def test_distances(self):
"""Tests that the periodicity is taken into account when calculating
distances.
"""
scaled_positions = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
system = System(
scaled_positions=scaled_positions,
symbols=["H", "H"],
cell=[
[5, 5, 0],
[0, -5, -5],
[5, 0, 5]
],
)
disp = system.get_displacement_tensor()
# For a non-periodic system, periodicity should not be taken into
# account even if cell is defined.
pos = system.get_positions()
assumed = np.array([
[pos[0] - pos[0], pos[1] - pos[0]],
[pos[0] - pos[1], pos[1] - pos[1]],
])
self.assertTrue(np.allclose(assumed, disp))
# For a periodic system, the nearest copy should be considered when
# comparing distances to neighbors or to self
system.set_pbc([True, True, True])
disp = system.get_displacement_tensor()
assumed = np.array([
[[5.0, 5.0, 0.0], [5, 0, 0]],
[[-5, 0, 0], [5.0, 5.0, 0.0]]])
self.assertTrue(np.allclose(assumed, disp))
# Tests that the displacement tensor is found correctly even for highly
# non-orthorhombic systems.
positions = np.array([
[1.56909, 2.71871, 6.45326],
[3.9248, 4.07536, 6.45326]
])
cell = np.array([
[4.7077, -2.718, 0.],
[0., 8.15225, 0.],
[0., 0., 50.]
])
system = System(
positions=positions,
symbols=["H", "H"],
cell=cell,
pbc=True,
)
# Fully periodic with minimum image convention
dist_mat = system.get_distance_matrix()
distance = dist_mat[0, 1]
# The minimum image should be within the same cell
expected = np.linalg.norm(positions[0, :] - positions[1, :])
self.assertTrue(np.allclose(distance, expected))
def create(self, system, positions, scaled_positions=False):
"""Return the local many-body tensor representation for the given
system and positions.
Args:
system (:class:`ase.Atoms` | :class:`.System`): Input system.
positions (iterable): Positions or atom index of points, from
which local_mbtr is created. Can be a list of integer numbers
or a list of xyz-coordinates.
scaled_positions (boolean): Controls whether the given positions
are given as scaled to the unit cell basis or not. Scaled
positions require that a cell is available for the system.
Returns:
1D ndarray: The local many-body tensor representations of given
positions, for k terms, as an array. These are ordered as given
in positions.
"""
# Transform the input system into the internal System-object
system = self.get_system(system)
# Ensure that the atomic number 0 is not present in the system
if 0 in system.get_atomic_numbers():
raise ValueError(
"Please do not use the atomic number 0 in local MBTR "
", as it is reserved for the ghost atom used by the "
"implementation.")
# Ensuring self is updated
self.update()
# Checking scaled position
if scaled_positions:
if np.linalg.norm(system.get_cell()) == 0:
raise ValueError(
"System doesn't have cell to justify scaled positions.")
# Figure out the atom index or atom location from the given positions
systems = []
# If virtual positions requested, create new atoms with atomic number 0
# at the requested position.
for i_pos in positions:
if self.virtual_positions:
if not isinstance(i_pos, (list, tuple, np.ndarray)):
raise ValueError(
"The given position of type '{}' could not be "
"interpreted as a valid location. If you wish to use "
"existing atoms as centers, please set "
"'virtual_positions' to False.".format(type(i_pos)))
if scaled_positions:
i_pos = np.dot(i_pos, system.get_cell())
else:
i_pos = np.array(i_pos)
i_pos = np.expand_dims(i_pos, axis=0)
new_system = System('X', positions=i_pos)
new_system += system
else:
if not np.issubdtype(type(i_pos), np.integer):
raise ValueError(
"The given position of type '{}' could not be "
"interpreted as a valid index. If you wish to use "
"custom locations as centers, please set "
"'virtual_positions' to True.".format(type(i_pos)))
new_system = Atoms()
center_atom = system[i_pos]
new_system += center_atom
new_system.set_atomic_numbers([0])
system_copy = system.copy()
del system_copy[i_pos]
new_system += system_copy
# Set the periodicity and cell to match the original system, as
# they are lost in the system concatenation
new_system.set_cell(system.get_cell())
new_system.set_pbc(system.get_pbc())
systems.append(new_system)
# Request MBTR for each position. Return type depends on flattening and
# whether a spares of dense result is requested.
n_pos = len(positions)
n_features = self.get_number_of_features()
if self._flatten and self._sparse:
data = []
cols = []
rows = []
row_offset = 0
for i, i_system in enumerate(systems):
i_res = super().create(i_system)
data.append(i_res.data)
rows.append(i_res.row + row_offset)
cols.append(i_res.col)
# Increase the row offset
row_offset += 1
# Saves the descriptors as a sparse matrix
data = np.concatenate(data)
rows = np.concatenate(rows)
cols = np.concatenate(cols)
desc = coo_matrix((data, (rows, cols)),
shape=(n_pos, n_features),
dtype=np.float32)
else:
if self._flatten and not self._sparse:
desc = np.empty((n_pos, n_features), dtype=np.float32)
else:
desc = np.empty((n_pos), dtype='object')
for i, i_system in enumerate(systems):
i_desc = super().create(i_system)
desc[i] = i_desc
return desc
def create_single(
self,
system,
positions,
):
"""Return the local many-body tensor representation for the given
system and positions.
Args:
system (:class:`ase.Atoms` | :class:`.System`): Input system.
positions (iterable): Positions or atom index of points, from
which local_mbtr is created. Can be a list of integer numbers
or a list of xyz-coordinates.
Returns:
1D ndarray: The local many-body tensor representations of given
positions, for k terms, as an array. These are ordered as given in
positions.
"""
# Transform the input system into the internal System-object
system = self.get_system(system)
# Check that the system does not have elements that are not in the list
# of atomic numbers
atomic_number_set = set(system.get_atomic_numbers())
self.check_atomic_numbers(atomic_number_set)
# Ensure that the atomic number 0 is not present in the system
if 0 in atomic_number_set:
raise ValueError(
"Please do not use the atomic number 0 in local MBTR"
", as it is reserved for the ghost atom used by the "
"implementation.")
# Figure out the atom index or atom location from the given positions
systems = []
# Positions specified, use them
if positions is not None:
# Check validity of position definitions and create final cartesian
# position list
list_positions = []
if len(positions) == 0:
raise ValueError(
"The argument 'positions' should contain a non-empty set of"
" atomic indices or cartesian coordinates with x, y and z "
"components.")
for i in positions:
if np.issubdtype(type(i), np.integer):
i_len = len(system)
if i >= i_len or i < 0:
raise ValueError(
"The provided index {} is not valid for the system "
"with {} atoms.".format(i, i_len))
list_positions.append(system.get_positions()[i])
elif isinstance(i, (list, tuple, np.ndarray)):
if len(i) != 3:
raise ValueError(
"The argument 'positions' should contain a "
"non-empty set of atomic indices or cartesian "
"coordinates with x, y and z components.")
list_positions.append(i)
else:
raise ValueError(
"Create method requires the argument 'positions', a "
"list of atom indices and/or positions.")
for i_pos in positions:
# Position designated as cartesian position, add a new atom at that
# location with the chemical element X and place is as the first
# atom in the system. The interaction limit makes sure that only
# interactions of this first atom to every other atom are
# considered.
if isinstance(i_pos, (list, tuple, np.ndarray)):
if len(i_pos) != 3:
raise ValueError(
"The argument 'positions' should contain a "
"non-empty set of atomic indices or cartesian "
"coordinates with x, y and z components.")
i_pos = np.array(i_pos)
i_pos = np.expand_dims(i_pos, axis=0)
new_system = System('X', positions=i_pos)
new_system += system
# Position designated as integer, use the atom at that index as
# center. For the calculation this central atoms is shifted to be
# the first atom in the system, and the interaction limit makes
# sure that only interactions of this first atom to every other
# atom are considered.
elif np.issubdtype(type(i_pos), np.integer):
new_system = Atoms()
center_atom = system[i_pos]
new_system += center_atom
new_system.set_atomic_numbers([0])
system_copy = system.copy()
del system_copy[i_pos]
new_system += system_copy
else:
raise ValueError(
"Create method requires the argument 'positions', a "
"list of atom indices and/or positions.")
# Set the periodicity and cell to match the original system, as
# they are lost in the system concatenation
new_system.set_cell(system.get_cell())
new_system.set_pbc(system.get_pbc())
systems.append(new_system)
# Request MBTR for each position. Return type depends on flattening and
# whether a spares of dense result is requested.
n_pos = len(positions)
n_features = self.get_number_of_features()
if self._flatten and self._sparse:
data = []
cols = []
rows = []
row_offset = 0
for i, i_system in enumerate(systems):
i_res = super().create_single(i_system)
data.append(i_res.data)
rows.append(i_res.row + row_offset)
cols.append(i_res.col)
# Increase the row offset
row_offset += 1
# Saves the descriptors as a sparse matrix
data = np.concatenate(data)
rows = np.concatenate(rows)
cols = np.concatenate(cols)
desc = coo_matrix((data, (rows, cols)),
shape=(n_pos, n_features),
dtype=np.float32)
else:
if self._flatten and not self._sparse:
desc = np.empty((n_pos, n_features), dtype=np.float32)
else:
desc = np.empty((n_pos), dtype='object')
for i, i_system in enumerate(systems):
i_desc = super().create_single(i_system)
desc[i] = i_desc
return desc