def test_elfcs():
""" Test whether the ElF algorithm reproduces the reference values for elf
"""
# Test the ElF alignment (ElF rule)
for i in [0, 3, 0]:
print('======Testing {} =========='.format(i))
angles1 = get_elfcs_angles(i, atoms.get_positions(), elf[i])
print(angles1)
rotated1 = rotate_tensor(elf[i], angles1, inverse=True)
for it in range(10):
rand_ang = np.random.rand(3) * 2 * np.pi
elf_rotated = rotate_tensor(elf[i], rand_ang)
coords_rotated = rotate_vector(atoms.get_positions()-\
atoms.get_positions()[i], rand_ang)
angles2 = get_elfcs_angles(i, coords_rotated, elf_rotated)
rotated2 = rotate_tensor(elf_rotated, angles2, inverse=True)
for key in rotated1:
assert np.allclose(rotated1[key],
rotated2[key],
atol=1e-3,
rtol=1e-3)
# pickle.dump(rotated1, open('./test/elf_elfcs.dat','wb'))
elf_ref = pickle.load(open('./test/elf_elfcs.dat', 'rb'))
for key in elf[0]:
assert np.allclose(rotated1[key], elf_ref[key])
def test_rotate_tensor():
"""Test certain algebraic properties of the rotate_tensor() routine
"""
# Test identity and inverse
id = rotate_tensor(elf[0], [0, 0, 0])
rotated = rotate_tensor(elf[0], [1.2, 0.3, 0.1])
rotated = rotate_tensor(rotated, [1.2, 0.3, 0.1], inverse=True)
for key in elf[0]:
assert np.allclose(rotated[key], elf[0][key])
assert np.allclose(id[key], elf[0][key])
# Test if rotation preserves l2-norm
for angles in [[1.0, 1.2, 0.2], [0.3, 3.6, 2.3]]:
rotated = rotate_tensor(elf[0], angles)
casimir = get_casimir(elf[0])
casimir_rotated = get_casimir(rotated)
for key in casimir:
assert np.allclose(casimir[key], casimir_rotated[key])
def change_alignment(path, traj_path, new_method, save_as=None):
""" Transform ElFs from one local coordinate system to another one specified in
new_method
Parameters
----------
path: str
file origin
traj_path: str
path to .traj or .xyz containing the atomic positions
new_method: str
{'elf','nn','water','neutral'}, method defining the local coordinate system
save_as: str
destination file to save ElFs, default=None (don't save)
Returns
---------
list of ElF
if save_as == None returns list of electronic descriptors (ElFs)
otherwise returns None
"""
elfs = hdf5_to_elfs(path)
atoms = read(traj_path, ':')
with File(path) as file:
basis = json.loads(file.attrs['basis'])
# if new_method == basis['alignment']:
# raise Exception('Already aligned with method: ' + new_method)
# else:
basis['alignment'] = new_method
#Rotate to neutral
for i, elf_system in enumerate(elfs):
for j, elf in enumerate(elf_system):
elfs[i][j].value = rotate_tensor(make_complex(
elf.value, basis['n_rad_' + elf.species.lower()],
basis['n_l_' + elf.species.lower()]),
elf.angles,
inverse=False)
elfs[i][j].angles = np.array([0, 0, 0])
elfs[i][j].unitcell = atoms[i].get_cell()
elfs[i][j].basis = basis
oriented_elfs = []
for elfs_system, atoms_system in zip(elfs, atoms):
oriented_elfs.append(orient_elfs(elfs_system, atoms_system,
new_method))
if save_as == None:
return oriented_elfs
else:
elfs_to_hdf5(oriented_elfs, save_as)
def test_watercs():
""" Test whether nearest neighbor reproduces the reference values for elf
"""
for i in [3, 1, 4, 0]:
angles1 = get_water_angles(i, atoms.get_positions())
rotated1 = rotate_tensor(elf[i], angles1, inverse=True)
for it in range(5):
rand_ang = np.random.rand(3) * 2 * np.pi
elf_rotated = rotate_tensor(elf[i], rand_ang)
coords_rotated = rotate_vector(atoms.get_positions()-\
atoms.get_positions()[i], rand_ang)
angles2 = get_water_angles(i, coords_rotated)
rotated2 = rotate_tensor(elf_rotated, angles2, inverse=True)
for key in rotated1:
np.allclose(rotated1[key], rotated2[key], atol=1e-6)
def test_nncs():
""" Test whether nearest neighbor reproduces the reference values for elf
"""
for i in [3, 1, 4, 0]:
angles1 = get_nncs_angles(i, atoms.get_positions())
rotated1 = rotate_tensor(elf[i], angles1, inverse=True)
for it in range(5):
rand_ang = np.random.rand(3) * 2 * np.pi
elf_rotated = rotate_tensor(elf[i], rand_ang)
coords_rotated = rotate_vector(atoms.get_positions()-\
atoms.get_positions()[i], rand_ang)
angles2 = get_nncs_angles(i, coords_rotated)
rotated2 = rotate_tensor(elf_rotated, angles2, inverse=True)
for key in rotated1:
np.allclose(rotated1[key], rotated2[key], atol=1e-6)
# pickle.dump(rotated1, open('./test/elf_nncs.dat','wb'))
elf_ref = pickle.load(open('./test/elf_nncs.dat', 'rb'))
for key in elf[0]:
assert np.allclose(rotated1[key], elf_ref[key])