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
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()
def __init__(self, atoms, siesta, indices=None, name='ram',
delta=0.01, nfree=2, directions=None, freq_pol=0.0, **kw):
Vibrations.__init__(self, atoms, indices=indices, name=name,
delta = delta, nfree=nfree)
if atoms.constraints:
warnings.warn('WARNING! \n Your Atoms object is constrained. ' +
'Some forces may be unintended set to zero. \n')
self.name = name + '-d%.3f' % delta
self.calc = atoms.get_calculator()
if directions is None:
self.directions = np.asarray([0, 1, 2])
else:
self.directions = np.asarray(directions)
self.ir = True
self.ram = True
self.siesta = siesta
if isinstance(freq_pol, list):
self.freq_pol = np.array(freq_pol)
elif isinstance(freq_pol, float):
self.freq_pol = np.array([freq_pol])
elif isinstance(freq_pol, float) or isinstance(freq_pol, np.ndarray):
self.freq_pol = freq_pol
else:
raise ValueError("wrong type for freq_pol, only float, list or array")
self.pyscf_arg = kw
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)
def ase_vib(embedder, coords, atomnos, logfunction=None, title='temp'):
'''
'''
atoms = Atoms(atomnos, positions=coords)
atoms.calc = get_ase_calc(embedder)
vib = Vibrations(atoms, name=title)
if os.path.isdir(title):
os.chdir(title)
for f in os.listdir():
os.remove(f)
os.chdir(os.path.dirname(os.getcwd()))
else:
os.mkdir(title)
os.chdir(title)
t_start = time.perf_counter()
with HiddenPrints():
vib.run()
# freqs = vib.get_frequencies()
freqs = vib.get_energies() * 8065.544 # from eV to cm-1
if logfunction is not None:
elapsed = time.perf_counter() - t_start
logfunction(
f'{title} - frequency calculation completed ({time_to_string(elapsed)})'
)
os.chdir(os.path.dirname(os.getcwd()))
return freqs, np.count_nonzero(freqs.imag > 1e-3)
def read(self, method='standard', direction='central'):
"""Read data from a pre-performed calculation."""
self.timer.start('read')
self.timer.start('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 Hessian
self.om_Q = self.hnu.real # energies in eV
self.om_v = self.om_Q
# pre-factors for one vibrational excitation
with np.errstate(divide='ignore'):
self.vib01_Q = np.where(self.om_Q > 0,
1. / np.sqrt(2 * self.om_Q), 0)
# -> sqrt(amu) * Angstrom
self.vib01_Q *= np.sqrt(u.Ha * u._me / u._amu) * u.Bohr
self.timer.stop('vibrations')
self.timer.start('excitations')
self.init_parallel_read()
if not hasattr(self, 'ex0E_p'):
if self.overlap:
self.read_excitations_overlap()
else:
self.read_excitations()
self.timer.stop('excitations')
self.timer.stop('read')
def vibname(tmp_path, relaxed):
atoms = relaxed.copy()
atoms.calc = relaxed.calc
name = str(tmp_path / 'vib')
vib = Vibrations(atoms, name=name)
vib.run()
return name
def vibname(relaxed):
atoms = relaxed.copy()
atoms.calc = relaxed.calc
name = 'vib'
vib = Vibrations(atoms, name=name)
vib.run()
return name
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
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.exobj = Excitations
self.exkwargs = exkwargs
self.timer = Timer()
self.txt = get_txt(txt, rank)
self.verbose = verbose
def test_Ag_Cu100():
from math import sqrt
from ase import Atom, Atoms
from ase.neb import NEB
from ase.constraints import FixAtoms
from ase.vibrations import Vibrations
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton, BFGS
# Distance between Cu atoms on a (100) surface:
d = 3.6 / sqrt(2)
initial = Atoms('Cu',
positions=[(0, 0, 0)],
cell=(d, d, 1.0),
pbc=(True, True, False))
initial *= (2, 2, 1) # 2x2 (100) surface-cell
# Approximate height of Ag atom on Cu(100) surfece:
h0 = 2.0
initial += Atom('Ag', (d / 2, d / 2, h0))
# Make band:
images = [initial.copy() for i in range(6)]
neb = NEB(images, climb=True)
# Set constraints and calculator:
constraint = FixAtoms(range(len(initial) - 1))
for image in images:
image.calc = EMT()
image.set_constraint(constraint)
# Displace last image:
images[-1].positions[-1] += (d, 0, 0)
# Relax height of Ag atom for initial and final states:
dyn1 = QuasiNewton(images[0])
dyn1.run(fmax=0.01)
dyn2 = QuasiNewton(images[-1])
dyn2.run(fmax=0.01)
# Interpolate positions between initial and final states:
neb.interpolate()
for image in images:
print(image.positions[-1], image.get_potential_energy())
dyn = BFGS(neb, trajectory='mep.traj')
dyn.run(fmax=0.05)
for image in images:
print(image.positions[-1], image.get_potential_energy())
a = images[0]
vib = Vibrations(a, [4])
vib.run()
print(vib.get_frequencies())
vib.summary()
print(vib.get_mode(-1))
vib.write_mode(-1, nimages=20)
def test_gs_minimum():
"""Test ground state minimum distance, energy and
vibrational frequency"""
atoms = H2Morse()
assert atoms.get_distance(0, 1) == pytest.approx(Re[0], 1.e-12)
assert atoms.get_potential_energy() == -De[0]
# check ground state vibrations
vib = Vibrations(atoms)
vib.run()
assert (vib.get_frequencies().real[-1] == pytest.approx(ome[0], 1e-2))
def run(self):
if self.overlap:
# XXXX stupid way to make a copy
self.atoms.get_potential_energy()
self.eq_calculator = self.atoms.get_calculator()
fname = self.exname + '.eq.gpw'
self.eq_calculator.write(fname, 'all')
self.eq_calculator = self.eq_calculator.__class__(fname)
self.eq_calculator.converge_wave_functions()
Vibrations.run(self)
def VibScript():
from ase.vibrations import Vibrations
import glob, json, cPickle, ase, os
#######################
print "Initializing..."
#----------------------
params, atoms = initialize(
) # Remove old .out/.err files, load from fw_spec, and write 'init.traj'
prev = glob.glob(
'*.pckl') #delete incomplete pckls - facilitating restarted jobs
if rank() == 0:
for p in prev:
if os.stat(p).st_size < 100: os.remove(p)
atoms.set_calculator(makeCalc(params))
vib = Vibrations(atoms,
delta=params['delta'],
indices=json.loads(params['vibids_json']))
vib.run()
vib.write_jmol()
##########################
print "Storing Results..."
#-------------------------
vib.summary(log='vibrations.txt')
with open('vibrations.txt', 'r') as f:
vibsummary = f.read()
ase.io.write('final.traj', atoms)
optAtoms = ase.io.read('final.traj')
vib_energies, vib_frequencies = vib.get_energies(), vib.get_frequencies()
resultDict = mergeDicts([
params,
trajDetails(optAtoms), {
'vibfreqs_pckl': cPickle.dumps(vib_frequencies),
'vibsummary': vibsummary,
'vibengs_pckl': cPickle.dumps(vib_energies)
}
])
with open('result.json', 'w') as outfile:
outfile.write(json.dumps(resultDict))
with open('result.json', 'r') as outfile:
json.loads(outfile.read()) #test that dictionary isn't 'corrupted'
if rank() == 0: log(params, optAtoms)
return 0
def characteriseTSinternal(self, mol):
os.chdir((self.workingDir + '/Raw/' + self.procNum))
if (self.lowMeth == 'nwchem'):
mol = tl.setCalc(mol, self.lowString, 'nwchem2', self.lowLev)
self.Reac.get_forces()
else:
mol = tl.setCalc(mol, self.lowString, self.lowMeth, self.lowLev)
vib = Vibrations(mol)
vib.clean()
vib.run()
viblist = vib.get_frequencies()
print("getting vibs")
TSFreqs, zpe = tl.getVibString(viblist, False, True)
print("vibs done " + str(zpe))
imaginaryFreq = tl.getImageFreq(viblist)
vib.clean()
os.chdir((self.workingDir))
# Finally get single point energy
mol = tl.setCalc(mol, self.singleString, self.singleMeth,
self.singleLev)
print("Getting single point energy for TS = " +
str(mol.get_potential_energy()) + "zpe = " + str(zpe) +
"reactant energy = " + str(self.reactantEnergy))
energy = mol.get_potential_energy() + zpe
return TSFreqs, imaginaryFreq, zpe, energy
def run(self):
if self.overlap:
# XXXX stupid way to make a copy
self.atoms.get_potential_energy()
calc = self.atoms.calc
fname = self.exname + '.eq.gpw'
calc.write(fname, 'all')
self.eq_calculator = calc.__class__.read(fname)
if hasattr(self.eq_calculator, 'converge_wave_functions'):
self.eq_calculator.converge_wave_functions()
Vibrations.run(self)
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()
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()
def __init__(self, atoms, indices=None, name='ir', delta=0.01,
nfree=2, directions=None):
Vibrations.__init__(self, atoms, indices=indices, name=name,
delta=delta, nfree=nfree)
if atoms.constraints:
print('WARNING! \n Your Atoms object is constrained. '
'Some forces may be unintended set to zero. \n')
if directions is None:
self.directions = np.asarray([0, 1, 2])
else:
self.directions = np.asarray(directions)
self.ir = True
self.ram = False
def characteriseFreqInternal(self, mol):
os.chdir((self.workingDir + '/' + '/Raw/' + self.procNum))
vib = Vibrations(mol)
vib.clean()
vib.run()
viblist = vib.get_frequencies()
freqs, zpe = tl.getVibString(viblist, False, False)
vib.clean()
os.chdir((self.workingDir))
return freqs, zpe
def test_ideal_gas_thermo():
atoms = Atoms('N2',
positions=[(0, 0, 0), (0, 0, 1.1)])
atoms.calc = EMT()
QuasiNewton(atoms).run(fmax=0.01)
energy = atoms.get_potential_energy()
vib = Vibrations(atoms, name='idealgasthermo-vib')
vib.run()
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies, geometry='linear',
atoms=atoms, symmetrynumber=2, spin=0,
potentialenergy=energy)
thermo.get_gibbs_energy(temperature=298.15, pressure=2 * 101325.)
def get_thermo_correction(
self,
coords: simtk.unit.quantity.Quantity) -> unit.quantity.Quantity:
"""
Returns the thermochemistry correction. This calls: https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html
and uses the Ideal gas rigid rotor harmonic oscillator approximation to calculate the Gibbs free energy correction that
needs to be added to the single point energy to obtain the Gibb's free energy
coords: [K][3]
Raises:
verror: if imaginary frequencies are detected a ValueError is raised
Returns:
float -- temperature correct [kT]
"""
if not (len(coords.shape) == 3 and coords.shape[2] == 3
and coords.shape[0] == 1):
raise RuntimeError(
f"Something is wrong with the shape of the provided coordinates: {coords.shape}. Only x.shape[0] == 1 is possible."
)
ase_mol = copy.deepcopy(self.ase_mol)
for atom, c in zip(ase_mol, coords[0]):
atom.x = c[0].value_in_unit(unit.angstrom)
atom.y = c[1].value_in_unit(unit.angstrom)
atom.z = c[2].value_in_unit(unit.angstrom)
calculator = self.model.ase()
ase_mol.set_calculator(calculator)
vib = Vibrations(ase_mol, name=f"/tmp/vib{random.randint(1,10000000)}")
vib.run()
vib_energies = vib.get_energies()
thermo = IdealGasThermo(
vib_energies=vib_energies,
atoms=ase_mol,
geometry="nonlinear",
symmetrynumber=1,
spin=0,
)
try:
G = thermo.get_gibbs_energy(
temperature=temperature.value_in_unit(unit.kelvin),
pressure=pressure.value_in_unit(unit.pascal),
)
except ValueError as verror:
logger.critical(verror)
vib.clean()
raise verror
# removes the vib tmp files
vib.clean()
return (
G * eV_to_kJ_mol
) * unit.kilojoule_per_mole # eV * conversion_factor(eV to kJ/mol)
def freq(atoms=None):
if atoms is None:
atoms = read('md.traj',index=0)
atoms.calc = IRFF(atoms=atoms,libfile='ffield.json',rcut=None,nn=True,massage=2)
# Compute frequencies
frequencies = Vibrations(atoms, name='freq')
frequencies.run()
# Print a summary
frequencies.summary()
frequencies.write_dos()
# Write jmol file if requested
# if write_jmol:
frequencies.write_jmol()
def run(self):
if self.overlap:
# XXXX stupid way to make a copy
self.atoms.get_potential_energy()
self.eq_calculator = self.atoms.calc
fname = 'tmp.gpw'
self.eq_calculator.write(fname, 'all')
self.eq_calculator = self.eq_calculator.__class__(restart=fname)
try:
# XXX GPAW specific
self.eq_calculator.converge_wave_functions()
except AttributeError:
pass
Vibrations.run(self)
def vib_zpe(self, job, atoms):
from ase.vibrations import Vibrations
self.log('-' * 60)
self.log('Run ZEP calculation: {0}'.format(job))
label = os.path.join(self.label, job)
label = os.path.join(label, 'vib')
# copy file
calculator = deepcopy(self.calculator)
dip = dipole_correction(atoms, edir=3)
calculator.update(dip)
calculator.update({
'calculation': 'scf',
'tstress': True,
'tprnfor': True,
'outdir': '../',
'prefix': '%s' % job,
'startingpot': 'file',
'startingwfc': 'file',
'etot_conv_thr': 1e-6,
'disk_io': 'none',
})
# better to restart from previous geo_relax calculation
calc = Espresso(
label=label,
**calculator,
)
atoms.calc = calc
if job[-1] == 'O':
indices = [-1]
elif job[-2:] == 'OH' and job[-3:] != 'OOH':
indices = [-1, -2]
elif job[-3:] == 'OOH':
indices = [-1, -2, -3]
elif job[-2:] == 'O2':
indices = [-1, -2]
else:
indices = []
# print('%!!!')
return job, 0
vib = Vibrations(atoms, name=os.path.join(label, job), indices=indices)
vib.run()
vib_energies = np.real(vib.get_energies())
zpe = 0.
for energy in vib_energies:
zpe += 0.5 * energy
self.zpes[job] = zpe
return job, zpe
def neural_hessian_ase(ase_atoms):
print("Calculating Numerical Hessian using ASE")
vib = Vibrations(ase_atoms, delta=0.05)
vib.run()
vib.summary()
hessian = np.array(vib.H) * (kcal/mol) * Bohr**2
vib.clean()
return hessian
def test_vibrations_restart_dir(self, testdir, random_dimer):
vib = Vibrations(random_dimer)
vib.run()
freqs = vib.get_frequencies()
assert freqs is not None
# write/read the data from another working directory
atoms = random_dimer.copy() # This copy() removes the Calculator
with ase.utils.workdir('run_from_here', mkdir=True):
vib = Vibrations(atoms, name=str(Path.cwd().parent / 'vib'))
assert_array_almost_equal(freqs, vib.get_frequencies())
assert vib.clean() == 13
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
def test_harmonic_vibrations(self, testdir):
"""Check the numerics with a trivial case: one atom in harmonic well"""
rng = np.random.RandomState(42)
k = rng.rand()
ref_atoms = Atoms('H', positions=np.zeros([1, 3]))
atoms = ref_atoms.copy()
mass = atoms.get_masses()[0]
atoms.calc = ForceConstantCalculator(D=np.eye(3) * k,
ref=ref_atoms,
f0=np.zeros((1, 3)))
vib = Vibrations(atoms, name='harmonic')
vib.run()
vib.read()
expected_energy = (
units._hbar # In J/s
* np.sqrt(k # In eV/A^2
* units._e # eV -> J
* units.m**2 # A^-2 -> m^-2
/ mass # in amu
/ units._amu # amu^-1 -> kg^-1
)) / units._e # J/s -> eV/s
assert np.allclose(vib.get_energies(), expected_energy)
def __init__(self, atoms, vibname, minfreq=-np.inf, maxfreq=np.inf):
"""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. / 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
def __init__(self, atoms, *args, **kwargs):
super().__init__(atoms, *args, **kwargs)
for key in ['txt', 'exext', 'exname']:
kwargs.pop(key, None)
kwargs['name'] = kwargs.get('name', self.name)
self.vibrations = Vibrations(atoms, *args, **kwargs)
self.delta = self.vibrations.delta
self.indices = self.vibrations.indices
def get_modes(self,atm,freqname="vib."):
for f in [f for f in os.listdir(".") if freqname in f and '.pckl' in f]:
os.remove(f)
new_target = open(os.devnull, "w")
old_target, sys.stdout = sys.stdout, new_target
atm.set_calculator(ANIENS(self.ens))
vib = Vibrations(atm, nfree=2, name=freqname)
vib.run()
freq = vib.get_frequencies()
modes = np.stack(vib.get_mode(i) for i in range(freq.size))
vib.clean()
sys.stdout = old_target
return modes
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)
def test_combine(testdir):
dirname = 'subdir'
vibname = 'ir'
with workdir(dirname, mkdir=True):
atoms = molecule('C2H6')
ir = Infrared(atoms)
assert ir.name == vibname
ir.calc = RandomCalculator()
ir.run()
freqs = ir.get_frequencies()
ints = ir.intensities
assert ir.combine() == 49
ir = Infrared(atoms)
assert (freqs == ir.get_frequencies()).all()
assert (ints == ir.intensities).all()
vib = Vibrations(atoms, name=vibname)
assert (freqs == vib.get_frequencies()).all()
# Read the data from other working directory
with workdir('..'):
ir = Infrared(atoms, name=f'{dirname}/{vibname}')
assert (freqs == ir.get_frequencies()).all()
ir = Infrared(atoms)
assert ir.split() == 1
assert (freqs == ir.get_frequencies()).all()
assert (ints == ir.intensities).all()
vib = Vibrations(atoms, name=vibname)
assert (freqs == vib.get_frequencies()).all()
assert ir.clean() == 49
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
def test_consistency_with_vibrationsdata(self, testdir, n2_emt):
atoms = n2_emt
vib = Vibrations(atoms)
vib.run()
vib_data = vib.get_vibrations()
assert_array_almost_equal(vib.get_energies(), vib_data.get_energies())
# Compare the last mode as the others may be re-ordered by negligible
# energy changes
assert_array_almost_equal(vib.get_mode(5), vib_data.get_modes()[5])
def test_co_vibespresso_vibrations(tmpdir):
tmpdir.chdir()
co = Atoms('CO', positions=[[1.19382389081, 0.0, 0.0], [0.0, 0.0, 0.0]])
co.set_cell(np.ones(3) * 12.0 * Bohr)
calc = Vibespresso(pw=34.0 * Rydberg,
dw=144.0 * Rydberg,
kpts='gamma',
xc='PBE',
calculation='scf',
ion_dynamics='None',
spinpol=False,
outdir='vibs')
co.set_calculator(calc)
# calculate the vibrations
vib = Vibrations(co, indices=range(len(co)), delta=0.01, nfree=2)
vib.run()
assert np.allclose(vib.get_energies(), REF_ENE)
from ase.vibrations import Vibrations
from __init__ import AnharmonicModes
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())
#!/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()
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],
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
from ase.build import bulk
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.vibrations import Vibrations
from ase.phonons import Phonons
from ase.thermochemistry import (IdealGasThermo, HarmonicThermo,
CrystalThermo)
from ase.calculators.emt import EMT
# Ideal gas thermo.
atoms = Atoms('N2',
positions=[(0, 0, 0), (0, 0, 1.1)],
calculator=EMT())
QuasiNewton(atoms).run(fmax=0.01)
energy = atoms.get_potential_energy()
vib = Vibrations(atoms, name='idealgasthermo-vib')
vib.run()
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies, geometry='linear',
atoms=atoms, symmetrynumber=2, spin=0,
potentialenergy=energy)
thermo.get_gibbs_energy(temperature=298.15, pressure=2 * 101325.)
# Harmonic thermo.
atoms = fcc100('Cu', (2, 2, 2), vacuum=10.)
atoms.set_calculator(EMT())
add_adsorbate(atoms, 'Pt', 1.5, 'hollow')
atoms.set_constraint(FixAtoms(indices=[atom.index for atom in atoms
if atom.symbol == 'Cu']))
# 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)
# 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
calc = espresso(pw = 500.,
dw = 5000.,
nbands = -10,
kpts=(1, 1, 1),
xc = 'BEEF',
outdir='outdir',
psppath = "/scratch/users/colinfd/psp/gbrv",
sigma = 10e-4)
atoms.set_calculator(calc)
dyn = QuasiNewton(atoms,logfile='out.log',trajectory='out.traj')
dyn.run(fmax=0.01)
electronicenergy = atoms.get_potential_energy()
vib = Vibrations(atoms) # run vibrations on all atoms
vib.run()
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies,
electronicenergy=electronicenergy,
atoms=atoms,
geometry='linear', # linear/nonlinear
symmetrynumber=2, spin=0) # symmetry numbers from point group
G = thermo.get_free_energy(temperature=300, pressure=101325.) # vapor pressure of water at room temperature
e = open('e_energy.out','w')
g = open('g_energy.out','w')
e.write(str(electronicenergy))
g.write(str(G))
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
#!/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)
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,
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)
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.)
sys.path.append("..")
from __init__ import AnharmonicModes
slab = fcc111('Au', size=(2, 2, 2), vacuum=4.0)
H = molecule('H')
add_adsorbate(slab, H, 3.0, 'ontop')
constraint = FixAtoms(mask=[a.symbol == 'Au' for a in slab])
slab.set_constraint(constraint)
slab.set_calculator(EMT())
QuasiNewton(slab).run(fmax=0.001)
vib = Vibrations(slab, indices=[8])
vib.run()
vib.summary()
vib.clean()
AM = AnharmonicModes(
vibrations_object=vib,
settings={
'plot_mode': True,
})
for i in range(len(vib.hnu)):
AM.define_vibration(mode_number=-1)
AM.inspect_anmodes()
AM.run()
import os
from ase.vibrations import Vibrations
from gpaw import GPAW
from gpaw.mpi import world
h2o = GPAW('h2o.gpw', txt=None).get_atoms()
# Test restart:
vib = Vibrations(h2o)
vib.run()
vib.summary(method='frederiksen')
# Remove a displacement file and redo it:
if world.rank == 0:
os.remove('vib.1z-.pckl')
world.barrier()
vib = Vibrations(h2o)
vib.run()
vib.summary(method='frederiksen')
"""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)