def test_thermochemistry():
"""Tests of the major methods (HarmonicThermo, IdealGasThermo,
CrystalThermo) from the thermochemistry module."""
# 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']))
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)
# Crystal thermo.
atoms = bulk('Al', 'fcc', a=4.05)
calc = EMT()
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
# Phonon calculator
N = 7
ph = Phonons(atoms, calc, supercell=(N, N, N), delta=0.05)
ph.run()
ph.read(acoustic=True)
phonon_energies, phonon_DOS = ph.dos(kpts=(4, 4, 4), npts=30, delta=5e-4)
thermo = CrystalThermo(phonon_energies=phonon_energies,
phonon_DOS=phonon_DOS,
potentialenergy=energy,
formula_units=4)
thermo.get_helmholtz_energy(temperature=298.15)
# Hindered translator / rotor.
# (Taken directly from the example given in the documentation.)
vibs = np.array([
3049.060670, 3040.796863, 3001.661338, 2997.961647, 2866.153162,
2750.855460, 1436.792655, 1431.413595, 1415.952186, 1395.726300,
1358.412432, 1335.922737, 1167.009954, 1142.126116, 1013.918680,
803.400098, 783.026031, 310.448278, 136.112935, 112.939853, 103.926392,
77.262869, 60.278004, 25.825447
])
vib_energies = vibs / 8065.54429 # Convert to eV from cm^-1.
trans_barrier_energy = 0.049313 # eV
rot_barrier_energy = 0.017675 # eV
sitedensity = 1.5e15 # cm^-2
rotationalminima = 6
symmetrynumber = 1
mass = 30.07 # amu
inertia = 73.149 # amu Ang^-2
thermo = HinderedThermo(vib_energies=vib_energies,
trans_barrier_energy=trans_barrier_energy,
rot_barrier_energy=rot_barrier_energy,
sitedensity=sitedensity,
rotationalminima=rotationalminima,
symmetrynumber=symmetrynumber,
mass=mass,
inertia=inertia)
helmholtz = thermo.get_helmholtz_energy(temperature=298.15)
target = 1.593 # Taken from documentation example.
assert (helmholtz - target) < 0.001
print "Ideal Gas Limit" ZPE = thermo.get_ZPE_correction() H = thermo.get_enthalpy(temperature=temp) S = thermo.get_entropy(temperature=temp,pressure=pres) G = thermo.get_gibbs_energy(temperature=temp,pressure=pres) print " " print "ZPE correction (ZPE) = ", ZPE, " eV" print "Ethalpy (H) = ", H, " eV" print "Entropy (S) = ", S, " eV/K" print "Gibbs Energy (G) = ", G, " eV" ## get the harmonic limit thermodynamic values thermo = HarmonicThermo(vib_energies=Freq, potentialenergy=scf_energy_eV) print print "Harmonic Approximation" ZPE = thermo.get_ZPE_correction() U = thermo.get_internal_energy(temperature=temp) S = thermo.get_entropy(temperature=temp) H = thermo.get_helmholtz_energy(temperature=temp) print " " print "ZPE correction (ZPE) = ", ZPE , " eV" print "Internal energy (U) = ", U, " eV" print "Entropy (S) = ", S, " eV/K" print "Helmholtz Energy (F) = ", F, " eV"
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']))
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)
# Crystal thermo.
atoms = bulk('Al', 'fcc', a=4.05)
calc = EMT()
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
# Phonon calculator
N = 7
ph = Phonons(atoms, calc, supercell=(N, N, N), delta=0.05)
ph.run()
ph.read(acoustic=True)
phonon_energies, phonon_DOS = ph.dos(kpts=(4, 4, 4), npts=30, delta=5e-4)
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']))
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)
# Crystal thermo.
atoms = bulk('Al', 'fcc', a=4.05)
calc = EMT()
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
# Phonon calculator
N = 7
ph = Phonons(atoms, calc, supercell=(N, N, N), delta=0.05)
ph.run()
ph.read(acoustic=True)
phonon_energies, phonon_DOS = ph.dos(kpts=(4, 4, 4), npts=30,
delta=5e-4)
