Пример #1
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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)
Пример #2
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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)
Пример #3
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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
Пример #4
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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:])
Пример #5
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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)
Пример #7
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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])
Пример #8
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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
Пример #11
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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)
Пример #12
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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)
Пример #13
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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)
Пример #14
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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])