Coverage for /builds/ase/ase/ase/ga/particle_comparator.py: 100.00%

1# fmt: off 

2 

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

4import numpy as np 

5 

6from ase.ga.utilities import get_nnmat 

7 

8 

9class NNMatComparator: 

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

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

12 of atoms. As specified in 

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

14 

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

16 self.d = d 

17 if elements is None: 

18 elements = [] 

19 self.elements = elements 

20 self.mic = mic 

21 

22 def looks_like(self, a1, a2): 

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

24 elements = self.elements 

25 if elements == []: 

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

27 a1, a2 = a1.copy(), a2.copy() 

28 a1.set_constraint() 

29 a2.set_constraint() 

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

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

32 

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

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

35 

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

37 

38 if diff < self.d: 

39 return True 

40 else: 

41 return False