def test_raises_error_when_direction_not_found(self):
path = "./files/water_on_graphene"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
with pytest.raises(analysis.KeyNotFound):
simulation.compute_density_profile(["O", "H"], direction="w")
def test_returns_profile_radial_direction_parallel_to_z_axis(self):
path = "./files/water_in_carbon_nanotube/m12_n12/classical"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.compute_density_profile(["O", "H"], direction="radial z")
assert simulation.density_profiles.get("O H - radial z")
def test_raises_error_when_correlation_time_is_too_high(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True, topology_file_name=topology_name)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
with pytest.raises(analysis.UnphysicalValue):
simulation.compute_mean_squared_displacement(["O", "H"], correlation_time=100000)
def test_returns_profile_in_z_direction(self):
path = "./files/water_on_graphene"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.compute_density_profile(["O", "H"], direction="z")
assert simulation.density_profiles.get("O H - z")
def test_raises_error_when_species_not_found(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True, topology_file_name=topology_name)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
with pytest.raises(analysis.KeyNotFound):
simulation.compute_rdf("O", "X")
def test_returns_error_for_three_periodic_directions(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True, topology_file_name=topology_name)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
with pytest.raises(analysis.UnphysicalValue):
simulation.get_water_contact_layer_on_interface()
def test_raises_error_when_unknown_fluid(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(
read_positions=True, topology_file_name=topology_name)
with pytest.raises(utils.UndefinedOption):
correction = (
utils.
compute_finite_size_correction_for_diffusion_coefficient_of_bulk_fluid(
simulation.topology, fluid="hexane", temperature=330))
def test_returns_correction(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(
read_positions=True, topology_file_name=topology_name)
correction = (
utils.
compute_finite_size_correction_for_diffusion_coefficient_of_bulk_fluid(
simulation.topology, fluid="water", temperature=330))
assert correction
def test_raises_error_when_number_of_blocks_is_too_high(self):
path = "./files/water_in_carbon_nanotube/m12_n12/quantum"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=False, read_summed_forces=True)
with pytest.raises(analysis.UnphysicalValue):
simulation.compute_friction_coefficient_via_green_kubo(
time_between_frames=1,
correlation_time=1000,
number_of_blocks=3000,
start_time=1000,
end_time=4500,
frame_frequency=1,
)
def test_raises_error_when_unknown_dimension(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True, topology_file_name=topology_name)
oxygens = simulation.position_universes[0].select_atoms("name O")
vectors_oxygen_1_to_others = oxygens.positions - oxygens[0].position
with pytest.raises(utils.UndefinedOption):
vectors_MIC = utils.apply_minimum_image_convention_to_interatomic_vectors(
vectors_oxygen_1_to_others, simulation.topology.cell, dimension="w"
)
def test_returns_MSD_for_bulk_water_based_on_water_COM(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True, topology_file_name=topology_name)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.compute_mean_squared_displacement(
["O", "H"], correlation_time=200, number_of_blocks=5
)
assert simulation.mean_squared_displacements.get("O H - ct: 200")
def test_returns_reorientational_relaxation_time_for_bulk_water_full(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True, topology_file_name=topology_name)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.compute_water_reorientational_relaxation_time(regime="Full", correlation_time=1000, number_of_blocks=1)
breakpoint()
assert simulation.reorientational_relaxation_time.get('reg: Full; ct: 1000')
def test_returns_profile_in_radial_direction_OH(self):
path = "./files/water_in_carbon_nanotube/m12_n12/classical"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.set_pbc_dimensions("z")
simulation.compute_water_orientation_profile(water_vector="O-H",frame_frequency=10)
assert (
np.max(simulation.water_orientations_spatially_resolved["O-H"][0][:, 0]) <= 1
and np.min(simulation.water_orientations_spatially_resolved["O-H"][0][:, 0]) >= -1
)
def test_returns_profile_in_z_direction(self):
path = "./files/water_on_graphene"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.set_pbc_dimensions("xy")
simulation.compute_water_orientation_profile(frame_frequency=10)
assert (
np.max(simulation.water_orientations_spatially_resolved["Dipole"][0][:, 0]) <= 1
and np.min(simulation.water_orientations_spatially_resolved["Dipole"][0][:, 0]) >= -1
)
def test_returns_contact_layer_for_one_dimensions(self):
path = "./files/water_in_carbon_nanotube/m12_n12/classical"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_pbc_dimensions("z")
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.compute_density_profile(["O", "H"], direction="radial z")
spatial_expansion_contact_layer = simulation.get_water_contact_layer_on_interface()
assert spatial_expansion_contact_layer > 0
def test_returns_reorientational_relaxation_time_for_nanotube_in_bulk_regime(self):
path = "./files/water_in_carbon_nanotube/m12_n12/classical"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.set_pbc_dimensions("z")
simulation.compute_density_profile(["O", "H"], direction="radial z")
simulation.compute_water_reorientational_relaxation_time(regime="Bulk", correlation_time=1000, number_of_blocks=1)
assert simulation.reorientational_relaxation_time.get('reg: Bulk; ct: 1000')
def test_returns_reorientational_relaxation_time_for_graphene_full(self):
path = "./files/water_on_graphene"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.set_pbc_dimensions("xy")
simulation.compute_density_profile(["O", "H"], direction="z")
simulation.compute_water_reorientational_relaxation_time(regime="Full", correlation_time=1000, number_of_blocks=1)
assert simulation.reorientational_relaxation_time.get('reg: Full; ct: 1000')
def test_returns_adjusted_vectors_2D(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True,
topology_file_name=topology_name)
oxygens = simulation.position_universes[0].select_atoms("name O")
vectors_oxygen_1_to_others = oxygens.positions - oxygens[0].position
vectors_MIC = utils.apply_minimum_image_convention_to_interatomic_vectors(
vectors_oxygen_1_to_others,
simulation.topology.cell,
)
assert (np.min(vectors_MIC) >= -simulation.topology.cell[0][0] / 2
and np.max(vectors_MIC) <= simulation.topology.cell[0][0] / 2)
def test_returns_pandas_dataframe_for_bulk_water(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True,
topology_file_name=topology_name)
hydrogen_bonding_analysis = hydrogen_bonding.HydrogenBonding(
simulation.position_universes[0], simulation.topology)
hydrogen_bonding_analysis.find_acceptor_donor_pairs(
start_frame=0,
end_frame=-1,
frame_frequency=10,
time_between_frames=20,
pbc_dimensions="xyz",
)
assert np.max(hydrogen_bonding_analysis.dataframe["Time"]) == 2000
def test_returns_diffusion_coefficient(self):
path = "./files/water_in_carbon_nanotube/m12_n12/classical"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(
read_positions=True, read_velocities=True, read_summed_forces=False
)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.compute_diffusion_coefficient_via_green_kubo(
species=["O"],
correlation_time=1000,
number_of_blocks=3,
start_time=1000,
end_time=20000,
)
assert len(simulation.diffusion_coefficients_via_GK["O - ct: 1000"]) == 3
def test_returns_correct_autocorrelation_function(self):
path = "./files/water_in_carbon_nanotube/m12_n12/classical"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True, read_summed_forces=True)
simulation.set_pbc_dimensions(pbc_dimensions="z")
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.compute_friction_coefficient_via_green_kubo(
time_between_frames=1,
correlation_time=1000,
number_of_blocks=3,
start_time=1000,
end_time=4500,
frame_frequency=1,
)
assert simulation.friction_coefficients.get("ct: 1000")
def test_returns_pandas_dataframe_for_carbon_nanotube(self):
path = "./files/water_in_carbon_nanotube/m12_n12/classical"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_pbc_dimensions("z")
hydrogen_bonding_analysis = hydrogen_bonding.HydrogenBonding(
simulation.position_universes[0], simulation.topology)
hydrogen_bonding_analysis.find_acceptor_donor_pairs(
start_frame=0,
end_frame=-1,
frame_frequency=10,
time_between_frames=20,
pbc_dimensions="z",
)
assert np.max(hydrogen_bonding_analysis.dataframe["Time"]) == 2000
def test_returns_pandas_dataframe_for_graphene(self):
path = "./files/water_on_graphene/"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True)
simulation.set_pbc_dimensions("xy")
hydrogen_bonding_analysis = hydrogen_bonding.HydrogenBonding(
simulation.position_universes[0], simulation.topology)
hydrogen_bonding_analysis.heavy_atoms_analysis(
start_frame=0,
end_frame=-1,
frame_frequency=10,
time_between_frames=20,
pbc_dimensions="xy",
spatial_extent_contact_layer=3.65)
assert len(
np.unique(hydrogen_bonding_analysis.
heavy_atoms_dataframe["Species"])) == 2
def test_returns_same_result_as_vmd(self):
path = "./files/bulk_water/classical"
vmd_data = pandas.read_csv(
os.path.join(path, "rdf_vmd.dat"), sep=r"\s", engine="python", header=None
)
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(read_positions=True, topology_file_name=topology_name)
simulation.set_sampling_times(
start_time=0, end_time=-1, frame_frequency=1, time_between_frames=20
)
simulation.compute_rdf("O", "O", spatial_range=6.2, spatial_resolution=309)
assert (
mean_squared_error(
vmd_data[1][1::], simulation.radial_distribution_functions["O-O"][1], squared=False
)
< 2e-2
)
def test_returns_correct_center_of_masses(self):
path = "./files/bulk_water/classical"
topology_name = "revPBE0-D3-w64-T300K-1bar"
simulation = analysis.Simulation(path)
simulation.read_in_simulation_data(
read_positions=True, topology_file_name=topology_name)
water_atoms = simulation.position_universes[0].select_atoms(
"name O H")
water_atoms.pack_into_box(
box=simulation.topology.get_cell_lengths_and_angles(),
inplace=True)
water_molecule_58 = water_atoms[174:177]
center_of_mass_MIC = utils.get_center_of_mass_of_atoms_in_accordance_with_MIC(
water_molecule_58, simulation.topology, dimension="xyz")
assert np.all(center_of_mass_MIC <= simulation.topology.
get_cell_lengths_and_angles()[0:3]) and np.all(
center_of_mass_MIC >= np.zeros(3))
