def vibname(relaxed):
atoms = relaxed.copy()
atoms.calc = relaxed.calc
name = 'vib'
vib = Vibrations(atoms, name=name)
vib.run()
return name
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(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 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 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 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 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 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_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 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_vibrations_on_surface(self, testdir):
atoms = self.n2_on_ag.copy()
atoms.calc = EMT()
vibs = Vibrations(atoms, indices=[-2, -1])
vibs.run()
freqs = vibs.get_frequencies()
vib_data = vibs.get_vibrations()
assert_array_almost_equal(freqs, vib_data.get_frequencies())
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 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 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_vib():
import os
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()
freqs = vib.get_frequencies()
print(freqs)
vib.summary()
print(vib.get_mode(-1))
vib.write_mode(n=None, nimages=20)
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
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
assert len(list(vib.iterimages())) == 13
d = dict(vib.iterdisplace(inplace=False))
for name, atoms in vib.iterdisplace(inplace=True):
assert d[name] == atoms
vib = Vibrations(n2)
vib.run()
assert vib.combine() == 13
assert (freqs == vib.get_frequencies()).all()
vib = Vibrations(n2)
assert vib.split() == 1
assert (freqs == vib.get_frequencies()).all()
assert vib.combine() == 13
# Read the data from other working directory
dirname = os.path.basename(os.getcwd())
os.chdir('..') # Change working directory
vib = Vibrations(n2, name=os.path.join(dirname, 'vib'))
assert (freqs == vib.get_frequencies()).all()
assert vib.clean() == 1
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 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 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 test_vibrations_methods(self, testdir, random_dimer):
vib = Vibrations(random_dimer)
vib.run()
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=vib.atoms,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15,
pressure=2 * 101325.,
verbose=False)
with open(self.logfile, 'w') as fd:
vib.summary(log=fd)
with open(self.logfile, 'rt') as fd:
log_txt = fd.read()
assert log_txt == '\n'.join(
VibrationsData._tabulate_from_energies(vib_energies)) + '\n'
last_mode = vib.get_mode(-1)
scale = 0.5
assert_array_almost_equal(
vib.show_as_force(-1, scale=scale, show=False).get_forces(),
last_mode * 3 * len(vib.atoms) * scale)
vib.write_mode(n=3, nimages=5)
for i in range(3):
assert not Path('vib.{}.traj'.format(i)).is_file()
mode_traj = ase.io.read('vib.3.traj', index=':')
assert len(mode_traj) == 5
assert_array_almost_equal(mode_traj[0].get_all_distances(),
random_dimer.get_all_distances())
with pytest.raises(AssertionError):
assert_array_almost_equal(mode_traj[4].get_all_distances(),
random_dimer.get_all_distances())
assert vib.clean(empty_files=True) == 0
assert vib.clean() == 13
assert len(list(vib.iterimages())) == 13
d = dict(vib.iterdisplace(inplace=False))
for name, image in vib.iterdisplace(inplace=True):
assert d[name] == random_dimer
def test_pickle_manipulation(self, n2_emt):
atoms = n2_emt
vib = Vibrations(atoms, name='interrupt')
vib.run()
disp_file = 'interrupt.1x-.pckl'
comb_file = 'interrupt.all.pckl'
assert os.path.isfile(disp_file)
assert not os.path.isfile(comb_file)
with pytest.raises(RuntimeError):
vib.split()
# Build a combined file
assert vib.combine() == 13
# Individual displacements should be gone, combination should exist
assert not os.path.isfile(disp_file)
assert os.path.isfile(comb_file)
# Not allowed to run after data has been combined
with pytest.raises(RuntimeError):
vib.run()
# But reading is allowed
vib.read()
# Splitting should fail if any split file already exists
with open(disp_file, 'w') as f:
f.write("hello")
with pytest.raises(RuntimeError):
vib.split()
os.remove(disp_file)
# Now split() for real: replace .all.pckl file with displacements
vib.split()
assert os.path.isfile(disp_file)
assert not os.path.isfile(comb_file)
# Not allowed to clobber existing combined file
with open(comb_file, 'w') as f:
f.write("Hello")
with pytest.raises(RuntimeError):
vib.combine()
os.remove(comb_file)
# Combining data also fails if some data is missing
os.remove('interrupt.1x-.pckl')
with pytest.raises(RuntimeError):
vib.combine()
vib.clean()
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 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 test_vibrations_example(testdir):
"""Test the example from the Vibrations.__init__() docstring"""
n2 = Atoms('N2', [(0, 0, 0), (0, 0, 1.1)], calculator=EMT())
BFGS(n2).run(fmax=0.01)
vib = Vibrations(n2)
vib.run()
with io.StringIO() as f:
vib.summary(log=f)
f.seek(0)
summary = f.read()
assert len(summary.split()) == len(expected_summary.split())
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 test_consistency_with_vibrationsdata(self, testdir, random_dimer):
vib = Vibrations(random_dimer, delta=1e-6, nfree=4)
vib.run()
vib_data = vib.get_vibrations()
assert_array_almost_equal(vib.get_energies(), vib_data.get_energies())
for mode_index in range(3 * len(vib.atoms)):
assert_array_almost_equal(vib.get_mode(mode_index),
vib_data.get_modes()[mode_index])
# Hessian should be close to the ForceConstantCalculator input
assert_array_almost_equal(random_dimer.calc.D,
vib_data.get_hessian_2d(),
decimal=6)
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 test_harmonic_thermo():
atoms = fcc100('Cu', (2, 2, 2), vacuum=10.)
atoms.calc = EMT()
add_adsorbate(atoms, 'Pt', 1.5, 'hollow')
atoms.set_constraint(FixAtoms(indices=[atom.index for atom in atoms
if atom.symbol == 'Cu']))
QuasiNewton(atoms).run(fmax=0.01)
vib = Vibrations(atoms, name='harmonicthermo-vib',
indices=[atom.index for atom in atoms
if atom.symbol != 'Cu'])
vib.run()
vib.summary()
vib_energies = vib.get_energies()
thermo = HarmonicThermo(vib_energies=vib_energies,
potentialenergy=atoms.get_potential_energy())
thermo.get_helmholtz_energy(temperature=298.15)
def compute_normal_modes(self, write_jmol=True):
"""
Use ase calculator to compute numerical frequencies for the molecule
Args:
write_jmol (bool): Write frequencies to input file for visualization in jmol (default=True)
"""
freq_file = os.path.join(self.working_dir, "normal_modes")
# Compute frequencies
frequencies = Vibrations(self.molecule, name=freq_file)
frequencies.run()
# Print a summary
frequencies.summary()
# Write jmol file if requested
if write_jmol:
frequencies.write_jmol()
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_json_manipulation(self, testdir, random_dimer):
vib = Vibrations(random_dimer, name='interrupt')
vib.run()
disp_file = Path('interrupt/cache.1x-.json')
comb_file = Path('interrupt/combined.json')
assert disp_file.is_file()
assert not comb_file.is_file()
# Should do nothing harmful as files are already split
# (It used to raise an error but this is no longer implemented.)
vib.split()
# Build a combined file
assert vib.combine() == 13
# Individual displacements should be gone, combination should exist
assert not disp_file.is_file()
assert comb_file.is_file()
# Not allowed to run after data has been combined
with pytest.raises(RuntimeError):
vib.run()
# But reading is allowed
vib.read()
# Splitting should fail if any split file already exists
with open(disp_file, 'w') as fd:
fd.write("hello")
with pytest.raises(AssertionError):
vib.split()
os.remove(disp_file)
# Now split() for real: replace .all.json file with displacements
vib.split()
assert disp_file.is_file()
assert not comb_file.is_file()
def run_task(self,fw_spec):
"""ONLY WORKS FOR QUANTUM ESPRESSO"""
from ase.vibrations import Vibrations
jobID = fw_spec['jobID']
job = db2object(jobID)
t0 = time.time()
atoms = job.atoms()
atoms.set_calculator(job.vibCalc())
vib = Vibrations(atoms,delta=job.delta(),indicies=job.vibids)
vib.run()
vib.summary(log='vibrations.txt')
vib.write_jmol()
vibs = vib.get_frequencies()
t = (time.time()-t0)/60.0 #min
return FWAction(stored_data= {'vibs':vibs,'avgtime':t},mod_spec=[{'_push': {'vibs':vibs,'time':t}}])
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())
assert abs(AM.get_ZPE() - 0.388) < 1e-3, AM.get_ZPE()
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
# 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
