def test_random_distance():
system = System(box_size=[10, 10, 10])
methane = Molecule(os.path.join(here, 'data', 'methane.xyz'))
system.add_molecules(methane, n=4)
config = system.random(min_dist_threshold=1.5)
for coord in config.coordinates():
assert np.min(coord) > 0.0
assert np.max(coord) < 10 - 1.5
def test_perturbation():
system = System(box_size=[7, 7, 7])
system.add_molecules(h2o, n=5)
config = system.random(min_dist_threshold=1.5, sigma=0.1, max_length=0.2)
pcoords = config.coordinates()
# Adding a displacement to each atom should still afford a reasonably
# sensible structure (no short distances)
dist_matrix = distance_matrix(pcoords, pcoords)
dist_matrix += np.identity(len(pcoords))
assert np.min(dist_matrix) > 0.6
def test_autode_parallel_orca():
if 'GT_ORCA' not in os.environ or not os.environ['GT_ORCA'] == 'True':
return
# Check that orca runs work
water = System(box_size=[10, 10, 10])
water.add_molecules(h2o, n=2)
configs = Data()
for _ in range(3):
configs += water.random(with_intra=True)
configs.parallel_orca()
def test_autode_xtb():
if 'GT_XTB' not in os.environ or not os.environ['GT_XTB'] == 'True':
return
# Check that orca and xtb runs work
water = System(box_size=[10, 10, 10])
water.add_molecules(h2o, n=5)
config = water.random()
config.run_xtb()
assert config.energy is not None
assert config.forces is not None
def test_random_grid_positions():
system = System(box_size=[10, 12, 14])
methane = Molecule(os.path.join(here, 'data', 'methane.xyz'))
system.add_molecules(methane, n=5)
config = system.random(grid=True)
config.save(filename='test_random.xyz')
# Minimum pairwise distance should be ~ the C-H distance (1.109 Å)
atoms = xyz_file_to_atoms('test_random.xyz')
coords = np.array([atom.coord for atom in atoms])
dist_matrix = distance_matrix(coords, coords)
# Distance matrix has zeros along the diagonals so add the identity
assert np.min(dist_matrix + 9 * np.identity(len(coords))) > 1.1
os.remove('test_random.xyz')
def test_histogram():
water_dimer = System(box_size=[7, 7, 7])
water_dimer.add_molecules(h2o, n=2)
data = Data(name='test')
data += water_dimer.random()
# Can't histogram energies and forces with no energies
with pytest.raises(NoEnergy):
data.histogram(name='test')
data[0].energy = 1
data[0].forces = np.zeros(shape=(6, 3))
data.histogram(name='test')
assert os.path.exists('test.png')
os.remove('test.png')
def test_gap():
water_dimer = System(box_size=[7, 7, 7])
water_dimer.add_molecules(h2o, n=2)
data = Data(name='test')
for _ in range(2):
data += water_dimer.random()
assert len(data) == 2
coords1 = data[0].coordinates()
assert coords1.shape == (6, 3)
coords2 = data[1].coordinates()
# Coordinates should be somewhat different
assert np.min(distance_matrix(coords1, coords2)) > 1E-3
def test_with_charges():
# Slightly modified ASE calculator to be compatible with the latest DFTB+
calculator = DFTB()
assert isinstance(calculator, Dftb)
# Can't get the fermi level with no calculation run
with pytest.raises(TypeError):
calculator.read_fermi_levels()
if 'GT_DFTB' not in os.environ or not os.environ['GT_DFTB'] == 'True':
return
# Check that charges work
na_water = System(box_size=[10, 10, 10])
na_water.add_molecules(Ion('Na', charge=1), n=1)
na_water.add_molecules(h2o, n=5)
assert na_water.charge() == 1
config = na_water.random()
config.run_dftb()
