def test_read_write_0():
xyz = 10 * np.random.randn(100, 11, 3)
lengths = np.ones(shape=(100, 3))
angles = np.empty(shape=(100, 3))
angles.fill(45)
with LAMMPSTrajectoryFile(temp, mode='w') as f:
f.write(xyz, lengths, angles)
with LAMMPSTrajectoryFile(temp) as f:
xyz2, new_lengths, new_angles = f.read()
eq(lengths, new_lengths)
eq(angles, new_angles)
eq(xyz, xyz2, decimal=3)
def test_multiread():
reference = md.load(get_fn('frame0.lammpstrj'), top=get_fn('native.pdb'))
with LAMMPSTrajectoryFile(get_fn('frame0.lammpstrj')) as f:
xyz0, _, _ = f.read(n_frames=1)
xyz1, _, _ = f.read(n_frames=1)
eq(reference.xyz[0], xyz0[0] / 10)
eq(reference.xyz[1], xyz1[0] / 10)
def test_seek():
reference = md.load(get_fn('frame0.lammpstrj'), top=get_fn('native.pdb'))
with LAMMPSTrajectoryFile(get_fn('frame0.lammpstrj')) as f:
f.seek(1)
eq(1, f.tell())
xyz1, _, _ = f.read(n_frames=1)
eq(reference.xyz[1], xyz1[0] / 10)
f.seek(10)
eq(10, f.tell())
xyz10, _, _ = f.read(n_frames=1)
eq(reference.xyz[10], xyz10[0] / 10)
eq(11, f.tell())
f.seek(-8, 1)
xyz3, _, _ = f.read(n_frames=1)
eq(reference.xyz[3], xyz3[0] / 10)
f.seek(4, 1)
xyz8, _, _ = f.read(n_frames=1)
eq(reference.xyz[8], xyz8[0] / 10)
def test_read_0():
with LAMMPSTrajectoryFile(get_fn('frame0.lammpstrj')) as f:
xyz, _, _ = f.read()
with LAMMPSTrajectoryFile(get_fn('frame0.lammpstrj')) as f:
xyz3, _, _ = f.read(stride=3)
eq(xyz[::3], xyz3)