# -*- coding: utf-8 -*-
"""Copyright 2019 DScribe developers
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
"""
import numpy as np
import ase.data
[docs]def symbols_to_numbers(symbols):
"""Transforms a set of chemical symbols into the corresponding atomic
numbers.
Args:
symbols(iterable): List of chemical symbols.
Returns:
np.ndarray: Atomic numbers as an array of integers.
"""
numbers = []
for symbol in symbols:
number = ase.data.atomic_numbers.get(symbol)
if number is None:
raise ValueError(
"Given chemical symbol {} is invalid and doesn't have an atomic"
" number associated with it.".format(symbol)
)
numbers.append(number)
return np.array(numbers, dtype=int)
[docs]def get_atomic_numbers(species):
"""Given a list of chemical species either as a atomic numbers or chemical
symbols, return the correponding list of ordered atomic numbers with
duplicates removed.
Args:
species(iterable of ints or strings):
Returns:
np.ndarray: list of atomic numbers as an integer array.
"""
# Check that an iterable is given
is_iterable = hasattr(species, '__iter__')
is_string = isinstance(species, str)
if not is_iterable or is_string:
raise ValueError(
"Please provide the species as an iterable, e.g. a list."
)
# Determine if the given species are atomic numbers or chemical symbols
if all(isinstance(x, (int, np.integer)) for x in species):
if not np.all(np.array(species) >= 0):
raise ValueError("The given list of species contains negative integers. Please use only non-negative integers")
atomic_numbers = species
elif all(isinstance(x, (str, np.str)) for x in species):
atomic_numbers = symbols_to_numbers(species)
else:
raise ValueError(
"The given list of species does not seem to contain strictly "
"chemical symbols or atomic numbers, but a mixture. Please use only"
" either one."
)
# Return species as atomic numbers with possible duplicates removed
new_atomic_numbers = np.array(sorted(list(set(atomic_numbers))))
return new_atomic_numbers