def test_extend_frame_props(self):
lattice = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
species = ["Si", "Si"]
frac_coords = [
[[0, 0, 0], [0.5, 0.5, 0.5]],
[[0.1, 0.1, 0.1], [0.6, 0.6, 0.6]],
[[0.2, 0.2, 0.2], [0.7, 0.7, 0.7]],
]
# Trajectories with constant site properties
frame_properties_1 = {"energy": [-3, -3.9, -4.1]}
traj_1 = Trajectory(lattice, species, frac_coords, frame_properties=frame_properties_1)
frame_properties_2 = {"energy": [-4.2, -4.25, -4.3]}
traj_2 = Trajectory(lattice, species, frac_coords, frame_properties=frame_properties_2)
# Test combining two trajectories with similar site_properties
traj_combined = traj_1.copy()
traj_combined.extend(traj_2)
expected_frame_properties = {"energy": [-3, -3.9, -4.1, -4.2, -4.25, -4.3]}
self.assertEqual(traj_combined.frame_properties, expected_frame_properties)
# Mismatched frame propertied
frame_properties_3 = {"energy": [-4.2, -4.25, -4.3], "pressure": [2, 2.5, 2.5]}
traj_3 = Trajectory(lattice, species, frac_coords, frame_properties=frame_properties_3)
traj_combined = traj_1.copy()
traj_combined.extend(traj_3)
expected_frame_properties = {
"energy": [-3, -3.9, -4.1, -4.2, -4.25, -4.3],
"pressure": [None, None, None, 2, 2.5, 2.5],
}
self.assertEqual(traj_combined.frame_properties, expected_frame_properties)
def test_extend_equivalent_site_props(self):
lattice = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
species = ["Si", "Si"]
frac_coords = [
[[0, 0, 0], [0.5, 0.5, 0.5]],
[[0.1, 0.1, 0.1], [0.6, 0.6, 0.6]],
[[0.2, 0.2, 0.2], [0.7, 0.7, 0.7]],
]
# Trajectories with constant site properties
site_properties_1 = [
{
"selective_dynamics": [[True, True, True], [False, False, False]],
"magmom": [5, 5],
}
]
traj_1 = Trajectory(lattice, species, frac_coords, site_properties=site_properties_1)
site_properties_2 = [
{
"selective_dynamics": [[True, True, True], [False, False, False]],
"magmom": [5, 5],
}
]
traj_2 = Trajectory(lattice, species, frac_coords, site_properties=site_properties_2)
# Test combining two trajectories with similar site_properties
traj_combined = traj_1.copy()
traj_combined.extend(traj_2)
self.assertEqual(traj_combined.site_properties, site_properties_1)
def test_extend_no_frame_props(self):
lattice = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
species = ['Si', 'Si']
frac_coords = [[[0, 0, 0], [0.5, 0.5, 0.5]],
[[0.1, 0.1, 0.1], [0.6, 0.6, 0.6]],
[[0.2, 0.2, 0.2], [0.7, 0.7, 0.7]]]
# Trajectory with no site_properties
traj_1 = Trajectory(lattice, species, frac_coords)
traj_2 = Trajectory(lattice, species, frac_coords)
# Test combining two trajectories with no site properties
traj_combined = traj_1.copy()
traj_combined.extend(traj_2)
self.assertEqual(traj_combined.frame_properties, None)
def test_extend_inequivalent_site_props(self):
lattice = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
species = ["Si", "Si"]
frac_coords = [
[[0, 0, 0], [0.5, 0.5, 0.5]],
[[0.1, 0.1, 0.1], [0.6, 0.6, 0.6]],
[[0.2, 0.2, 0.2], [0.7, 0.7, 0.7]],
]
# Trajectories with constant site properties
site_properties_1 = [
{
"selective_dynamics": [[False, False, False], [False, False, False]],
"magmom": [5, 5],
}
]
traj_1 = Trajectory(lattice, species, frac_coords, site_properties=site_properties_1)
site_properties_2 = [
{
"selective_dynamics": [[True, True, True], [False, False, False]],
"magmom": [5, 5],
}
]
traj_2 = Trajectory(lattice, species, frac_coords, site_properties=site_properties_2)
# Test combining two trajectories with similar site_properties
traj_combined = traj_1.copy()
traj_combined.extend(traj_2)
expected_site_props = [
{
"selective_dynamics": [[False, False, False], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[False, False, False], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[False, False, False], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, True, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, True, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, True, True], [False, False, False]],
"magmom": [5, 5],
},
]
self.assertEqual(traj_combined.site_properties, expected_site_props)
# Trajectory with const site_properties and trajectory with changing site properties
site_properties_1 = [
{
"selective_dynamics": [[True, False, False], [False, False, False]],
"magmom": [5, 5],
}
]
traj_1 = Trajectory(lattice, species, frac_coords, site_properties=site_properties_1)
site_properties_2 = [
{
"selective_dynamics": [[False, True, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, True, False], [False, False, False]],
"magmom": [5, 5],
},
]
traj_2 = Trajectory(lattice, species, frac_coords, site_properties=site_properties_2)
# Test combining two trajectories with similar site_properties
traj_combined = traj_1.copy()
traj_combined.extend(traj_2)
expected_site_props = [
{
"selective_dynamics": [[True, False, False], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, False], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, False], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[False, True, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, True, False], [False, False, False]],
"magmom": [5, 5],
},
]
self.assertEqual(traj_combined.site_properties, expected_site_props)
# The other way around
traj_combined = traj_2.copy()
traj_combined.extend(traj_1)
expected_site_props = [
{
"selective_dynamics": [[False, True, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, True, False], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, False], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, False], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, False], [False, False, False]],
"magmom": [5, 5],
},
]
self.assertEqual(traj_combined.site_properties, expected_site_props)
# Trajectory with no and trajectory with changing site properties
site_properties_1 = None
traj_1 = Trajectory(lattice, species, frac_coords, site_properties=site_properties_1)
site_properties_2 = [
{
"selective_dynamics": [[False, True, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, True, False], [False, False, False]],
"magmom": [5, 5],
},
]
traj_2 = Trajectory(lattice, species, frac_coords, site_properties=site_properties_2)
# Test combining two trajectories with similar site_properties
traj_combined = traj_1.copy()
traj_combined.extend(traj_2)
expected_site_props = [
None,
None,
None,
{
"selective_dynamics": [[False, True, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, True, False], [False, False, False]],
"magmom": [5, 5],
},
]
self.assertEqual(traj_combined.site_properties, expected_site_props)
# The other way around
traj_combined = traj_2.copy()
traj_combined.extend(traj_1)
expected_site_props = [
{
"selective_dynamics": [[False, True, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, False, True], [False, False, False]],
"magmom": [5, 5],
},
{
"selective_dynamics": [[True, True, False], [False, False, False]],
"magmom": [5, 5],
},
None,
None,
None,
]
self.assertEqual(traj_combined.site_properties, expected_site_props)
