Coverage for icet/core/orbit.py: 87%

1""" 

2This module provides the Orbit class. 

3""" 

4 

5from _icet import Orbit 

6from numpy.typing import NDArray 

7__all__ = ['Orbit'] 

8 

9 

10def __str__(self) -> str: 

11 """ String representation. """ 

12 s = f'Order: {self.order}\n' 

13 s += f'Multiplicity: {len(self)}\n' 

14 s += f'Radius: {self.radius:.4f}\n' 

15 

16 # Representative cluster 

17 s += 'Representative cluster:\n' 

18 for site, off, pos in zip(self.sites, self.site_offsets, self.positions): 

19 offset = ''.join([f'{x:3}' for x in off]) 

20 position = ''.join([f' {x:6.2f}' for x in pos]) 

21 s += f'\tSite: {site},\tOffset: {offset},\tPosition:{position}\n' 

22 

23 return s 

24 

25 

26def __repr__(self) -> str: 

27 """ Representation. """ 

28 s = type(self).__name__ + '(' 

29 s += f'order={self.order}' 

30 s += f', multiplicity={len(self)}' 

31 s += f', radius={self.radius:.4f}' 

32 s += f', sites={self.sites}' 

33 s += ')' 

34 return s 

35 

36 

37def _repr_html_(self) -> str: 

38 """ HTML representation. Used, e.g., in jupyter notebooks. """ 

39 s = ['<h4>Orbit</h4>'] 

40 s += ['<table border="1" class="dataframe">'] 

41 s += ['<thead><tr><th style="text-align: left;">Field</th><th>Value</th></tr></thead>'] 

42 s += ['<tbody>'] 

43 s += [f'<tr><td style="text-align: left;">Order</td><td>{self.order}</td></tr>'] 

44 s += [f'<tr><td style="text-align: left;">Multiplicity</td><td>{len(self)}</td></tr>'] 

45 s += [f'<tr><td style="text-align: left;">Radius</td><td>{self.radius:.4f}</td></tr>'] 

46 s += [f'<tr><td style="text-align: left;">Sites</td><td>{self.sites}</td></tr>'] 

47 s += ['</tbody>'] 

48 s += ['</table>'] 

49 return ''.join(s) 

50 

51 

52@property 

53def distances(self) -> list[float]: 

54 """ Distances between all sites in the representative cluster. """ 

55 return self.representative_cluster.distances 

56 

57 

58@property 

59def sites(self) -> list[int]: 

60 """ The indices of all sites in the representative cluster.""" 

61 return [site.index for site in self.representative_cluster.lattice_sites] 

62 

63 

64@property 

65def site_offsets(self) -> list[NDArray[int]]: 

66 """ Unit cell offsets of all sites in the representative cluster. """ 

67 return [site.unitcell_offset.astype(int) 

68 for site in self.representative_cluster.lattice_sites] 

69 

70 

71@property 

72def positions(self) -> list[NDArray[float]]: 

73 """ Positions of all sites in the representative cluster. """ 

74 return self.representative_cluster.positions 

75 

76 

77@property 

78def all_distances(self) -> list[list[float]]: 

79 """ Distances between all sites in all clusters. """ 

80 return [cluster.distances for cluster in self.clusters] 

81 

82 

83@property 

84def all_sites(self) -> list[list[int]]: 

85 """ The site indices of all sites in all clusters.""" 

86 return [[site.index for site in cluster.lattice_sites] 

87 for cluster in self.clusters] 

88 

89 

90@property 

91def all_site_offsets(self) -> list[list[NDArray[int]]]: 

92 """ Unit cell offsets of all sites in all clusters. """ 

93 return [[site.unitcell_offset.astype(int) for site in cluster.lattice_sites] 

94 for cluster in self.clusters] 

95 

96 

97@property 

98def all_positions(self) -> list[list[NDArray[float]]]: 

99 """ Positions of all sites in all clusters. """ 

100 return [cluster.positions for cluster in self.clusters] 

101 

102 

103Orbit.__str__ = __str__ 

104Orbit.__repr__ = __repr__ 

105Orbit._repr_html_ = _repr_html_ 

106 

107Orbit.distances = distances 

108Orbit.sites = sites 

109Orbit.site_offsets = site_offsets 

110Orbit.positions = positions 

111 

112Orbit.all_distances = all_distances 

113Orbit.all_sites = all_sites 

114Orbit.all_site_offsets = all_site_offsets 

115Orbit.all_positions = all_positions