1"""Comparators originally meant to be used with particles""" 

2import numpy as np 

3from ase.ga.utilities import get_nnmat 

4 

5 

6class NNMatComparator: 

7 """Use the nearest neighbor matrix to determine differences 

8 in the distribution (and to a slighter degree structure) 

9 of atoms. As specified in 

10 S. Lysgaard et al., Top. Catal., 57 (1-4), pp 33-39, (2014)""" 

11 def __init__(self, d=0.2, elements=None, mic=False): 

12 self.d = d 

13 if elements is None: 

14 elements = [] 

15 self.elements = elements 

16 self.mic = mic 

17 

18 def looks_like(self, a1, a2): 

19 """ Return if structure a1 or a2 are similar or not. """ 

20 elements = self.elements 

21 if elements == []: 

22 elements = sorted(set(a1.get_chemical_symbols())) 

23 a1, a2 = a1.copy(), a2.copy() 

24 a1.set_constraint() 

25 a2.set_constraint() 

26 del a1[[a.index for a in a1 if a.symbol not in elements]] 

27 del a2[[a.index for a in a2 if a.symbol not in elements]] 

28 

29 nnmat_a1 = get_nnmat(a1, mic=self.mic) 

30 nnmat_a2 = get_nnmat(a2, mic=self.mic) 

31 

32 diff = np.linalg.norm(nnmat_a1 - nnmat_a2) 

33 

34 if diff < self.d: 

35 return True 

36 else: 

37 return False