def test_trajectory_write_method(tmpdir):
""" Test trajectory class write method """
ref_traj = os.path.join(mof_trial_dir, 'Run1', 'traj.xyz')
traj = Trajectory(read=ref_traj)
temp_file = tmpdir.join('traj-temp.xyz')
traj.write(temp_file.strpath)
assert filecmp.cmp(ref_traj, temp_file.strpath)
def test_trajectory_stretch_method():
""" Test trajectory class stretch method for non-interpenetrated ideal MOF """
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
xyz_stretch1 = traj.stretch(1)
assert len(traj.xyz) == len(xyz_stretch1)
xyz_stretch3 = traj.stretch(3)
assert len(traj.xyz[0]) == len(xyz_stretch3[0])
assert len(traj.xyz[-1]) == len(xyz_stretch3[-1])
assert len(traj.xyz) * 3 == len(xyz_stretch3)
def load_sample_trajectory(mof='single', tests_dir=tests_dir):
""" Load a sample trajectory file from tests directory """
from thermof import Trajectory
if mof == 'single':
sample_traj = Trajectory(read=os.path.join(
tests_dir, 'ideal-mof-trial', 'Run1', 'traj.xyz'))
else:
sample_traj = Trajectory(
read=os.path.join(tests_dir, 'ip-mof-trial', 'Run1', 'traj.xyz'))
return sample_traj
def test_trajectory_subdivide_method_example_case():
""" Test trajectory class subdivision for non-interpenetrated ideal MOF example case """
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
div_traj = traj.subdivide(atoms=list(range(10, 20)),
frames=list(range(5, 10)),
dimensions=[1, 2])
assert (div_traj.n_frames, div_traj.n_atoms,
div_traj.n_dimensions) == (5, 10, 2)
assert div_traj.atoms == [frame[10:20] for frame in traj.atoms[5:10]]
assert np.allclose(div_traj.coordinates[0][0], traj.coordinates[5][10][1:])
assert np.allclose(div_traj.coordinates[4][3], traj.coordinates[9][13][1:])
def test_trajectory_stretch_method_with_write(tmpdir):
""" Test trajectory class stretch method for non-interpenetrated ideal MOF """
ref_traj = os.path.join(mof_trial_dir, 'Run1', 'traj.xyz')
traj = Trajectory(read=ref_traj)
with open(ref_traj, 'r') as rt:
ref_traj_lines = rt.readlines()
temp_file = tmpdir.join('traj-temp.xyz')
xyz_stretch = traj.stretch(2, temp_file.strpath)
with open(temp_file.strpath, 'r') as tf:
tmp_traj_lines = tf.readlines()
assert len(tmp_traj_lines) == len(ref_traj_lines) * 2
def test_calculate_mean_squared_disp_for_single_ideal_mof():
""" Test trajectory class calculate_mean_squared_disp function for single ideal mof """
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
traj.set_cell([80, 80, 80])
traj.calculate_distances()
traj.calculate_mean_squared_disp()
assert np.all(traj.mean_squared_disp > 0.0)
assert np.all(traj.mean_squared_disp < 0.4)
def test_trajectory_read_method_for_interpenetrated_ideal_mof():
""" Test trajectory class read method for interpenetrated ideal MOF """
traj = Trajectory(read=os.path.join(ipmof_trial_dir, 'Run1', 'traj.xyz'))
assert len(traj.xyz[0]) == 7170
assert traj.n_atoms == len(traj.atoms[0]) == 7168
assert len(traj.coordinates[0]) == 7168
assert len(traj) == traj.n_frames == 61
assert traj.coordinates[0][0] == [0, 0, 0]
assert np.allclose(traj.coordinates[-1][-1], [74.1941, 74.2373, 0.916302])
def test_trajectory_read_method_for_single_ideal_mof():
""" Test trajectory class read method for non-interpenetrated ideal MOF """
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
assert len(traj.xyz[0]) == 3586
assert traj.n_atoms == len(traj.atoms[0]) == 3584
assert len(traj.coordinates[0]) == 3584
assert len(traj) == traj.n_frames == 61
assert traj.coordinates[0][0] == [0, 0, 0]
assert np.allclose(traj.coordinates[-1][-1], [69.4517, 69.960, 76.5111])
def test_trajectory_change_atoms_for_interpenetrated_ideal_mof():
""" Test trajectory class change atoms method for interpenetrated ideal MOF """
traj = Trajectory(read=os.path.join(ipmof_trial_dir, 'Run1', 'traj.xyz'))
assert Counter(traj.get_unique_atoms()) == Counter(['1', '2'])
traj.change_atoms({'1': 'C', '2': 'O'})
assert Counter(traj.get_unique_atoms()) == Counter(['C', 'O'])
ref_atoms = ['C'] * int(traj.n_atoms / 2) + ['O'] * int(traj.n_atoms / 2)
assert [line.split()[0] for line in traj.xyz[0][2:]] == ref_atoms
assert traj.atoms[0] == ref_atoms
def test_trajectory_change_atoms_for_single_ideal_mof():
""" Test trajectory class change atoms method for non-interpenetrated ideal MOF """
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
assert traj.get_unique_atoms() == ['1']
traj.change_atoms({'1': 'C'})
assert traj.get_unique_atoms() == ['C']
ref_atoms = ['C'] * traj.n_atoms
assert [line.split()[0] for line in traj.xyz[0][2:]] == ref_atoms
assert traj.atoms[0] == ref_atoms
def test_calculate_distances_with_trajectory_calculate_distances(max_dist=5):
"""
Tests interatomic distance calculation for the Trajectory class
- Test first frame is all zeros
- Make sure all distances are less than max distance (5 A)
- Test a known distance
"""
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
traj.set_cell([80, 80, 80])
traj.calculate_distances()
distances = calculate_distances(traj.coordinates, [80, 80, 80],
reference_frame=0)
assert np.allclose(traj.distances, distances)
def test_trajectory_calculate_distances_nonzero_reference_frame(max_dist=5):
"""
Tests interatomic distance calculation for the Trajectory class
- Test seventh frame (reference frame) is all zeros
- Make sure all distances are less than max distance (5 A)
- Test a known distance
"""
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
traj.set_cell([80, 80, 80])
traj.calculate_distances(reference_frame=7)
assert np.allclose(traj.distances[7], np.zeros(traj.n_atoms))
for frame in traj.distances:
assert np.all(frame < max_dist)
assert np.isclose(traj.distances[0][3], 0.23030113908032163)
def test_trajectory_calculate_distances(max_dist=5):
"""
Tests interatomic distance calculation for the Trajectory class
- Test first frame is all zeros
- Make sure all distances are less than max distance (5 A)
- Test a known distance
"""
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
traj.set_cell([80, 80, 80])
traj.calculate_distances()
assert np.allclose(traj.distances[0], np.zeros(traj.n_atoms))
for frame in traj.distances:
assert np.all(frame < max_dist)
assert np.isclose(traj.distances[3][3], 0.5159079779340517)
def test_trajectory_subdivide_method_returns_same_trajectory_without_kwargs():
""" Test trajectory class subdivision method for non-interpenetrated ideal MOF with no kwargs """
traj = Trajectory(read=os.path.join(mof_trial_dir, 'Run1', 'traj.xyz'))
div_traj = traj.subdivide()
assert traj == div_traj
def test_calculate_mean_disp_and_mean_squared_disp_for_linear_motion_of_particles():
""" Test trajectory class calculate_mean_disp and calculate_mean_squared_disp functions
for 6 particles with linear motion with alternative calculation """
n_atoms, n_frames = 6, 6
traj = Trajectory()
traj.coordinates = [[[i + j, i + j, i + j] for i in range(n_atoms)] for j in range(n_frames)]
traj.n_atoms, traj.n_frames = n_atoms, n_frames
traj.set_cell([10, 10, 10])
traj.calculate_distances()
traj.calculate_mean_disp()
traj.calculate_mean_squared_disp()
assert np.allclose([np.sum(range(n_frames)) / n_frames * np.sqrt(3)] * n_atoms, traj.mean_disp)
for i in range(traj.n_atoms):
c0 = traj.coordinates[0][i]
x2 = (np.array([f[i][0] for f in traj.coordinates]) - c0[0]) ** 2
y2 = (np.array([f[i][1] for f in traj.coordinates]) - c0[1]) ** 2
z2 = (np.array([f[i][2] for f in traj.coordinates]) - c0[2]) ** 2
mean_squared_disp = sum(x2 + y2 + z2) / n_frames
mean_disp = sum(np.sqrt(x2 + y2 + z2)) / n_frames
assert np.allclose(mean_disp, traj.mean_disp[i])
assert np.allclose(mean_squared_disp, traj.mean_squared_disp[i])
def test_center_of_mass_for_interpenetrated_ideal_mof():
""" Test trajectory class read method for interpenetrated ideal MOF """
traj = Trajectory(read=os.path.join(ipmof_trial_dir, 'Run1', 'traj.xyz'))
traj.change_atoms({'1': 'C', '2': 'O'})
traj.calculate_com()
assert np.isclose(traj.com[0][0], traj.com[0][1], traj.com[0][2])