def test_msd_com_removal(self, universe):
msd = MSD(universe, **self.kwargs, com_removal_sel="all")
msd.run(stop=2)
reference = {
'n_residues': 1,
'n_frames': 2,
'msd': [[0.0, 0.0]],
'lagtimes': [0.0, 5.0]
}
assert msd.msd.shape == (reference['n_residues'], reference['n_frames'])
assert_array_almost_equal(msd.msd, reference['msd'])
assert_array_almost_equal(msd.lagtimes, reference['lagtimes'])
def test_diffusion_coefficient_lipid_sel(self, universe):
msd = MSD(universe, **self.kwargs)
msd.msd = np.asarray([np.arange(100)])
msd.lagtimes = np.arange(100)
reference = {
'd': 0.25 * 1e-5
}
d, sem = msd.diffusion_coefficient(lipid_sel="all")
assert d == reference['d']
assert np.isnan(sem) # we only have 1 molecule, so there is no SEM
def test_msd(self, universe):
msd = MSD(universe, **self.kwargs)
msd.run(stop=2)
reference = {
'n_residues': 1,
'n_frames': 2,
'msd': [[0.0, 0.04394855]],
'lagtimes': [0.0, 5000.0]
}
assert msd.msd.shape == (reference['n_residues'], reference['n_frames'])
assert_array_almost_equal(msd.msd, reference['msd'])
assert_array_almost_equal(msd.lagtimes, reference['lagtimes'])