1import os 

2import warnings 

3from ase.io import iread 

4from ase.geometry.dimensionality import analyze_dimensionality 

5 

6 

7class CLICommand: 

8 """Analyze the dimensionality of the bonded clusters in a structure, using 

9 the scoring parameter described in: 

10 

11 "Definition of a scoring parameter to identify low-dimensional materials 

12 components", P.M. Larsen, M. Pandey, M. Strange, and K. W. Jacobsen 

13 Phys. Rev. Materials 3 034003, 2019, 

14 https://doi.org/10.1103/PhysRevMaterials.3.034003 

15 https://arxiv.org/abs/1808.02114 

16 

17 A score in the range [0-1] is assigned to each possible dimensionality 

18 classification. The scores sum to 1. A bonded cluster can be a molecular 

19 (0D), chain (1D), layer (2D), or bulk (3D) cluster. Mixed dimensionalities, 

20 such as 0D+3D are possible. Input files may use any format supported by 

21 ASE. 

22 

23 Example usage: 

24 

25 * ase dimensionality --display-all structure.cif 

26 * ase dimensionality structure1.cif structure2.cif 

27 

28 For each structure the following data is printed: 

29 

30 * type - the dimensionalities present 

31 * score - the score of the classification 

32 * a - the start of the k-interval (see paper) 

33 * b - the end of the k-interval (see paper) 

34 * component counts - the number of clusters with each dimensionality type 

35 

36 If the `--display-all` option is used, all dimensionality classifications 

37 are displayed. 

38 """ 

39 

40 @staticmethod 

41 def add_arguments(parser): 

42 add = parser.add_argument 

43 add('filenames', nargs='+', help='input file(s) to analyze') 

44 add('--display-all', dest='full', action='store_true', 

45 help='display all dimensionality classifications') 

46 add('--no-merge', dest='no_merge', action='store_true', 

47 help='do not merge k-intervals with same dimensionality') 

48 

49 @staticmethod 

50 def run(args, parser): 

51 

52 files = [os.path.split(path)[1] for path in args.filenames] 

53 lmax = max([len(f) for f in files]) + 2 

54 

55 print('file'.ljust(lmax) + 

56 'type score a b component counts') 

57 print('=' * lmax + '===============================================') 

58 

59 merge = not args.no_merge 

60 

61 # reading CIF files can produce a ton of distracting warnings 

62 with warnings.catch_warnings(): 

63 warnings.filterwarnings('ignore') 

64 for path, f in zip(args.filenames, files): 

65 for atoms in iread(path): 

66 result = analyze_dimensionality(atoms, merge=merge) 

67 if not args.full: 

68 result = result[:1] 

69 

70 for i, entry in enumerate(result): 

71 dimtype = entry.dimtype.rjust(4) 

72 score = '{:.3f}'.format(entry.score).ljust(5) 

73 a = '{:.3f}'.format(entry.a).ljust(5) 

74 b = '{:.3f}'.format(entry.b).ljust(5) 

75 if i == 0: 

76 name = f.ljust(lmax) 

77 else: 

78 name = ' ' * lmax 

79 

80 line = ('{}{}' + ' {}' * 4).format(name, dimtype, 

81 score, a, b, 

82 entry.h) 

83 print(line) 

84 

85 if args.full: 

86 print()