 3.9
definition_of_atomic_species=[['C', 'C5.0-s1p1', 'C_PBE13'],
['H', 'H5.0-s1', 'H_PBE13']],
kpts=(1, 1, 1),
eigensolver='Band')
bud.calc = calc
with Trajectory('example.traj', 'w', bud) as traj:
ucf = UnitCellFilter(bud,
mask=[True, True, False, False, False, False])
dyn = QuasiNewton(ucf)
dyn.attach(traj.write)
dyn.run(fmax=0.1)
bud.get_potential_energy()
def require_version(self, version):
from ase.utils import tokenize_version
installed_version = self.factory.version()
old = tokenize_version(installed_version) < tokenize_version(version)
if old:
pytest.skip('Version too old: Requires {}; got {}'
.format(version, installed_version))
def test_dftb_bandstructure(dftb_factory):
# We need to get the DFTB+ version to know
# whether to skip this test or not.
# For this, we need to run DFTB+ and grep
# the version from the output header.
# cmd = os.environ['ASE_DFTB_COMMAND'].split()[0]
# cmd = dftb_factory.ex
version = dftb_factory.version()
if tokenize_version(version) < tokenize_version('17.1'):
pytest.skip('Band structure requires DFTB 17.1+')
calc = dftb_factory.calc(label='dftb',
kpts=(3, 3, 3),
Hamiltonian_SCC='Yes',
Hamiltonian_SCCTolerance=1e-5,
Hamiltonian_MaxAngularMomentum_Si='d')
atoms = bulk('Si')
atoms.calc = calc
atoms.get_potential_energy()
efermi = calc.get_fermi_level()
assert abs(efermi - -2.90086680996455) < 1.
# DOS does not currently work because of
# missing "get_k_point_weights" function
#from ase.dft.dos import DOS
#dos = DOS(calc, width=0.2)
#d = dos.get_dos()
#e = dos.get_energies()
#print(d, e)
calc = dftb_factory.calc(atoms=atoms,
label='dftb',
kpts={
'path': 'WGXWLG',
'npoints': 50
},
Hamiltonian_SCC='Yes',
Hamiltonian_MaxSCCIterations=1,
Hamiltonian_ReadInitialCharges='Yes',
Hamiltonian_MaxAngularMomentum_Si='d')
atoms.calc = calc
calc.calculate(atoms)
#calc.results['fermi_levels'] = [efermi]
calc.band_structure()
def read_atoms(backend,
header: Tuple = None,
traj: TrajectoryReader = None,
_try_except: bool = True) -> Atoms:
if _try_except:
try:
return read_atoms(backend, header, traj, False)
except Exception as ex:
if (traj is not None and tokenize_version(__version__) <
tokenize_version(traj.ase_version)):
msg = ('You are trying to read a trajectory file written '
f'by ASE-{traj.ase_version} from ASE-{__version__}. '
'It might help to update your ASE')
raise VersionTooOldError(msg) from ex
else:
raise
b = backend
if header:
pbc, numbers, masses, constraints = header
else:
pbc = b.pbc
numbers = b.numbers
masses = b.get('masses')
constraints = b.get('constraints', '[]')
atoms = Atoms(positions=b.positions,
numbers=numbers,
cell=b.cell,
masses=masses,
pbc=pbc,
info=b.get('info'),
constraint=[dict2constraint(d) for d in decode(constraints)],
momenta=b.get('momenta'),
magmoms=b.get('magmoms'),
charges=b.get('charges'),
tags=b.get('tags'))
return atoms
def test_tokenize_version_equal():
version = '3.8x.xx'
assert tokenize_version(version) == tokenize_version(version)
def test_tokenize_version_lessthan(v1, v2):
v1 = tokenize_version(v1)
v2 = tokenize_version(v2)
assert v1 < v2