Coverage for eminus/data.py: 100.00%

1# SPDX-FileCopyrightText: 2021 The eminus developers

2# SPDX-License-Identifier: Apache-2.0

3"""Atomic data collections."""

5import math

7#: Map atom symbols and atom numbers.

8SYMBOL2NUMBER = {

9 "X": 0,

10 "H": 1,

11 "He": 2,

12 "Li": 3,

13 "Be": 4,

14 "B": 5,

15 "C": 6,

16 "N": 7,

17 "O": 8,

18 "F": 9,

19 "Ne": 10,

20 "Na": 11,

21 "Mg": 12,

22 "Al": 13,

23 "Si": 14,

24 "P": 15,

25 "S": 16,

26 "Cl": 17,

27 "Ar": 18,

28 "K": 19,

29 "Ca": 20,

30 "Sc": 21,

31 "Ti": 22,

32 "V": 23,

33 "Cr": 24,

34 "Mn": 25,

35 "Fe": 26,

36 "Co": 27,

37 "Ni": 28,

38 "Cu": 29,

39 "Zn": 30,

40 "Ga": 31,

41 "Ge": 32,

42 "As": 33,

43 "Se": 34,

44 "Br": 35,

45 "Kr": 36,

46 "Rb": 37,

47 "Sr": 38,

48 "Y": 39,

49 "Zr": 40,

50 "Nb": 41,

51 "Mo": 42,

52 "Tc": 43,

53 "Ru": 44,

54 "Rh": 45,

55 "Pd": 46,

56 "Ag": 47,

57 "Cd": 48,

58 "In": 49,

59 "Sn": 50,

60 "Sb": 51,

61 "Te": 52,

62 "I": 53,

63 "Xe": 54,

64 "Cs": 55,

65 "Ba": 56,

66 "La": 57,

67 "Ce": 58,

68 "Pr": 59,

69 "Nd": 60,

70 "Pm": 61,

71 "Sm": 62,

72 "Eu": 63,

73 "Gd": 64,

74 "Tb": 65,

75 "Dy": 66,

76 "Ho": 67,

77 "Er": 68,

78 "Tm": 69,

79 "Yb": 70,

80 "Lu": 71,

81 "Hf": 72,

82 "Ta": 73,

83 "W": 74,

84 "Re": 75,

85 "Os": 76,

86 "Ir": 77,

87 "Pt": 78,

88 "Au": 79,

89 "Hg": 80,

90 "Tl": 81,

91 "Pb": 82,

92 "Bi": 83,

93 "Po": 84,

94 "At": 85,

95 "Rn": 86,

96 # "Fr": 87,

97 # "Ra": 88,

98 "Ac": 89,

99 "Th": 90,

100 "Pa": 91,

101 "U": 92,

102 "Np": 93,

103 "Pu": 94,

104 "Am": 95,

105 "Cm": 96,

106 "Bk": 97,

107 "Cf": 98,

108 "Es": 99,

109 "Fm": 100,

110 "Md": 101,

111 "No": 102,

112 "Lr": 103,

113}

114

115#: Map atom numbers and atom symbols.

116NUMBER2SYMBOL = {value: key for key, value in SYMBOL2NUMBER.items()}

117

118#: Covalent radii per atom.

119#: Reference: Dalton Trans., 2832.

120COVALENT_RADII = {

121 "X": 0.3779452249251541,

122 "H": 0.5858150986339887,

123 "He": 0.5291233148952157,

124 "Li": 2.418849439520986,

125 "Be": 1.8141370796407394,

126 "B": 1.5873699446856468,

127 "C": 1.4361918547155854,

128 "N": 1.3417055484842968,

129 "O": 1.2472192422530084,

130 "F": 1.0771438910366888,

131 "Ne": 1.0960411522829467,

132 "Na": 3.1369453668787783,

133 "Mg": 2.6645138357223357,

134 "Al": 2.286568610797182,

135 "Si": 2.0975959983346053,

136 "P": 2.022006953349574,

137 "S": 1.9842124308570588,

138 "Cl": 1.9275206471182857,

139 "Ar": 2.0031096921033167,

140 "K": 3.836144032990313,

141 "Ca": 3.3259179793413556,

142 "Sc": 3.2125344118638095,

143 "Ti": 3.0235617994012327,

144 "V": 2.8912809706774283,

145 "Cr": 2.6267193132298203,

146 "Mn": 2.6267193132298203,

147 "Fe": 2.494438484506017,

148 "Co": 2.3810549170284707,

149 "Ni": 2.343260394535955,

150 "Cu": 2.494438484506017,

151 "Zn": 2.3054658720434396,

152 "Ga": 2.3054658720434396,

153 "Ge": 2.267671349550924,

154 "As": 2.2487740883046663,

155 "Se": 2.267671349550924,

156 "Br": 2.267671349550924,

157 "Kr": 2.1920823045658935,

158 "Rb": 4.157397474176695,

159 "Sr": 3.6849659430202517,

160 "Y": 3.590479636788963,

161 "Zr": 3.3070207180950977,

162 "Nb": 3.099150844386263,

163 "Mo": 2.910178231923686,

164 "Tc": 2.777897403199882,

165 "Ru": 2.7590001419536243,

166 "Rh": 2.6834110969685936,

167 "Pd": 2.6267193132298203,

168 "Ag": 2.740102880707367,

169 "Cd": 2.721205619461109,

170 "In": 2.6834110969685936,

171 "Sn": 2.6267193132298203,

172 "Sb": 2.6267193132298203,

173 "Te": 2.607822051983563,

174 "I": 2.6267193132298203,

175 "Xe": 2.6456165744760782,

176 "Cs": 4.610931744086879,

177 "Ba": 4.062911167945406,

178 "La": 3.911733077975344,

179 "Ce": 3.8550412942365715,

180 "Pr": 3.836144032990313,

181 "Nd": 3.798349510497798,

182 "Pm": 3.760554988005283,

183 "Sm": 3.741657726759025,

184 "Eu": 3.741657726759025,

185 "Gd": 3.7038632042665096,

186 "Tb": 3.6660686817739943,

187 "Dy": 3.628274159281479,

188 "Ho": 3.628274159281479,

189 "Er": 3.5715823755427056,

190 "Tm": 3.590479636788963,

191 "Yb": 3.5337878530501907,

192 "Lu": 3.5337878530501907,

193 "Hf": 3.3070207180950977,

194 "Ta": 3.2125344118638095,

195 "W": 3.061356321893748,

196 "Re": 2.853486448184913,

197 "Os": 2.721205619461109,

198 "Ir": 2.6645138357223357,

199 "Pt": 2.5700275294910475,

200 "Au": 2.5700275294910475,

201 "Hg": 2.494438484506017,

202 "Tl": 2.740102880707367,

203 "Pb": 2.7590001419536243,

204 "Bi": 2.79679466444614,

205 "Po": 2.6456165744760782,

206 "At": 2.8345891869386555,

207 "Rn": 2.8345891869386555,

208 "Ac": 4.913287924027003,

209 "Th": 4.176294735422952,

210 "Pa": 4.062911167945406,

211 "U": 3.892835816729087,

212 "Np": 3.7794522492515403,

213 "Pu": 3.7038632042665096,

214 "Am": 3.590479636788963,

215 "Cm": 3.5337878530501907,

216 "Bk": 3.4015070243263863,

217 "Cf": 3.1936371506175516,

218 "Es": 0.3779452249251541,

219 "Fm": 0.3779452249251541,

220 "Md": 0.3779452249251541,

221 "No": 0.3779452249251541,

222 "Lr": 0.3779452249251541,

223}

224

225#: CPK colors per atom.

226#: Reference: https://gitlab.com/ase/ase/-/blob/master/ase/data/colors.py

227CPK_COLORS = {

228 "X": "#ff0000",

229 "H": "#ffffff",

230 "He": "#ffc0ca",

231 "Li": "#b12121",

232 "Be": "#ff1392",

233 "B": "#00ff00",

234 "C": "#c7c7c7",

235 "N": "#8f8fff",

236 "O": "#ef0000",

237 "F": "#daa41f",

238 "Ne": "#ff1392",

239 "Na": "#0000ff",

240 "Mg": "#218a21",

241 "Al": "#808090",

242 "Si": "#daa41f",

243 "P": "#ffa400",

244 "S": "#ffc731",

245 "Cl": "#00ff00",

246 "Ar": "#ff1392",

247 "K": "#ff1392",

248 "Ca": "#808090",

249 "Sc": "#ff1392",

250 "Ti": "#808090",

251 "V": "#ff1392",

252 "Cr": "#808090",

253 "Mn": "#808090",

254 "Fe": "#ffa400",

255 "Co": "#ff1392",

256 "Ni": "#a42a2a",

257 "Cu": "#a42a2a",

258 "Zn": "#a42a2a",

259 "Ga": "#ff1392",

260 "Ge": "#ff1392",

261 "As": "#ff1392",

262 "Se": "#ff1392",

263 "Br": "#a42a2a",

264 "Kr": "#ff1392",

265 "Rb": "#ff1392",

266 "Sr": "#ff1392",

267 "Y": "#ff1392",

268 "Zr": "#ff1392",

269 "Nb": "#ff1392",

270 "Mo": "#ff1392",

271 "Tc": "#ff1392",

272 "Ru": "#ff1392",

273 "Rh": "#ff1392",

274 "Pd": "#ff1392",

275 "Ag": "#808090",

276 "Cd": "#ff1392",

277 "In": "#ff1392",

278 "Sn": "#ff1392",

279 "Sb": "#ff1392",

280 "Te": "#ff1392",

281 "I": "#9f1fef",

282 "Xe": "#ff1392",

283 "Cs": "#ff1392",

284 "Ba": "#ffa400",

285 "La": "#ff1392",

286 "Ce": "#ff1392",

287 "Pr": "#ff1392",

288 "Nd": "#ff1392",

289 "Pm": "#ff1392",

290 "Sm": "#ff1392",

291 "Eu": "#ff1392",

292 "Gd": "#ff1392",

293 "Tb": "#ff1392",

294 "Dy": "#ff1392",

295 "Ho": "#ff1392",

296 "Er": "#ff1392",

297 "Tm": "#ff1392",

298 "Yb": "#ff1392",

299 "Lu": "#ff1392",

300 "Hf": "#ff1392",

301 "Ta": "#ff1392",

302 "W": "#ff1392",

303 "Re": "#ff1392",

304 "Os": "#ff1392",

305 "Ir": "#ff1392",

306 "Pt": "#ff1392",

307 "Au": "#daa41f",

308 "Hg": "#ff1392",

309 "Tl": "#ff1392",

310 "Pb": "#ff1392",

311 "Bi": "#ff1392",

312 "Po": "#ff1392",

313 "At": "#ff1392",

314 "Rn": "#ffffff",

315 "Ac": "#ffffff",

316 "Th": "#ffffff",

317 "Pa": "#ffffff",

318 "U": "#ff1392",

319 "Np": "#ffffff",

320 "Pu": "#ff1392",

321 "Am": "#ffffff",

322 "Cm": "#ffffff",

323 "Bk": "#ffffff",

324 "Cf": "#ffffff",

325 "Es": "#ffffff",

326 "Fm": "#ffffff",

327 "Md": "#ffffff",

328 "No": "#ffffff",

329 "Lr": "#ffffff",

330}

331

332#: Special points in Brillouin zones of different crystal systems.

333#: Reference: Comput. Mater. Sci. 49, 299.

334SPECIAL_POINTS = {

335 "sc": {

336 "G": [0, 0, 0],

337 "M": [1 / 2, 1 / 2, 0],

338 "R": [1 / 2, 1 / 2, 1 / 2],

339 "X": [0, 1 / 2, 0],

340 },

341 "fcc": {

342 "G": [0, 0, 0],

343 "K": [3 / 8, 3 / 8, 3 / 4],

344 "L": [1 / 2, 1 / 2, 1 / 2],

345 "U": [5 / 8, 1 / 4, 5 / 8],

346 "W": [1 / 2, 1 / 4, 3 / 4],

347 "X": [1 / 2, 0, 1 / 2],

348 },

349 "bcc": {

350 "G": [0, 0, 0],

351 "H": [1 / 2, -1 / 2, 1 / 2],

352 "P": [1 / 4, 1 / 4, 1 / 4],

353 "N": [0, 0, 1 / 2],

354 },

355 "tetragonal": {

356 "G": [0, 0, 0],

357 "A": [1 / 2, 1 / 2, 1 / 2],

358 "M": [1 / 2, 1 / 2, 0],

359 "R": [0, 1 / 2, 1 / 2],

360 "X": [0, 1 / 2, 0],

361 "Z": [0, 0, 1 / 2],

362 },

363 "orthorhombic": {

364 "G": [0, 0, 0],

365 "R": [1 / 2, 1 / 2, 1 / 2],

366 "S": [1 / 2, 1 / 2, 0],

367 "T": [0, 1 / 2, 1 / 2],

368 "U": [1 / 2, 0, 1 / 2],

369 "X": [1 / 2, 0, 0],

370 "Y": [0, 1 / 2, 0],

371 "Z": [0, 0, 1 / 2],

372 },

373 "hexagonal": {

374 "G": [0, 0, 0],

375 "A": [0, 0, 1 / 2],

376 "H": [1 / 3, 1 / 3, 1 / 2],

377 "K": [1 / 3, 1 / 3, 0],

378 "L": [1 / 2, 0, 1 / 2],

379 "M": [1 / 2, 0, 0],

380 },

381}

382

383#: Primitive lattice vectors of different crystal systems.

384#: Reference: Comput. Mater. Sci. 49, 299.

385LATTICE_VECTORS = {

386 "sc": [

387 [1, 0, 0],

388 [0, 1, 0],

389 [0, 0, 1],

390 ],

391 "fcc": [

392 [0, 1 / 2, 1 / 2],

393 [1 / 2, 0, 1 / 2],

394 [1 / 2, 1 / 2, 0],

395 ],

396 "bcc": [

397 [-1 / 2, 1 / 2, 1 / 2],

398 [1 / 2, -1 / 2, 1 / 2],

399 [1 / 2, 1 / 2, -1 / 2],

400 ],

401 "hexagonal": [

402 [1 / 2, -math.sqrt(3) / 2, 0],

403 [1 / 2, math.sqrt(3) / 2, 0],

404 [0, 0, 1],

405 ],

406}