def test_rdf_multiple_center():
""" Test if the first argument allows to use multiple centers"""
stack = load_structure(TEST_FILE)
# calculate oxygen RDF for water with and without a selection
oxygen = stack[:, stack.atom_name == 'OW']
interval = np.array([0, 10])
n_bins = 100
# averaging individual calculations
bins1, g_r1 = rdf(oxygen[:, 1].coord,
oxygen[:, 2:],
interval=interval,
bins=n_bins,
periodic=False)
bins2, g_r2 = rdf(oxygen[:, 0].coord,
oxygen[:, 2:],
interval=interval,
bins=n_bins,
periodic=False)
mean = np.mean([g_r1, g_r2], axis=0)
# this should give the same result as averaging for oxygen 0 and 1
bins, g_r = rdf(oxygen[:, 0:2].coord,
oxygen[:, 2:],
interval=interval,
bins=n_bins,
periodic=False)
assert np.allclose(g_r, mean, rtol=0.0001)
def test_rdf_periodic():
""" Test if the periodic argument gives the correct results"""
test_file = TEST_FILE
stack = load_structure(test_file)
# calculate oxygen RDF for water
oxygen = stack[:, stack.atom_name == 'OW']
interval = np.array([0, 10])
n_bins = 100
bins, g_r = rdf(oxygen[:, 0].coord,
oxygen[:, 1:],
interval=interval,
bins=n_bins,
periodic=True)
# Compare with MDTraj
import mdtraj
traj = mdtraj.load(TEST_FILE)
ow = [a.index for a in traj.topology.atoms if a.name == 'O']
pairs = itertools.product([ow[0]], ow[1:])
mdt_bins, mdt_g_r = mdtraj.compute_rdf(traj,
list(pairs),
r_range=interval / 10,
n_bins=n_bins,
periodic=True)
assert np.allclose(bins, mdt_bins * 10)
assert np.allclose(g_r, mdt_g_r, rtol=0.0001)
def test_rdf():
""" General test to reproduce oxygen RDF for a box of water"""
test_file = TEST_FILE
stack = load_structure(test_file)
# calculate oxygen RDF for water
oxygen = stack[:, stack.atom_name == 'OW']
interval = np.array([0, 10])
n_bins = 100
bins, g_r = rdf(oxygen[:, 0].coord,
oxygen,
interval=interval,
bins=n_bins,
periodic=False)
# Compare with MDTraj
import mdtraj
traj = mdtraj.load(TEST_FILE)
ow = [a.index for a in traj.topology.atoms if a.name == 'O']
pairs = itertools.product([ow[0]], ow)
mdt_bins, mdt_g_r = mdtraj.compute_rdf(traj,
list(pairs),
r_range=interval / 10,
n_bins=n_bins,
periodic=False)
assert np.allclose(bins, mdt_bins * 10)
assert np.allclose(g_r, mdt_g_r, rtol=0.0001)
def test_rdf_bins():
""" Test if RDF produce correct bin ranges """
stack = load_structure(TEST_FILE)
center = stack[:, 0]
num_bins = 44
bin_range = (0, 11.7)
bins, g_r = rdf(center, stack, bins=num_bins, interval=bin_range)
assert (len(bins) == num_bins)
assert (bins[0] > bin_range[0])
assert (bins[1] < bin_range[1])
def test_rdf_atom_argument():
""" Test if the first argument allows to use AtomArrayStack """
stack = load_structure(TEST_FILE)
# calculate oxygen RDF for water with and without a selection
oxygen = stack[:, stack.atom_name == 'OW']
interval = np.array([0, 10])
n_bins = 100
bins, g_r = rdf(oxygen[:, 0],
stack,
interval=interval,
bins=n_bins,
periodic=False)
atom_bins, atoms_g_r = rdf(oxygen[:, 0].coord,
stack,
interval=interval,
bins=n_bins,
periodic=False)
assert np.allclose(g_r, atoms_g_r)
def test_rdf_with_selection():
""" Test if the selection argument of rdf function works as expected """
stack = load_structure(TEST_FILE)
# calculate oxygen RDF for water with and without a selection
oxygen = stack[:, stack.atom_name == 'OW']
interval = np.array([0, 10])
n_bins = 100
sele = (stack.atom_name == 'OW') & (stack.res_id >= 3)
bins, g_r = rdf(oxygen[:, 0].coord,
stack,
selection=sele,
interval=interval,
bins=n_bins,
periodic=False)
nosel_bins, nosel_g_r = rdf(oxygen[:, 0].coord,
oxygen[:, 1:],
interval=interval,
bins=n_bins,
periodic=False)
assert np.allclose(bins, nosel_bins)
assert np.allclose(g_r, nosel_g_r)
def test_rdf_normalized():
""" Assert that the RDF tail is normalized to 1"""
test_file = TEST_FILE
stack = load_structure(test_file)
# calculate oxygen RDF for water
oxygen = stack[:, stack.atom_name == 'OW']
interval = np.array([0, 5])
n_bins = 100
bins, g_r = rdf(oxygen.coord,
oxygen,
interval=interval,
bins=n_bins,
periodic=True)
assert np.allclose(g_r[-10:], np.ones(10), atol=0.1)
def test_rdf_box():
""" Test correct use of simulation boxes """
stack = load_structure(TEST_FILE)
box = vectors_from_unitcell(1, 1, 1, 90, 90, 90)
box = np.repeat(box[np.newaxis, :, :], len(stack), axis=0)
# Use box attribute of stack
rdf(stack[:, 0], stack)
# Use box attribute and dont fail because stack has no box
stack.box = None
rdf(stack[:, 0], stack, box=box)
# Fail if no box is present
with pytest.raises(ValueError):
rdf(stack[:, 0], stack)
# Fail if box is of wrong size
with pytest.raises(ValueError):
rdf(stack[:, 0], stack, box=box[0])