def thermo(vib_path, temp):
"""Calculate vibrational contributions to U, ZPE, Cv, and S
vib_path (str): path to vibrational frequency data file (cm^-1 units)
"""
# Read in vibrational frequencies (assumes cm^-1 units)
vib = np.loadtxt(vib_path)
# convert from cm-1 to eV
vib_energies = vib * ase.units.invcm
# initialize Harmonic-oscillator-approximated thermochemistry object
thermo = HarmonicThermo(vib_energies)
# Calculate U, ZPE, Cv, S, and ST.
# Note that when E_pot = 0, U = ZPE + Cv
u = thermo.get_internal_energy(temp, verbose=False)
zpe = thermo.get_ZPE_correction()
cv = u - zpe
s = thermo.get_entropy(temp, verbose=False)
ts = s * temp
# calculate the G correction term
g_correction = zpe + cv - ts
# convert the results into a dictionary
results = {
'E_ZPE': zpe,
'Cv_harm (0->T)': cv,
'U': u,
'S_harm': s,
'T*S': ts,
f'G_correction @ {temp} K': g_correction
}
# print the results in a nice format
center = 50
line = '=' * center
print(line)
print(f'Harmonic Thermochem Results at T = {temp} K'.center(center))
print(line)
# iteratively print each result in table format
for name in results:
lbl = 'eV/K' if name == 'S_harm' else 'eV'
space = center - len(name) - 5
val = results[name]
print(f'{name}{val:>{space}.9f} {lbl}')
print(line)
ediff=1e-8,
ediffg=-0.01,
algo="Fast",
gga="RP",
xc="PBE",
kpts=(4, 4, 1),
# isif = 0,
# ibrion = 5,
# nsw = 0,
# nfree = 2
)
adsorbedH.set_calculator(calc)
electronicenergy = adsorbedH.get_potential_energy()
print("electronic energy is %.5f" % electronicenergy)
vib = Vibrations(adsorbedH, indices=[23], delta=0.01, nfree=2)
vib.run()
print(vib.get_frequencies())
vib.summary()
print(vib.get_mode(-1))
vib.write_mode(-1)
vib_energies = vib.get_energies()
thermo = HarmonicThermo(vib_energies=vib_energies,
electronicenergy=electronicenergy)
thermo.get_entropy(temperature=298.15)
thermo.get_internal_energy(temperature=298.15)
thermo.get_free_energy(temperature=298.15)
'nmix':10,
'maxsteps': maxsteps,
'diag': 'david'},
#mode = 'scf',
output = {'avoidio':False,
'removewf':True,
'wf_collect':False},
outdirprefix='vibdir'
)
atoms.set_calculator(calc)
vib = Vibrations(atoms, delta=0.04, indices=vib_atoms)
vib.run()
vib.summary(log='vibrations.txt')
vib.write_jmol()
#dyn = QuasiNewton(atoms, logfile='qn.log', trajectory='qn.traj')
#dyn.run(fmax=0.05)
energy = atoms.get_potential_energy()
vibs = vib.get_energies()
with open('vibrations.txt','r') as f: ZPE = f.readlines()[-1]
gibbs = HarmonicThermo(vib_energies=vibs)
entropy = gibbs.get_entropy(temperature)
with open('converged.log', 'w') as f: f.write("Energy: %f eV\nEntropy: %f eV/K \n%s"%(energy,entropy,ZPE))
