Source code for ase.build.molecule

from ase.atoms import Atoms
from ase.collections import g2


[docs]def molecule(name, vacuum=None, **kwargs): if name in extra: kwargs.update(extra[name]) mol = Atoms(**kwargs) else: mol = g2[name] if kwargs: mol = Atoms(mol, **kwargs) if vacuum is not None: mol.center(vacuum=vacuum) return mol
extra = { 'Be2': { 'symbols': 'BeBe', 'positions': [[0, 0, 1.0106], [0, 0, -1.0106]]}, 'C7NH5': { 'symbols': 'C7NH5', 'positions': [[-1.593581, -1.142601, 0.], [-2.235542, 0.095555, 0.], [-0.204885, -1.210726, 0.], [0.549645, -0.025355, 0.], [1.976332, -0.085321, 0.], [-0.099258, 1.220706, 0.], [-1.488628, 1.273345, 0.], [3.136871, -0.128138, 0.], [-2.177996, -2.060896, 0.], [-3.323594, 0.141242, 0.], [0.301694, -2.173705, 0.], [0.488716, 2.136782, 0.], [-1.987765, 2.240495, 0.]]}, 'BDA': { # 1,4-Benzodiamine # aka p-Aminoaniline; p-Benzenediamine; p-Diaminobenzene; # p-Phenylenediamine; Paraphenylen-diamine # PBE-gpaw relaxed 'symbols': 'C6H4N2H4', 'positions': [[0.004212, 1.406347, 0.061073], [1.193490, 0.687096, 0.029481], [1.190824, -0.690400, -0.028344], [0.000295, -1.406191, -0.059503], [-1.186974, -0.685668, -0.045413], [-1.185376, 0.690203, 0.009452], [2.147124, 1.219997, 0.064477], [2.141593, -1.227477, -0.054266], [-2.138408, -1.222814, -0.095050], [-2.137740, 1.226930, 0.023036], [-0.006314, 2.776024, 0.186278], [-0.007340, -2.777839, -0.159936], [0.844710, -3.256543, 0.110098], [-0.854965, -3.253324, 0.130125], [0.845826, 3.267270, -0.055549], [-0.854666, 3.254654, -0.092676]]}, 'biphenyl': { # PBE-gpaw relaxed 'symbols': 'C6H5C6H5', 'positions': [[-0.74081, -0.00000, -0.00003], [-1.46261, -1.20370, -0.00993], [-2.85531, -1.20350, -0.00663], [-3.55761, -0.00000, -0.00003], [-2.85531, 1.20350, 0.00667], [-1.46261, 1.20370, 0.00997], [-0.92071, -2.14850, 0.00967], [-3.38981, -2.15110, -0.00083], [-4.64571, -0.00000, -0.00003], [-3.38981, 2.15110, 0.00077], [-0.92071, 2.14850, -0.00963], [3.55849, -0.00000, -0.00003], [2.85509, -0.86640, -0.83553], [1.46289, -0.87000, -0.83153], [0.73969, -0.00000, -0.00003], [1.46289, 0.87000, 0.83157], [2.85509, 0.86640, 0.83547], [4.64659, -0.00000, -0.00003], [3.39189, -1.53770, -1.50253], [0.91869, -1.53310, -1.50263], [0.91869, 1.53310, 1.50267], [3.39189, 1.53770, 1.50257]]}, 'C60': { # Buckminsterfullerene, I*h symm. # The Buckyball has two degrees of freedom, the C-C bond, and the # C=C bond. This is an LDA-gpaw relaxed structure with bond lengths # 1.437 and 1.385. # Experimentally, the two bond lengths are 1.45 and 1.40 Angstrom. 'symbols': 'C60', 'positions': [[2.2101953, 0.5866631, 2.6669504], [3.1076393, 0.1577008, 1.6300286], [1.3284430, -0.3158939, 3.2363232], [3.0908709, -1.1585005, 1.2014240], [3.1879245, -1.4574599, -0.1997005], [3.2214623, 1.2230966, 0.6739440], [3.3161210, 0.9351586, -0.6765151], [3.2984981, -0.4301142, -1.1204138], [-0.4480842, 1.3591484, 3.2081020], [0.4672056, 2.2949830, 2.6175264], [-0.0256575, 0.0764219, 3.5086259], [1.7727917, 1.9176584, 2.3529691], [2.3954623, 2.3095689, 1.1189539], [-0.2610195, 3.0820935, 1.6623117], [0.3407726, 3.4592388, 0.4745968], [1.6951171, 3.0692446, 0.1976623], [-2.1258394, -0.8458853, 2.6700963], [-2.5620990, 0.4855202, 2.3531715], [-0.8781521, -1.0461985, 3.2367302], [-1.7415096, 1.5679963, 2.6197333], [-1.6262468, 2.6357030, 1.6641811], [-3.2984810, 0.4301871, 1.1204208], [-3.1879469, 1.4573895, 0.1996030], [-2.3360261, 2.5813627, 0.4760912], [-0.5005210, -2.9797771, 1.7940308], [-1.7944338, -2.7729087, 1.2047891], [-0.0514245, -2.1328841, 2.7938830], [-2.5891471, -1.7225828, 1.6329715], [-3.3160705, -0.9350636, 0.6765268], [-1.6951919, -3.0692581, -0.1976564], [-2.3954901, -2.3096853, -1.1189862], [-3.2214182, -1.2231835, -0.6739581], [2.1758234, -2.0946263, 1.7922529], [1.7118619, -2.9749681, 0.7557198], [1.3130656, -1.6829416, 2.7943892], [0.3959024, -3.4051395, 0.7557638], [-0.3408219, -3.4591883, -0.4745610], [2.3360057, -2.5814499, -0.4761050], [1.6263757, -2.6357349, -1.6642309], [0.2611352, -3.0821271, -1.6622618], [-2.2100844, -0.5868636, -2.6670300], [-1.7726970, -1.9178969, -2.3530466], [-0.4670723, -2.2950509, -2.6175105], [-1.3283500, 0.3157683, -3.2362375], [-2.1759882, 2.0945383, -1.7923294], [-3.0909663, 1.1583472, -1.2015749], [-3.1076090, -0.1578453, -1.6301627], [-1.3131365, 1.6828292, -2.7943639], [0.5003224, 2.9799637, -1.7940203], [-0.3961148, 3.4052817, -0.7557272], [-1.7120629, 2.9749122, -0.7557988], [0.0512824, 2.1329478, -2.7937450], [2.1258630, 0.8460809, -2.6700534], [2.5891853, 1.7227742, -1.6329562], [1.7943010, 2.7730684, -1.2048262], [0.8781323, 1.0463514, -3.2365313], [0.4482452, -1.3591061, -3.2080510], [1.7416948, -1.5679557, -2.6197714], [2.5621724, -0.4853529, -2.3532026], [0.0257904, -0.0763567, -3.5084446]]}}