Coverage for /builds/kinetik161/ase/ase/build/molecule.py: 100.00%

1from ase.atoms import Atoms 

2from ase.collections import g2 

3 

4 

5def molecule(name, vacuum=None, **kwargs): 

6 """Create an atomic structure from a database. 

7 

8 This is a helper function to easily create molecules from the g2 and 

9 extra databases. 

10 

11 Parameters 

12 ---------- 

13 name : str 

14 Name of the molecule to build. 

15 vacuum : float, optional 

16 Amount of vacuum to pad the molecule with on all sides. 

17 Additional keyword arguments (kwargs) can be supplied, which are passed 

18 to ase.Atoms. 

19 

20 Returns 

21 ------- 

22 ase.atoms.Atoms 

23 An ASE Atoms object corresponding to the specified molecule. 

24 

25 Notes 

26 ----- 

27 To see a list of allowed names, try: 

28 

29 >>> from ase.collections import g2 

30 >>> print(g2.names) #doctest:+NORMALIZE_WHITESPACE 

31 ['PH3', 'P2', 'CH3CHO', 'H2COH', 'CS', 'OCHCHO', 'C3H9C', 'CH3COF', 

32 'CH3CH2OCH3', 'HCOOH', 'HCCl3', 'HOCl', 'H2', 'SH2', 'C2H2', 

33 'C4H4NH', 'CH3SCH3', 'SiH2_s3B1d', 'CH3SH', 'CH3CO', 'CO', 'ClF3', 

34 'SiH4', 'C2H6CHOH', 'CH2NHCH2', 'isobutene', 'HCO', 'bicyclobutane', 

35 'LiF', 'Si', 'C2H6', 'CN', 'ClNO', 'S', 'SiF4', 'H3CNH2', 

36 'methylenecyclopropane', 'CH3CH2OH', 'F', 'NaCl', 'CH3Cl', 

37 'CH3SiH3', 'AlF3', 'C2H3', 'ClF', 'PF3', 'PH2', 'CH3CN', 

38 'cyclobutene', 'CH3ONO', 'SiH3', 'C3H6_D3h', 'CO2', 'NO', 

39 'trans-butane', 'H2CCHCl', 'LiH', 'NH2', 'CH', 'CH2OCH2', 

40 'C6H6', 'CH3CONH2', 'cyclobutane', 'H2CCHCN', 'butadiene', 'C', 

41 'H2CO', 'CH3COOH', 'HCF3', 'CH3S', 'CS2', 'SiH2_s1A1d', 'C4H4S', 

42 'N2H4', 'OH', 'CH3OCH3', 'C5H5N', 'H2O', 'HCl', 'CH2_s1A1d', 

43 'CH3CH2SH', 'CH3NO2', 'Cl', 'Be', 'BCl3', 'C4H4O', 'Al', 'CH3O', 

44 'CH3OH', 'C3H7Cl', 'isobutane', 'Na', 'CCl4', 'CH3CH2O', 'H2CCHF', 

45 'C3H7', 'CH3', 'O3', 'P', 'C2H4', 'NCCN', 'S2', 'AlCl3', 'SiCl4', 

46 'SiO', 'C3H4_D2d', 'H', 'COF2', '2-butyne', 'C2H5', 'BF3', 'N2O', 

47 'F2O', 'SO2', 'H2CCl2', 'CF3CN', 'HCN', 'C2H6NH', 'OCS', 'B', 'ClO', 

48 'C3H8', 'HF', 'O2', 'SO', 'NH', 'C2F4', 'NF3', 'CH2_s3B1d', 

49 'CH3CH2Cl', 'CH3COCl', 'NH3', 'C3H9N', 'CF4', 'C3H6_Cs', 'Si2H6', 

50 'HCOOCH3', 'O', 'CCH', 'N', 'Si2', 'C2H6SO', 'C5H8', 'H2CF2', 'Li2', 

51 'CH2SCH2', 'C2Cl4', 'C3H4_C3v', 'CH3COCH3', 'F2', 'CH4', 'SH', 

52 'H2CCO', 'CH3CH2NH2', 'Li', 'N2', 'Cl2', 'H2O2', 'Na2', 'BeH', 

53 'C3H4_C2v', 'NO2'] 

54 >>> from ase.build.molecule import extra 

55 >>> print(extra.keys()) #doctest:+NORMALIZE_WHITESPACE 

56 dict_keys(['Be2', 'C7NH5', 'BDA', 'biphenyl', 'C60']) 

57 

58 Examples 

59 -------- 

60 >>> from ase.build import molecule 

61 >>> atoms = molecule('H2O') 

62 

63 """ 

64 if name in extra: 

65 kwargs.update(extra[name]) 

66 mol = Atoms(**kwargs) 

67 else: 

68 mol = g2[name] 

69 if kwargs: 

70 mol = Atoms(mol, **kwargs) 

71 if vacuum is not None: 

72 mol.center(vacuum=vacuum) 

73 return mol 

74 

75 

76extra = { 

77 'Be2': { 

78 'symbols': 'BeBe', 

79 'positions': [[0, 0, 1.0106], 

80 [0, 0, -1.0106]]}, 

81 'C7NH5': { 

82 'symbols': 'C7NH5', 

83 'positions': [[-1.593581, -1.142601, 0.], 

84 [-2.235542, 0.095555, 0.], 

85 [-0.204885, -1.210726, 0.], 

86 [0.549645, -0.025355, 0.], 

87 [1.976332, -0.085321, 0.], 

88 [-0.099258, 1.220706, 0.], 

89 [-1.488628, 1.273345, 0.], 

90 [3.136871, -0.128138, 0.], 

91 [-2.177996, -2.060896, 0.], 

92 [-3.323594, 0.141242, 0.], 

93 [0.301694, -2.173705, 0.], 

94 [0.488716, 2.136782, 0.], 

95 [-1.987765, 2.240495, 0.]]}, 

96 'BDA': { 

97 # 1,4-Benzodiamine 

98 # aka p-Aminoaniline; p-Benzenediamine; p-Diaminobenzene; 

99 # p-Phenylenediamine; Paraphenylen-diamine 

100 # PBE-gpaw relaxed 

101 'symbols': 'C6H4N2H4', 

102 'positions': [[0.004212, 1.406347, 0.061073], 

103 [1.193490, 0.687096, 0.029481], 

104 [1.190824, -0.690400, -0.028344], 

105 [0.000295, -1.406191, -0.059503], 

106 [-1.186974, -0.685668, -0.045413], 

107 [-1.185376, 0.690203, 0.009452], 

108 [2.147124, 1.219997, 0.064477], 

109 [2.141593, -1.227477, -0.054266], 

110 [-2.138408, -1.222814, -0.095050], 

111 [-2.137740, 1.226930, 0.023036], 

112 [-0.006314, 2.776024, 0.186278], 

113 [-0.007340, -2.777839, -0.159936], 

114 [0.844710, -3.256543, 0.110098], 

115 [-0.854965, -3.253324, 0.130125], 

116 [0.845826, 3.267270, -0.055549], 

117 [-0.854666, 3.254654, -0.092676]]}, 

118 'biphenyl': { 

119 # PBE-gpaw relaxed 

120 'symbols': 'C6H5C6H5', 

121 'positions': [[-0.74081, -0.00000, -0.00003], 

122 [-1.46261, -1.20370, -0.00993], 

123 [-2.85531, -1.20350, -0.00663], 

124 [-3.55761, -0.00000, -0.00003], 

125 [-2.85531, 1.20350, 0.00667], 

126 [-1.46261, 1.20370, 0.00997], 

127 [-0.92071, -2.14850, 0.00967], 

128 [-3.38981, -2.15110, -0.00083], 

129 [-4.64571, -0.00000, -0.00003], 

130 [-3.38981, 2.15110, 0.00077], 

131 [-0.92071, 2.14850, -0.00963], 

132 [3.55849, -0.00000, -0.00003], 

133 [2.85509, -0.86640, -0.83553], 

134 [1.46289, -0.87000, -0.83153], 

135 [0.73969, -0.00000, -0.00003], 

136 [1.46289, 0.87000, 0.83157], 

137 [2.85509, 0.86640, 0.83547], 

138 [4.64659, -0.00000, -0.00003], 

139 [3.39189, -1.53770, -1.50253], 

140 [0.91869, -1.53310, -1.50263], 

141 [0.91869, 1.53310, 1.50267], 

142 [3.39189, 1.53770, 1.50257]]}, 

143 'C60': { 

144 # Buckminsterfullerene, I*h symm. 

145 # The Buckyball has two degrees of freedom, the C-C bond, and the 

146 # C=C bond. This is an LDA-gpaw relaxed structure with bond lengths 

147 # 1.437 and 1.385. 

148 # Experimentally, the two bond lengths are 1.45 and 1.40 Angstrom. 

149 'symbols': 'C60', 

150 'positions': [[2.2101953, 0.5866631, 2.6669504], 

151 [3.1076393, 0.1577008, 1.6300286], 

152 [1.3284430, -0.3158939, 3.2363232], 

153 [3.0908709, -1.1585005, 1.2014240], 

154 [3.1879245, -1.4574599, -0.1997005], 

155 [3.2214623, 1.2230966, 0.6739440], 

156 [3.3161210, 0.9351586, -0.6765151], 

157 [3.2984981, -0.4301142, -1.1204138], 

158 [-0.4480842, 1.3591484, 3.2081020], 

159 [0.4672056, 2.2949830, 2.6175264], 

160 [-0.0256575, 0.0764219, 3.5086259], 

161 [1.7727917, 1.9176584, 2.3529691], 

162 [2.3954623, 2.3095689, 1.1189539], 

163 [-0.2610195, 3.0820935, 1.6623117], 

164 [0.3407726, 3.4592388, 0.4745968], 

165 [1.6951171, 3.0692446, 0.1976623], 

166 [-2.1258394, -0.8458853, 2.6700963], 

167 [-2.5620990, 0.4855202, 2.3531715], 

168 [-0.8781521, -1.0461985, 3.2367302], 

169 [-1.7415096, 1.5679963, 2.6197333], 

170 [-1.6262468, 2.6357030, 1.6641811], 

171 [-3.2984810, 0.4301871, 1.1204208], 

172 [-3.1879469, 1.4573895, 0.1996030], 

173 [-2.3360261, 2.5813627, 0.4760912], 

174 [-0.5005210, -2.9797771, 1.7940308], 

175 [-1.7944338, -2.7729087, 1.2047891], 

176 [-0.0514245, -2.1328841, 2.7938830], 

177 [-2.5891471, -1.7225828, 1.6329715], 

178 [-3.3160705, -0.9350636, 0.6765268], 

179 [-1.6951919, -3.0692581, -0.1976564], 

180 [-2.3954901, -2.3096853, -1.1189862], 

181 [-3.2214182, -1.2231835, -0.6739581], 

182 [2.1758234, -2.0946263, 1.7922529], 

183 [1.7118619, -2.9749681, 0.7557198], 

184 [1.3130656, -1.6829416, 2.7943892], 

185 [0.3959024, -3.4051395, 0.7557638], 

186 [-0.3408219, -3.4591883, -0.4745610], 

187 [2.3360057, -2.5814499, -0.4761050], 

188 [1.6263757, -2.6357349, -1.6642309], 

189 [0.2611352, -3.0821271, -1.6622618], 

190 [-2.2100844, -0.5868636, -2.6670300], 

191 [-1.7726970, -1.9178969, -2.3530466], 

192 [-0.4670723, -2.2950509, -2.6175105], 

193 [-1.3283500, 0.3157683, -3.2362375], 

194 [-2.1759882, 2.0945383, -1.7923294], 

195 [-3.0909663, 1.1583472, -1.2015749], 

196 [-3.1076090, -0.1578453, -1.6301627], 

197 [-1.3131365, 1.6828292, -2.7943639], 

198 [0.5003224, 2.9799637, -1.7940203], 

199 [-0.3961148, 3.4052817, -0.7557272], 

200 [-1.7120629, 2.9749122, -0.7557988], 

201 [0.0512824, 2.1329478, -2.7937450], 

202 [2.1258630, 0.8460809, -2.6700534], 

203 [2.5891853, 1.7227742, -1.6329562], 

204 [1.7943010, 2.7730684, -1.2048262], 

205 [0.8781323, 1.0463514, -3.2365313], 

206 [0.4482452, -1.3591061, -3.2080510], 

207 [1.7416948, -1.5679557, -2.6197714], 

208 [2.5621724, -0.4853529, -2.3532026], 

209 [0.0257904, -0.0763567, -3.5084446]]}}