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 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 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)))
def test7(self): atoms = self.atoms atoms.update_attrs() assert_true(np.allclose(atoms.coordination_numbers, atoms.neighbor_counts(2.0)))