本文整理汇总了Python中ase.vibrations.Vibrations类的典型用法代码示例。如果您正苦于以下问题:Python Vibrations类的具体用法?Python Vibrations怎么用?Python Vibrations使用的例子?那么, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Vibrations类的15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: __init__
def __init__(self, atoms, Excitations,
indices=None,
gsname='rraman', # name for ground state calculations
exname=None, # name for excited state calculations
delta=0.01,
nfree=2,
directions=None,
approximation='Profeta',
observation={'geometry': '-Z(XX)Z'},
exkwargs={}, # kwargs to be passed to Excitations
exext='.ex.gz', # extension for Excitation names
txt='-',
verbose=False,):
assert(nfree == 2)
Vibrations.__init__(self, atoms, indices, gsname, delta, nfree)
self.name = gsname + '-d%.3f' % delta
if exname is None:
exname = gsname
self.exname = exname + '-d%.3f' % delta
self.exext = exext
if directions is None:
self.directions = np.array([0, 1, 2])
else:
self.directions = np.array(directions)
self.approximation = approximation
self.observation = observation
self.exobj = Excitations
self.exkwargs = exkwargs
self.timer = Timer()
self.txt = convert_string_to_fd(txt)
self.verbose = verbose
示例2: run
def run(job, atoms):
kwargs = {'mode': 0,
'label': 'vib-{0}'.format(job, job),
'xc': 'PBE',
'scf_guess': 'atomic',
'max_scf': 500,
'EPS_SCF': 5.0E-7,
'added_mos': 500,
'sme/method': 'fermi_dirac',
'ELECTRONIC_TEMPERATURE': 300,
'DIA/ALGORITHM': 'STANDARD',
'mix/METHOD': 'BROYDEN_MIXING',
'ALPHA': 0.1,
'BETA': 1.5,
'NBUFFER': 8,
'cpu': 36,
'cutoff': 300,
'run_type': 'ENERGY_FORCE', # ENERGY_FORCE, GEO_OPT, CELL_OPT, MD
'atoms': atoms,
}
calc = CP2K(**kwargs)
atoms.set_calculator(calc)
vib = Vibrations(atoms, indices = [65, 69])
vib.run()
vib.summary()
示例3: __init__
def __init__(self, atoms, Excitations,
indices=None,
gsname='rraman', # name for ground state calculations
exname=None, # name for excited state calculations
delta=0.01,
nfree=2,
directions=None,
exkwargs={}, # kwargs to be passed to Excitations
txt='-'):
assert(nfree == 2)
Vibrations.__init__(self, atoms, indices, gsname, delta, nfree)
self.name = gsname + '-d%.3f' % delta
if exname is None:
exname = gsname
self.exname = exname + '-d%.3f' % delta
if directions is None:
self.directions = np.array([0, 1, 2])
else:
self.directions = np.array(directions)
self.exobj = Excitations
self.exkwargs = exkwargs
self.timer = Timer()
self.txt = get_txt(txt, rank)
示例4: read
def read(self, method='standard', direction='central'):
"""Read data from a pre-performed calculation."""
if not hasattr(self, 'modes'):
self.timer.start('read vibrations')
Vibrations.read(self, method, direction)
# we now have:
# self.H : Hessian matrix
# self.im : 1./sqrt(masses)
# self.modes : Eigenmodes of the mass weighted H
self.om_r = self.hnu.real # energies in eV
self.timer.stop('read vibrations')
if not hasattr(self, 'ex0E_p'):
self.read_excitations()
示例5: __init__
def __init__(self, atoms, vibname, minfreq=None, maxfreq=None):
"""Input is a atoms object and the corresponding vibrations.
With minfreq and maxfreq frequencies can
be excluded from the calculation"""
self.atoms = atoms
# V = a * v is the combined atom and xyz-index
self.mm05_V = np.repeat(1.0 / np.sqrt(atoms.get_masses()), 3)
self.minfreq = minfreq
self.maxfreq = maxfreq
self.shape = (len(self.atoms), 3)
vib = Vibrations(atoms, name=vibname)
self.energies = np.real(vib.get_energies(method="frederiksen")) # [eV]
self.frequencies = np.real(vib.get_frequencies(method="frederiksen")) # [cm^-1]
self.modes = vib.modes
self.H = vib.H
示例6: run
def run(label, atoms):
#calc.mode = 1
calc.directory = 'vib/pt/{0}'.format(label)
calc.prefix = 'al2o3-pt-{0}'.format(label)
calc.results = {}
calc.CP2K_INPUT.FORCE_EVAL_list[0].DFT.Wfn_restart_file_name = 'al2o3-pt-{0}-RESTART.wfn'.format(label)
calc.CP2K_INPUT.MOTION.CONSTRAINT.FIXED_ATOMS_list = []
#===============================================================================
atoms.set_calculator(calc)
###calc.write_input_file()
#e = atoms.get_potential_energy()
#t = calc.get_time()
print(' {0} '.format(label))
vib = Vibrations(atoms, indices = [120])
vib.run()
vib.summary()
import os, shutil
for file in os.listdir('.'):
if "pckl" in file:
shutil.move(file,calc.directory)
示例7: len
grid='nodisk',
tolerances='tight',
maxiter=777,
convergence={'lshift': 0.0},
basis=basis,
basispar='spherical',
direct='noio',
raw='set int:txs:limxmem 134217728\nmemory total 8000 Mb noverify\n',
label=label)
atoms.set_calculator(calc)
t = time.time()
if len(atoms) > 1:
# need a copy of atoms for calculation of vibrations
vibatoms = atoms.copy()
vibatoms.set_calculator(calc)
vib = Vibrations(vibatoms, name=label + '_fixed')
vib.run()
f = vib.get_frequencies()[-1].real
# clean nwchem restart
if os.path.exists(name + '_' + code + '.db'):
os.remove(name + '_' + code + '.db')
atoms.get_potential_energy()
c.write(atoms, name=name, relaxed=False, basis=basis,
frequency=f,
time=time.time()-t)
else:
atoms.get_potential_energy()
c.write(atoms, name=name, relaxed=False, basis=basis,
time=time.time()-t)
if len(atoms) > 1:
opt = BFGS(atoms,
示例8: Vibrations
# 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9: GPAW
"""Calculate the vibrational modes of a H2O molecule."""
from ase.vibrations import Vibrations
from gpaw import GPAW
h2o = GPAW('h2o.gpw', txt=None).get_atoms()
# Create vibration calculator
vib = Vibrations(h2o)
vib.run()
vib.summary(method='frederiksen')
# Make trajectory files to visualize normal modes:
for mode in range(9):
vib.write_mode(mode)
示例10: Atoms
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
示例11: connect
#!/usr/bin/env python
from ase.db import connect
from ase.calculators.aims import Aims
from ase.lattice.surface import fcc111, add_adsorbate
from ase.constraints import FixAtoms
from ase import Atoms, Atom
from ase.io.aims import read_aims
from ase.optimize import BFGS
from ase.vibrations import Vibrations
mydb = connect("mydb.db")
atoms = mydb.get_atoms(name='pt-co-relax')
calc = Aims(label='cluster/pt-co-vib-cons',
xc='pbe',
spin='none',
relativistic = 'atomic_zora scalar',
sc_accuracy_etot=1e-7,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-4,
sc_accuracy_forces=1e-3)
atoms.set_calculator(calc)
vib = Vibrations(atoms, indices=[1, 2], name='cluster/pt-co-vib-cons/vib')
vib.run()
vib.summary()
示例12: calculate
def calculate(element, ref_data, p):
values_dict = {}
values_dict[p['xc']] = {}
for XY, data in ref_data[p['xc']].items():
X = XY.split('-')[0]
Y = XY.split('-')[1]
if (X == Y and X == element) or (X != Y and (X == element or Y == element)):
# compound contains the requested element
re_ref = data['re']
we_ref = data['we']
m0_ref = data.get('m0', 0.0)
#
compound = Atoms(X+Y,
[
(0, 0, 0.5 ),
(0, 0, 0.5+re_ref/a),
],
pbc=0)
compound.set_cell([a, b, c], scale_atoms=1)
compound.center()
# calculation on the reference geometry
calc = Calculator(**p)
compound.set_calculator(calc)
e_compound = compound.get_potential_energy()
finegd = calc.density.finegd
dip = finegd.calculate_dipole_moment(calc.density.rhot_g)*calc.a0
vib = Vibrations(compound)
vib.run()
vib_compound = vib.get_frequencies(method='frederiksen').real[-1]
world.barrier()
vib_pckl = glob('vib.*.pckl')
if rank == 0:
for file in vib_pckl: remove(file)
# calculation on the relaxed geometry
qn = QuasiNewton(compound)
#qn.attach(PickleTrajectory('compound.traj', 'w', compound).write)
qn.run(fmax=0.05)
e_compound_r = compound.get_potential_energy()
dist_compound_r = compound.get_distance(0,1)
dip_r = finegd.calculate_dipole_moment(calc.density.rhot_g)*calc.a0
vib = Vibrations(compound)
vib.run()
vib_compound_r = vib.get_frequencies(method='frederiksen').real[-1]
world.barrier()
vib_pckl = glob('vib.*.pckl')
if rank == 0:
for file in vib_pckl: remove(file)
del compound
e = e_compound
we = vib_compound
m0 = dip
e_r = e_compound_r
we_r = vib_compound_r
re_r = dist_compound_r
m0_r = dip_r
#
values_dict[p['xc']][XY] = {'re': re_r, 'we': (we_r, we), 'm0': (m0_r, m0)}
#
return values_dict
示例13: Cluster
H 5.320549047980879 3.220584852467720 3.974551561510350
H 7.723359150977955 3.224855971783890 4.574146712279462
H 7.580803493981530 5.034479218283977 4.877211530909463
"""
h = 0.3
atoms = Cluster(read_xyz(StringIO.StringIO(butadiene)))
atoms.minimal_box(3.0, h)
atoms.set_calculator(GPAW(h=h))
if 0:
dyn = FIRE(atoms)
dyn.run(fmax=0.05)
atoms.write("butadiene.xyz")
vibname = "fcvib"
vib = Vibrations(atoms, name=vibname)
vib.run()
# Modul
a = FranckCondon(atoms, vibname, minfreq=250)
# excited state forces
F = np.array(
[
[-2.11413, 0.07317, -0.91682],
[3.23569, -0.74520, 0.76758],
[-3.44847, 0.63846, -0.81080],
[2.77345, 0.01272, 0.74811],
[-0.06544, -0.01078, -0.03209],
[-0.01245, -0.01123, -0.00040],
[0.00186, -0.05864, -0.00371],
示例14: molecule
#!/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15: Vibrations
# the valence electrons
sigma=0.1,
psppath='/home/vossj/suncat/psp/gbrv1.5pbe', # pseudopotential
convergence={'energy': 1e-5,
'mixing': 0.1,
'nmix': 10,
'mix': 4,
'maxsteps': 500,
'diag': 'david'
}, # convergence parameters
outdirprefix='calcdirv') # output directory for Quantum Espresso files
atoms.set_calculator(calcvib)
vib = Vibrations(atoms, indices=vibrateatoms, delta=0.03)
vib.run()
vib.summary(method='standard')
# Make trajectory files to visualize the modes.
for mode in range(len(vibrateatoms) * 3):
vib.write_mode(mode)
# Calculate free energy
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies,
electronicenergy=energy,
atoms=atoms,
geometry='linear',
symmetrynumber=2, spin=0)