def test_manager_iteration_2(self):
'''
Compare the distances and direction vector between the reference and
librascal sctrict neighbourlist
'''
frame = self.frame
structure = self.structure
for pbc in self.pbcs:
frame['pbc'] = pbc
structure['pbc'] = pbc
manager = get_neighbourlist(frame, self.nl_options)
neighpos, neighlist, neightype, neighdist, neighdirVec = get_NL_strict_reference(
self.cutoff, **structure)
for ii, center in enumerate(manager):
dists, dirVecs = [], []
for jj, neigh in enumerate(center):
dist = np.linalg.norm(neigh.position - center.position)
dists.append(dist)
dirVecs.append((neigh.position - center.position) / dist)
ref_dists, dists = np.array(neighdist[ii]), np.array(dists)
ref_dirVecs, dirVecs = np.array(neighdirVec[ii]).reshape(
(-1, 3)), np.array(dirVecs)
# sort because the order is not the same
ref_sort_ids, sort_ids = np.argsort(ref_dists), np.argsort(
dists)
def test_manager_iteration(self):
manager = get_neighbourlist(self.frame, self.nl_options)
ii = 0
for center in manager:
self.assertTrue(ii == center.atom_tag)
self.assertTrue(
self.structure["atom_types"][ii] == center.atom_type)
self.assertTrue(
np.allclose(self.structure["positions"][:, ii],
center.position))
ii += 1
def test_manager_iteration_2(self):
frame = self.frame
structure = self.structure
for pbc in self.pbcs:
frame["pbc"] = pbc
structure["pbc"] = pbc
manager = get_neighbourlist(frame, self.nl_options)
neighpos, neighlist, neightype, neighdist = get_NL_reference(
self.cutoff, **structure)
for center in manager:
for neigh in center.pairs():
dist = np.linalg.norm(neigh.position - center.position)
def test_manager_iteration_2(self):
frame = self.frame
structure = self.structure
for pbc in self.pbcs:
frame['pbc'] = pbc
structure['pbc'] = pbc
manager = get_neighbourlist(frame, self.nl_options)
neighpos, neighlist, neightype, neighdist = get_NL_reference(
self.cutoff, **structure)
for ii, center in enumerate(manager):
for jj, neigh in enumerate(center):
dist = np.linalg.norm(neigh.position - center.position)
