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 

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

13 self.d = d 

14 if elements is None: 

15 elements = [] 

16 self.elements = elements 

17 self.mic = mic 

18 

19 def looks_like(self, a1, a2): 

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

21 elements = self.elements 

22 if elements == []: 

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

24 a1, a2 = a1.copy(), a2.copy() 

25 a1.set_constraint() 

26 a2.set_constraint() 

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

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

29 

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

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

32 

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

34 

35 if diff < self.d: 

36 return True 

37 else: 

38 return False