def test8(self):
atoms = self.atoms
atoms.update_attrs()
# print(atoms.bonds.lengths)
# print(atoms.neighbor_distances)
assert_true(np.allclose(atoms.bonds.lengths,
atoms.neighbor_distances))
def test6(self):
atoms = self.atoms
atoms.update_attrs()
assert_equal(atoms.filtered(atoms.coordination_numbers == 1).Natoms,
atoms.coordination_counts[1])
assert_equal(atoms.filtered(atoms.coordination_numbers == 3).Natoms,
atoms.coordination_counts[3])
def test5(self):
atoms = self.atoms
assert_true(np.allclose(atoms.coords, atoms.atom_tree.data))
atoms.kNN = 3
atoms.NNrc = 2.0
atoms.update_attrs()
assert_equals(len(atoms.nearest_neighbors), atoms.Natoms)
assert_equals(len(atoms.coordination_numbers), atoms.Natoms)
def test5(self):
atoms = self.atoms
assert_true(np.allclose(atoms.coords, atoms.atom_tree.data))
atoms.kNN = 3
atoms.NNrc = 2.0
atoms.update_attrs()
assert_equals(len(atoms.nearest_neighbors), atoms.Natoms)
assert_equals(len(atoms.coordination_numbers), atoms.Natoms)
def test6(self):
atoms = self.atoms
atoms.update_attrs()
assert_equal(
atoms.filtered(atoms.coordination_numbers == 1).Natoms,
atoms.coordination_counts[1])
assert_equal(
atoms.filtered(atoms.coordination_numbers == 3).Natoms,
atoms.coordination_counts[3])
def test2(self):
atoms = self.atoms
atoms.kNN = 3
atoms.NNrc = 2.0
atoms.update_attrs()
print(atoms.ids)
for atom in atoms:
print('atom: {}, bond.lengths: {}'.format(atom.id,
atom.bonds.lengths))
def test2(self):
atoms = self.atoms
atoms.kNN = 3
atoms.NNrc = 2.0
atoms.update_attrs()
print(atoms.ids)
for atom in atoms:
print('atom: {}, bond.lengths: {}'.format(
atom.id, atom.bonds.lengths))
def test1(self):
atoms = self.atoms
atoms.kNN = 6
atoms.NNrc = 9.0
for atom in atoms:
assert_equals(atom.CN, 0)
atom.CN = 3
assert_equals(atom.CN, 3)
atoms.update_attrs()
atoms = atoms.filtered((atoms.z >= -5) & (atoms.z <= 5))
print('Natoms: {}'.format(atoms.Natoms))
for atom in atoms:
assert_equals(atom.CN, atoms.kNN)
def test1(self):
atoms = self.atoms
atoms.kNN = 6
atoms.NNrc = 9.0
for atom in atoms:
assert_equals(atom.CN, 0)
atom.CN = 3
assert_equals(atom.CN, 3)
atoms.update_attrs()
atoms = atoms.filtered((atoms.z >= -5) & (atoms.z <= 5))
print('Natoms: {}'.format(atoms.Natoms))
for atom in atoms:
assert_equals(atom.CN, atoms.kNN)
def test9(self):
atoms = self.atoms
atoms.update_attrs()
assert_true(np.allclose(atoms.volume, atoms.bounds.volume))
def test8(self):
atoms = self.atoms
atoms.update_attrs()
# print(atoms.bonds.lengths)
# print(atoms.neighbor_distances)
assert_true(np.allclose(atoms.bonds.lengths, atoms.neighbor_distances))
def test7(self):
atoms = self.atoms
atoms.update_attrs()
assert_true(
np.allclose(atoms.coordination_numbers,
atoms.neighbor_counts(2.0)))
def test9(self):
atoms = self.atoms
atoms.update_attrs()
assert_true(np.allclose(atoms.volume, atoms.bounds.volume))
def test7(self):
atoms = self.atoms
atoms.update_attrs()
assert_true(np.allclose(atoms.coordination_numbers,
atoms.neighbor_counts(2.0)))
