Coverage for /builds/ase/ase/ase/calculators/siesta/parameters.py: 100.00%

1# fmt: off 

2 

3from ase.calculators.calculator import Parameters 

4 

5""" 

62017.04 - Pedro Brandimarte: changes for python 2-3 compatible 

7""" 

8 

9 

10class PAOBasisBlock(Parameters): 

11 """ 

12 Representing a block in PAO.Basis for one species. 

13 """ 

14 

15 def __init__(self, block): 

16 """ 

17 Parameters: 

18 -block : String. A block defining the basis set of a single 

19 species using the format of a PAO.Basis block. 

20 The initial label should be left out since it is 

21 determined programatically. 

22 Example1: 2 nodes 1.0 

23 n=2 0 2 E 50.0 2.5 

24 3.50 3.50 

25 0.95 1.00 

26 1 1 P 2 

27 3.50 

28 Example2: 1 

29 0 2 S 0.2 

30 5.00 0.00 

31 See siesta manual for details. 

32 """ 

33 assert isinstance(block, str) 

34 Parameters.__init__(self, block=block) 

35 

36 def script(self, label): 

37 """ 

38 Write the fdf script for the block. 

39 

40 Parameters: 

41 -label : The label to insert in front of the block. 

42 """ 

43 return label + ' ' + self['block'] 

44 

45 

46class Species(Parameters): 

47 """ 

48 Parameters for specifying the behaviour for a single species in the 

49 calculation. If the tag argument is set to an integer then atoms with 

50 the specified element and tag will be a separate species. 

51 

52 Pseudopotential and basis set can be specified. Additionally the species 

53 can be set be a ghost species, meaning that they will not be considered 

54 atoms, but the corresponding basis set will be used. 

55 """ 

56 

57 def __init__(self, 

58 symbol, 

59 basis_set='DZP', 

60 pseudopotential=None, 

61 tag=None, 

62 ghost=False, 

63 excess_charge=None): 

64 kwargs = locals() 

65 kwargs.pop('self') 

66 Parameters.__init__(self, **kwargs) 

67 

68 

69def format_fdf(key, value): 

70 """ 

71 Write an fdf key-word value pair. 

72 

73 Parameters: 

74 - key : The fdf-key 

75 - value : The fdf value. 

76 """ 

77 if isinstance(value, (list, tuple)) and len(value) == 0: 

78 return '' 

79 

80 key = format_key(key) 

81 new_value = format_value(value) 

82 

83 if isinstance(value, list): 

84 string = '%block ' + key + '\n' +\ 

85 new_value + '\n' + \ 

86 '%endblock ' + key + '\n' 

87 else: 

88 string = f'{key}\t{new_value}\n' 

89 

90 return string 

91 

92 

93def format_value(value): 

94 """ 

95 Format python values to fdf-format. 

96 

97 Parameters: 

98 - value : The value to format. 

99 """ 

100 if isinstance(value, tuple): 

101 sub_values = [format_value(v) for v in value] 

102 value = '\t'.join(sub_values) 

103 elif isinstance(value, list): 

104 sub_values = [format_value(v) for v in value] 

105 value = '\n'.join(sub_values) 

106 else: 

107 value = str(value) 

108 

109 return value 

110 

111 

112def format_key(key): 

113 """ Fix the fdf-key replacing '_' with '.' and '__' with '_' """ 

114 key = key.replace('__', '#') 

115 key = key.replace('_', '.') 

116 key = key.replace('#', '_') 

117 

118 return key