本文整理汇总了Python中ase.lattice.cubic.FaceCenteredCubic.center方法的典型用法代码示例。如果您正苦于以下问题：Python FaceCenteredCubic.center方法的具体用法？Python FaceCenteredCubic.center怎么用？Python FaceCenteredCubic.center使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类ase.lattice.cubic.FaceCenteredCubic的用法示例。
在下文中一共展示了FaceCenteredCubic.center方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: fcc211
# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import center [as 别名]
def fcc211(symbol, size, a=None, vacuum=None, orthogonal=True):
"""FCC(211) surface.
Does not currently support special adsorption sites.
Currently only implemented for *orthogonal=True* with size specified
as (i, j, k), where i, j, and k are number of atoms in each direction.
i must be divisible by 3 to accommodate the step width.
"""
if not orthogonal:
raise NotImplementedError('Only implemented for orthogonal '
'unit cells.')
if size[0] % 3 != 0:
raise NotImplementedError('First dimension of size must be '
'divisible by 3.')
atoms = FaceCenteredCubic(symbol,
directions=[[1, -1, -1],
[0, 2, -2],
[2, 1, 1]],
miller=(None, None, (2, 1, 1)),
latticeconstant=a,
size=(1, 1, 1),
pbc=True)
z = (size[2] + 1) // 2
atoms = atoms.repeat((size[0] // 3, size[1], z))
if size[2] % 2: # Odd: remove bottom layer and shrink cell.
remove_list = [atom.index for atom in atoms
if atom.z < atoms[1].z]
del atoms[remove_list]
dz = atoms[0].z
atoms.translate((0., 0., -dz))
atoms.cell[2][2] -= dz
atoms.cell[2] = 0.0
atoms.pbc[1] = False
if vacuum:
atoms.center(vacuum, axis=2)
# Renumber systematically from top down.
orders = [(atom.index, round(atom.x, 3), round(atom.y, 3),
-round(atom.z, 3), atom.index) for atom in atoms]
orders.sort(key=itemgetter(3, 1, 2))
newatoms = atoms.copy()
for index, order in enumerate(orders):
newatoms[index].position = atoms[order[0]].position.copy()
return newatoms示例2: print
# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import center [as 别名]
if rank == 0:
print("#"*60)
print("GPAW benchmark: Copper Sheet")
print(" dimensions: x=%d, y=%d, z=%d" % (x, y, z))
print(" grid spacing: h=%f" % h)
print(" Brillouin-zone sampling: kpts=" + str(kpts))
print(" MPI task: %d out of %d" % (rank, size))
print(" using MICs: " + str(use_mic))
print("#"*60)
print("")
# setup the system
atoms = FaceCenteredCubic(directions=[[1,-1,0], [1,1,-2], [1,1,1]],
size=(x,y,z), symbol='Cu', pbc=(1,1,0))
#add_vacuum(atoms, 10.0)
atoms.center(vacuum=6.0, axis=2)
calc = GPAW(h=h, nbands=-20, width=0.2,
kpts=kpts, xc='PBE',
maxiter=maxiter,
txt=txt, eigensolver=RMM_DIIS(niter=2),
parallel={'sl_auto': True},
mixer=Mixer(0.1, 5, 100),
)
atoms.set_calculator(calc)
# execute the run
try:
atoms.get_potential_energy()
except ConvergenceError:
pass
示例3: FaceCenteredCubic
# 需要导入模块: from ase.lattice.cubic import FaceCenteredCubic [as 别名]
# 或者: from ase.lattice.cubic.FaceCenteredCubic import center [as 别名]
symb = "Cu"
Z = data.atomic_numbers[symb]
a0 = data.reference_states[Z]['a']
# (100) oriented block
atoms = FaceCenteredCubic(size=(5,5,5), symbol="Cu", pbc=(1,1,0))
assert len(atoms) == 5*5*5*4
c = atoms.get_cell()
checkang(c[0], c[1], pi/2)
checkang(c[0], c[2], pi/2)
checkang(c[1], c[2], pi/2)
assert np.abs(5 * a0 - c[2,2]) < 1e-10
# Add vacuum in one direction
vac = 10.0
atoms.center(axis=2, vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi/2)
checkang(c[0], c[2], pi/2)
checkang(c[1], c[2], pi/2)
assert np.abs(4.5 * a0 + 2* vac - c[2,2]) < 1e-10
# Add vacuum in all directions
vac = 4.0
atoms.center(vacuum=vac)
c = atoms.get_cell()
checkang(c[0], c[1], pi/2)
checkang(c[0], c[2], pi/2)
checkang(c[1], c[2], pi/2)
assert np.abs(4.5 * a0 + 2* vac - c[0,0]) < 1e-10
assert np.abs(4.5 * a0 + 2* vac - c[1,1]) < 1e-10