本文整理汇总了Python中ase.vibrations.Vibrations.write_mode方法的典型用法代码示例。如果您正苦于以下问题：Python Vibrations.write_mode方法的具体用法？Python Vibrations.write_mode怎么用？Python Vibrations.write_mode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.vibrations.Vibrations的用法示例。
在下文中一共展示了Vibrations.write_mode方法的5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: Vibrations
# 需要导入模块: from ase.vibrations import Vibrations [as 别名]
# 或者: from ase.vibrations.Vibrations import write_mode [as 别名]
# name of output file for free energies
output_name = 'out.energy'
### At 300K and 101325 Pa
### change for your operating conditions
T = 300 # K
P = 101325 # Pa
#########################################################################################################
##### END #####
#########################################################################################################
energy = atoms.get_potential_energy() # caclulate the energy, to be used to determine G
vibrateatoms = [atom.index for atom in atoms if atom.symbol in ['H','N']] # calculate the vibrational modes for all N and H atoms
# Calculate vibrations
vib = Vibrations(atoms,indices=vibrateatoms,delta=0.03) # define a vibration calculation
vib.run() # run the vibration calculation
vib.summary(method='standard') # summarize the calculated results
for mode in range(len(vibrateatoms)*3): # Make trajectory files to visualize the modes.
vib.write_mode(mode)
vibenergies=vib.get_energies()
vibenergies=[vib for vib in vibenergies if not isinstance(vib,complex)] # only take the real modes
gibbs = HarmonicThermo(vib_energies = vibenergies, electronicenergy = energy)
freeenergy = gibbs.get_gibbs_energy(T,P)
f=open(output_name,'w')
f.write('Potential energy: '+str(energy)+'\n'+'Free energy: '+str(freeenergy)+'\n')
f.close示例2: Atoms
# 需要导入模块: from ase.vibrations import Vibrations [as 别名]
# 或者: from ase.vibrations.Vibrations import write_mode [as 别名]
from ase import *
from ase.vibrations import Vibrations
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(-1, nimages=20)
示例3: molecule
# 需要导入模块: from ase.vibrations import Vibrations [as 别名]
# 或者: from ase.vibrations.Vibrations import write_mode [as 别名]
#!/usr/bin/env python
from ase import Atom, Atoms
from ase.structure import molecule
from ase.calculators.cp2k import CP2K
from ase.optimize import BFGS
from ase.vibrations import Vibrations
from multiprocessing import Pool
import os
atoms = molecule('CO')
atoms.center(vacuum=2.0)
calc = CP2K(label = 'molecules/co/vib',
xc='PBE')
atoms.set_calculator(calc)
gopt = BFGS(atoms, logfile=None)
gopt.run(fmax=1e-2)
e = atoms.get_potential_energy()
pos = atoms.get_positions()
d = ((pos[0] - pos[1])**2).sum()**0.5
print('{0:1.4f} {1:1.4f} '.format( e, d))
vib = Vibrations(n2)
vib.run()
vib.summary()
vib.write_mode(-1)
示例4: Atoms
# 需要导入模块: from ase.vibrations import Vibrations [as 别名]
# 或者: from ase.vibrations.Vibrations import write_mode [as 别名]
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.)
示例5: molecule
# 需要导入模块: from ase.vibrations import Vibrations [as 别名]
# 或者: from ase.vibrations.Vibrations import write_mode [as 别名]
CH3 = molecule('CH3')
add_adsorbate(slab, CH3, 3.0, 'ontop')
constraint = FixAtoms(mask=[a.symbol == 'Al' for a in slab])
slab.set_constraint(constraint)
slab.set_calculator(EMT())
dyn = QuasiNewton(slab, trajectory='relax.traj')
dyn.run(fmax=0.01)
vib = Vibrations(slab, indices=[8, 9, 10, 11])
vib.run()
vib.summary()
vib.write_mode()
print('\n >> Anharmonics <<\n')
AM = AnharmonicModes(
vibrations_object=vib,
pre_names='an_mode_',
settings={
'use_forces': True,
# 'plot_mode': True,
'temperature': 298.15,
# 'rot_nsamples': 15,
# 'max_step_iterations': 1,
# 'min_step_iterations': 1,
'plot_mode_each_iteration': True,
# 'rot_nsamples': 9,