def get_system(self, system):
"""Used to convert the given atomic system into a custom System-object
that is used internally. The System class inherits from ase.Atoms, but
includes built-in caching for geometric quantities that may be re-used
by the descriptors.
Args:
system (:class:`ase.Atoms` | :class:`.System`): Input system.
Returns:
:class:`.System`: The given system transformed into a corresponding
System-object.
"""
if isinstance(system, Atoms):
if type(system) == System:
return system
else:
return System.from_atoms(system)
else:
raise ValueError("Invalid system with type: '{}'.".format(
type(system)))
def system_stats(system_iterator):
"""
Args:
system_stats(iterable containing ASE.Atoms or System): The atomic
systems for which to gather statistics.
Returns:
Dict: A dictionary of different statistics for the system. The
dictionary will contain:
n_atoms_max: The maximum number of atoms in a system.
max_atomic_number: The highest atomic number
min_atomic_number: The lowest atomic number
atomic_numbers: List of present atomic numbers
element_symbols: List of present atomic symbols
min_distance: Minimum distance in the system
"""
n_atoms_max = 0
atomic_numbers = set()
symbols = set()
min_distance = None
for system in system_iterator:
n_atoms = len(system)
# Make ASE.Atoms into a System object
if isinstance(system, Atoms):
system = System.from_atoms(system)
i_atomic_numbers = set(system.get_atomic_numbers())
i_symbols = set(system.get_chemical_symbols())
distance_matrix = system.get_distance_matrix()
# Gather atomic numbers and symbols
atomic_numbers = atomic_numbers.union(i_atomic_numbers)
symbols = symbols.union(i_symbols)
# Gather maximum number of atoms
if n_atoms > n_atoms_max:
n_atoms_max = n_atoms
# Gather min distance. For periodic systems we must also consider
# distances from an atom to it's periodic copy, as given by
# get_distance_matrix() on the diagonal.
if np.any(system.get_pbc()):
triu_indices = np.triu_indices(len(distance_matrix), k=0)
else:
triu_indices = np.triu_indices(len(distance_matrix), k=1)
distances = distance_matrix[triu_indices]
i_min_dist = distances.min()
if min_distance is None or i_min_dist < min_distance:
min_distance = i_min_dist
return {
"n_atoms_max": n_atoms_max,
"max_atomic_number": max(list(atomic_numbers)),
"min_atomic_number": min(list(atomic_numbers)),
"atomic_numbers": list(atomic_numbers),
"element_symbols": list(symbols),
"min_distance": min_distance,
}