本文整理匯總了Python中ase.vibrations.Vibrations.clean方法的典型用法代碼示例。如果您正苦於以下問題：Python Vibrations.clean方法的具體用法？Python Vibrations.clean怎麽用？Python Vibrations.clean使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類ase.vibrations.Vibrations的用法示例。
在下文中一共展示了Vibrations.clean方法的2個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: fcc111
# 需要導入模塊: from ase.vibrations import Vibrations [as 別名]
# 或者: from ase.vibrations.Vibrations import clean [as 別名]
slab = fcc111('Al', size=(2, 2, 2), vacuum=3.0)
CH3 = molecule('CH3')
add_adsorbate(slab, CH3, 2.5, 'ontop')
constraint = FixAtoms(mask=[a.symbol == 'Al' for a in slab])
slab.set_constraint(constraint)
slab.set_calculator(EMT())
dyn = QuasiNewton(slab, logfile='/dev/null')
dyn.run(fmax=0.05)
vib = Vibrations(slab, indices=[8, 9, 10, 11])
vib.run()
vib.summary(log='/dev/null')
vib.clean()
AM = AnharmonicModes(vibrations_object=vib)
rot_mode = AM.define_rotation(
basepos=[0., 0., -1.],
branch=[9, 10, 11],
symnumber=3)
AM.run()
AM.summary(log='/dev/null')
AM.clean()
# print(AM.get_ZPE(), AM.get_entropic_energy())
assert abs(AM.get_ZPE() - 0.388) < 1e-3, AM.get_ZPE()
assert abs(AM.get_entropic_energy() - (0.091)) < 1e-3, (
AM.get_entropic_energy())示例2: Atoms
# 需要導入模塊: from ase.vibrations import Vibrations [as 別名]
# 或者: from ase.vibrations.Vibrations import clean [as 別名]
from __future__ import print_function
from ase import Atoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.vibrations import Vibrations
from ase.thermochemistry import IdealGasThermo
n2 = Atoms('N2',
positions=[(0, 0, 0), (0, 0, 1.1)],
calculator=EMT())
QuasiNewton(n2).run(fmax=0.01)
vib = Vibrations(n2)
vib.run()
print(vib.get_frequencies())
vib.summary()
print(vib.get_mode(-1))
vib.write_mode(n=None, nimages=20)
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies, geometry='linear',
atoms=n2, symmetrynumber=2, spin=0)
thermo.get_gibbs_energy(temperature=298.15, pressure=2 * 101325.)
assert vib.clean(empty_files=True) == 0
assert vib.clean() == 13