Coverage for /builds/kinetik161/ase/ase/ga/particle_comparator.py: 100.00%

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

2import numpy as np 

3 

4from ase.ga.utilities import get_nnmat 

5 

6 

7class NNMatComparator: 

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

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

10 of atoms. As specified in 

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

12 

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

14 self.d = d 

15 if elements is None: 

16 elements = [] 

17 self.elements = elements 

18 self.mic = mic 

19 

20 def looks_like(self, a1, a2): 

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

22 elements = self.elements 

23 if elements == []: 

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

25 a1, a2 = a1.copy(), a2.copy() 

26 a1.set_constraint() 

27 a2.set_constraint() 

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

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

30 

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

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

33 

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

35 

36 if diff < self.d: 

37 return True 

38 else: 

39 return False