def __init__(self, symbol):
atoms = Atoms(
[ Atom(symbol, ( 0, 0, 0, )), ],
cell=(30.0, 30.0, 30., ),
pbc=False,
)
Molecule.__init__(self, atoms)
def __init__(self, symbol):
self.__symbol = symbol
bond_length = {'O': 1.21}[symbol]
atoms = Atoms(symbol*2, positions=[[0,-bond_length/2., 0], [0, bond_length/2., 0]],
cell=(10, 10, 10+bond_length)
)
atoms.set_initial_magnetic_moments([1,1])
Molecule.__init__(self, atoms)
def __init__(self, symbol, name=DEFAULT, parameters=DEFAULT):
self.__symbol = symbol
number = atomic_numbers[symbol]
radius = covalent_radii[number]
atoms = Atoms(symbol + '2', positions=[[-radius, 0, 0], [radius, 0, 0]])
Molecule.__init__(
self,
atoms=atoms,
name=name,
parameters=parameters,
)
def __init__(self, symbol):
self.__symbol = symbol
atoms = Atoms(symbols=symbol + '10H15',
pbc=np.array([False, False, False], dtype=bool),
cell=np.array(
[[ 42., 0., 0.],
[ 0., 43., 0.],
[ 0., 0., 31.]]),
positions=np.array([
[ 0.00000000 , 0.00000000 , 0.00000000],
[ 2.18427300 , -0.00001600 ,- 1.00453600],
[ -1.09434500 , 1.89303000 ,- 1.00282400],
[ -1.09431700 , -1.89301600 ,- 1.00282400],
[ 4.43153700 , -0.00001800 ,- 1.81223000],
[ 1.10633700 , 1.91978200 ,- 1.81223000],
[ -2.21886300 , 3.83958200 ,- 1.81223000],
[ 1.10633700 , -1.91981800 ,- 1.81223000],
[ -2.21886300 , -0.00001800 ,- 1.81223000],
[ -2.21886300 , -3.83961800 ,- 1.81223000],
[ 5.36233700 , -0.00001800 ,- 0.66163000],
[ 4.66473700 , -1.20821800 ,- 2.63453000],
[ 4.66473700 , 1.20818200 ,- 2.63453000],
[ 1.10613700 , 1.91938200 ,- 3.29223000],
[ 1.80393700 , 3.12808200 ,- 1.31863000],
[ -2.68466300 , 4.64548200 ,- 0.66163000],
[ -1.28896300 , 4.64588200 ,- 2.63423000],
[ -3.38166300 , 3.43748200 ,- 2.63483000],
[ 1.80393700 , -3.12811800 ,- 1.31863000],
[ 1.10613700 , -1.91941800 ,- 3.29223000],
[ -2.21846300 , -0.00001800 ,- 3.29223000],
[ -3.61406300 , -0.00001800 ,- 1.31863000],
[ -2.68466300 , -4.64551800 ,- 0.66163000],
[ -3.38166300 , -3.43751800 ,- 2.63483000],
[ -1.28896300 , -4.64591800 ,- 2.63423000],
]))
normal_vector = np.array([0,0,1])
constraints = []
for i in range(4, 10):
constraint = FixedPlane(i, normal_vector)
constraints.append(constraint)
atoms.set_constraint(constraints)
Molecule.__init__(self, atoms)
def name(self):
return self.__symbol + Molecule.name(self)
def __init__(self, parameters=DEFAULT):
atoms = Atoms(
[
Atom("C", (8.46865, 12.3316, 5.1)),
Atom("C", (8.45722, 13.7215, 5.1)),
Atom("C", (7.24847, 14.4039, 5.1)),
Atom("H", (7.23946, 15.4976, 5.1)),
Atom("C", (6.05114, 13.6965, 5.1)),
Atom("H", (5.1, 14.2335, 5.1)),
Atom("C", (6.0626, 12.3066, 5.1)),
Atom("H", (5.12044, 11.7499, 5.1)),
Atom("C", (7.27133, 11.6242, 5.1)),
Atom("H", (7.28039, 10.5305, 5.1)),
Atom("C", (9.95115, 12.3316, 5.1)),
Atom("C", (9.96258, 13.7215, 5.1)),
Atom("C", (11.1713, 14.4039, 5.1)),
Atom("H", (11.1803, 15.4976, 5.1)),
Atom("C", (12.3687, 13.6965, 5.1)),
Atom("C", (12.3572, 12.3066, 5.1)),
Atom("C", (11.1485, 11.6242, 5.1)),
Atom("H", (11.1394, 10.5305, 5.1)),
Atom("C", (15.4761, 17.7423, 5.1)),
Atom("C", (16.6856, 17.0572, 5.1)),
Atom("C", (17.8809, 17.7628, 5.1)),
Atom("H", (18.8326, 17.2238, 5.1)),
Atom("C", (17.8669, 19.1535, 5.1)),
Atom("H", (18.8075, 19.7087, 5.1)),
Atom("C", (16.6575, 19.8385, 5.1)),
Atom("H", (16.6465, 20.9327, 5.1)),
Atom("C", (15.4622, 19.1329, 5.1)),
Atom("H", (14.5105, 19.6719, 5.1)),
Atom("C", (14.7349, 16.4584, 5.1)),
Atom("C", (15.9329, 15.7535, 5.1)),
Atom("C", (15.9195, 14.3655, 5.1)),
Atom("H", (16.8622, 13.8109, 5.1)),
Atom("C", (14.7082, 13.6823, 5.1)),
Atom("C", (13.5102, 14.3872, 5.1)),
Atom("C", (13.5236, 15.7752, 5.1)),
Atom("H", (12.5809, 16.3299, 5.1)),
Atom("C", (16.6582, 8.96828, 5.1)),
Atom("C", (15.4602, 8.26342, 5.1)),
Atom("C", (15.4736, 6.87542, 5.1)),
Atom("H", (14.5309, 6.32074, 5.1)),
Atom("C", (16.6849, 6.19221, 5.1)),
Atom("H", (16.6954, 5.1, 5.1)),
Atom("C", (17.8829, 6.89708, 5.1)),
Atom("H", (18.836, 6.35947, 5.1)),
Atom("C", (17.8695, 8.28507, 5.1)),
Atom("H", (18.8121, 8.83977, 5.1)),
Atom("C", (15.917, 10.2522, 5.1)),
Atom("C", (14.7075, 9.5671, 5.1)),
Atom("C", (13.5122, 10.2727, 5.1)),
Atom("H", (12.5605, 9.73365, 5.1)),
Atom("C", (13.5262, 11.6633, 5.1)),
Atom("C", (14.7356, 12.3484, 5.1)),
Atom("C", (15.9309, 11.6428, 5.1)),
Atom("H", (16.8826, 12.1818, 5.1)),
],
cell=(23.9360246543, 26.0327464664, 10.2),
pbc=False,
)
cell = atoms.cell.sum(axis=0)
atoms.positions -= cell / 2.0
atoms.positions[:, 0] -= 1.58
Molecule.__init__(self, atoms=atoms, parameters=parameters)
def __init__(self, parameters=DEFAULT):
Molecule.__init__(self, atoms=st_atoms, parameters=parameters)
def __init__(self, parameters=DEFAULT):
group1 = makeEneEndGroup(3)
atoms = triplicateEndGroup(group1)
Molecule.__init__(self, atoms=atoms, parameters=parameters)
def __init__(self, number, name=DEFAULT):
self.__name = name
self.__number = number
atoms = makeEnes(number)
Molecule.__init__(self, atoms, name=name)
