def test_gsd_rdf_pair_order(self, gsdfile_bond):
rdf, norm = gsd_rdf(gsdfile_bond, "A", "B")
rdf_y = rdf.rdf*norm
rdf2, norm2 = gsd_rdf(gsdfile_bond, "B", "A")
rdf_y2 = rdf2.rdf*norm2
for i,j in zip(rdf_y, rdf_y2):
assert np.allclose(i,j,atol=1e-4)
def get_state_rdf(self, state, query):
"""Calculate the RDF of a Pair at a State."""
if query:
traj = state.query_traj
else:
traj = state.traj_file
rdf, norm = gsd_rdf(
traj,
self.type1,
self.type2,
start=-state._opt.max_frames,
r_max=state._opt.rdf_cutoff,
bins=state._opt.n_rdf_points,
exclude_bonded=state._opt.rdf_exclude_bonded
)
return np.stack((rdf.bin_centers, rdf.rdf*norm)).T
def test_gsd_rdf_samename(self, gsdfile_bond):
rdf_ex, norm = gsd_rdf(gsdfile_bond, "A", "A")
rdf_noex, norm2 = gsd_rdf(gsdfile_bond, "A", "A", exclude_bonded=False)
assert norm2 == 1
assert not np.array_equal(rdf_noex, rdf_ex)
def test_gsd_rdf(self, gsdfile_bond):
rdf_ex, norm = gsd_rdf(gsdfile_bond, "A", "B")
rdf_noex, norm2 = gsd_rdf(gsdfile_bond, "A", "B", exclude_bonded=False)
assert np.isclose(norm2, 2/3, 1e-4)
assert not np.array_equal(rdf_noex, rdf_ex)