def gas_chemical_potential(species, temperature, fugacity):
"""For a gas, given its temperature (K) and fugacity (Pa), returns
its chemical potential.
Args:
species (string)
temperature (float)
fugacity (float)
Raises:
RuntimeError
"""
if not gasprops.has_key(species):
raise RuntimeError('Data for this gas (%s) is not in gasprops'
'dictionary. Add to hori.thermo.gasprops' % species)
d = io.gasdata(species)
p = gasprops[species]
electronic_energy = (d['electronic energy'] +
p['electronic energy correction'])
thermo = IdealGasThermo(vib_energies=d['vibrations'],
electronicenergy=electronic_energy,
geometry=p['geometry'],
atoms=d['atoms'],
symmetrynumber=p['symmetrynumber'],
spin=p['spin'])
mu = thermo.get_gibbs_energy(temperature=temperature, pressure=fugacity)
#mu = thermo.get_gibbs_energy(temperature=temperature,pressure=fugacity)
return mu
def gas_chemical_potential(species, temperature, fugacity):
"""For a gas, given its temperature (K) and fugacity (Pa), returns
its chemical potential.
Args:
species (string)
temperature (float)
fugacity (float)
Raises:
RuntimeError
"""
if not gasprops.has_key(species):
raise RuntimeError('Data for this gas (%s) is not in gasprops'
'dictionary. Add to hori.thermo.gasprops' %
species)
d = io.gasdata(species)
p = gasprops[species]
electronic_energy = (d['electronic energy'] +
p['electronic energy correction'])
thermo = IdealGasThermo(vib_energies=d['vibrations'],
electronicenergy=electronic_energy,
geometry=p['geometry'],
atoms=d['atoms'],
symmetrynumber=p['symmetrynumber'],
spin=p['spin'])
mu = thermo.get_gibbs_energy(temperature=temperature, pressure=fugacity)
#mu = thermo.get_gibbs_energy(temperature=temperature,pressure=fugacity)
return mu
def get_enthalpy(self, temperature=T_std, electronic_energy='Default'):
"""Returns the internal energy of an adsorbed molecule.
Parameters
----------
temperature : numeric
temperature in K
electronic_energy : numeric
energy in eV
Returns
-------
internal_energy : numeric
Internal energy in eV
"""
if not temperature: # either None or 0
return (0, 0, 0)
if electronic_energy == 'Default':
electronic_energy = molecule_dict[self.name]['electronic_energy']
else:
ideal_gas_object = IdealGasThermo(
vib_energies=self.get_vib_energies(),
potentialenergy=electronic_energy,
atoms=self.atom_object,
geometry=molecule_dict[self.name]['geometry'],
symmetrynumber=molecule_dict[self.name]['symmetrynumber'],
spin=molecule_dict[self.name]['spin'])
energy = ideal_gas_object.get_enthalpy(temperature=temperature,
verbose=False)
self.enthalpy = energy
return (self.enthalpy)
def setUp(self):
unittest.TestCase.setUp(self)
# Testing Ideal Gas Model
CO2 = molecule('CO2')
CO2_pmutt_parameters = {
'name':
'CO2',
'elements': {
'C': 1,
'O': 2
},
'trans_model':
trans.FreeTrans,
'n_degrees':
3,
'molecular_weight':
get_molecular_weight('CO2'),
'rot_model':
rot.RigidRotor,
'rot_temperatures':
rot.get_rot_temperatures_from_atoms(CO2, geometry='linear'),
'geometry':
'linear',
'symmetrynumber':
2,
'elec_model':
elec.GroundStateElec,
'potentialenergy':
-22.994202,
'spin':
0.,
'vib_model':
vib.HarmonicVib,
'vib_wavenumbers': [3360., 954., 954., 1890.],
}
CO2_ase_parameters = {
'atoms':
CO2,
'potentialenergy':
-22.994202,
'vib_energies': [
c.wavenumber_to_energy(x) *
c.convert_unit(initial='J', final='eV')
for x in CO2_pmutt_parameters['vib_wavenumbers']
],
'geometry':
'linear',
'symmetrynumber':
2,
'spin':
0.
}
self.CO2_pmutt = StatMech(**CO2_pmutt_parameters)
self.CO2_ASE = IdealGasThermo(**CO2_ase_parameters)
self.T0 = c.T0('K') # K
self.P0 = c.P0('Pa')
self.V0 = c.V0('m3')
self.mw = get_molecular_weight({'C': 1, 'O': 2})
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_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 _calculate_one_G(self, gas, verbose=False):
d = self.gas_dict[gas]
thermo = IdealGasThermo(vib_energies=d['vibrations'],
electronicenergy=(d['electronic energy'] +
d['electronic energy correction']),
geometry=d['geometry'],
atoms=d['atoms'],
symmetrynumber=d['symmetrynumber'],
spin=d['spin'])
self.G[gas] = thermo.get_gibbs_energy(d['temperature'],
d['fugacity'], verbose=verbose)
def _calculate_one_G(self, gas, verbose=False):
d = self.gas_dict[gas]
thermo = IdealGasThermo(
vib_energies=d['vibrations'],
electronicenergy=(d['electronic energy'] +
d['electronic energy correction']),
geometry=d['geometry'],
atoms=d['atoms'],
symmetrynumber=d['symmetrynumber'],
spin=d['spin'])
self.G[gas] = thermo.get_gibbs_energy(d['temperature'],
d['fugacity'],
verbose=verbose)
def get_free_energy(self,
temperature,
pressure='Default',
electronic_energy='Default',
overbinding=True):
"""Returns the internal energy of an adsorbed molecule.
Parameters
----------
temperature : numeric
temperature in K
electronic_energy : numeric
energy in eV
pressure : numeric
pressure in mbar
Returns
-------
internal_energy : numeric
Internal energy in eV
"""
if not temperature or not pressure: # either None or 0
return (0)
else:
if electronic_energy == 'Default':
electronic_energy = molecule_dict[
self.name]['electronic_energy']
if overbinding == True:
electronic_energy += molecule_dict[
self.name]['overbinding']
else:
pass
if pressure == 'Default':
pressure = molecule_dict[self.name]['pressure']
else:
pass
pressure = pressure * 100 # gives Pa
ideal_gas_object = IdealGasThermo(
vib_energies=self.get_vib_energies(),
potentialenergy=electronic_energy,
atoms=self.atom_object,
geometry=molecule_dict[self.name]['geometry'],
symmetrynumber=molecule_dict[self.name]['symmetrynumber'],
spin=molecule_dict[self.name]['spin'])
# Returns the Gibbs free energy, in eV, in the ideal gas
# approximation at a specified temperature (K) and pressure (Pa).
self.free_energy = ideal_gas_object.get_gibbs_energy(
temperature=temperature, pressure=pressure, verbose=False)
return self.free_energy
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 get_mu(p, T):
# calculates mu for a given pressure and temperature
os.chdir('vibO2')
atoms = read('relax.traj')
vib = InfraRed(atoms)
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies,
atoms=atoms,
geometry='linear',
symmetrynumber=2, spin=1)
G = thermo.get_gibbs_energy(temperature=T, pressure=p, verbose=False)
delta_mu = 0.5*G#-thermo.get_ZPE_correction())
os.chdir('..')
return delta_mu+en_o
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_p(mu, T):
# calculates p for a given mu and temperature
os.chdir('vibO2')
atoms = read('relax.traj')
vib = InfraRed(atoms)
vib_energies = vib.get_energies()
thermo = IdealGasThermo(vib_energies=vib_energies,
atoms=atoms,
geometry='linear',
symmetrynumber=2, spin=1)
G = thermo.get_gibbs_energy(temperature=T, pressure=thermo.referencepressure, verbose=False)
mu_0 = 0.5*G+en_o
p=thermo.referencepressure*np.exp(2*(mu-mu_0)/(T*kB))
os.chdir('..')
return p
def __init__(self, temperature, voltage, functional):
self.temperature = temperature
self.voltage = voltage
self.functional = functional
d = io.gasdata('H2') # hydrogen electrode
d['electronic energy correction'] = gasprops['H2'][
'electronic energy correction']
d['geometry'] = gasprops['H2']['geometry']
d['symmetrynumber'] = gasprops['H2']['symmetrynumber']
d['spin'] = gasprops['H2']['spin']
if functional == 'BEEF':
d['electronic energy correction'] = gasprops_BEEF['H2'][
'electronic energy correction']
self.referencepressure = 101325. # Pa, RHE definition
self._previous = {'temperature': None, 'voltage': None}
thermo = IdealGasThermo(
vib_energies=d['vibrations'],
electronicenergy=(d['electronic energy'] +
d['electronic energy correction']),
geometry=d['geometry'],
atoms=d['atoms'],
symmetrynumber=d['symmetrynumber'],
spin=d['spin'])
self._thermo = thermo
self._calculate_G()
def get_gas_Gcorr(self,atoms,vibs,symmetrynumber,spin,geometry,verbose=False):
gibbs = IdealGasThermo(vib_energies=vibs,
potentialenergy=0,
atoms=atoms,
geometry=geometry,
symmetrynumber=symmetrynumber,
spin=spin,
)
return gibbs
def setUp(self):
unittest.TestCase.setUp(self)
# Testing Ideal Gas Model
CO2 = molecule('CO2')
CO2_PyMuTT_parameters = {
'trans_model':
trans.IdealTrans,
'n_degrees':
3,
'molecular_weight':
get_molecular_weight('CO2'),
'rot_model':
rot.RigidRotor,
'rot_temperatures':
rot.get_rot_temperatures_from_atoms(CO2, geometry='linear'),
'geometry':
'linear',
'symmetrynumber':
2,
'elec_model':
elec.IdealElec,
'potentialenergy':
-22.994202,
'spin':
0.,
'vib_model':
vib.HarmonicVib,
'vib_wavenumbers': [3360., 954., 954., 1890.],
}
CO2_ase_parameters = {
'atoms': CO2,
'potentialenergy': -22.994202,
'vib_energies': [c.wavenumber_to_energy(x) \
for x in CO2_PyMuTT_parameters['vib_wavenumbers']],
'geometry':'linear',
'symmetrynumber': 2,
'spin': 0.
}
self.CO2_PyMuTT = StatMech(**CO2_PyMuTT_parameters)
self.CO2_ASE = IdealGasThermo(**CO2_ase_parameters)
self.T0 = c.T0('K') # K
self.P0 = c.P0('Pa')
self.V0 = c.V0('m3')
def __init__(
self,
surf_name=None,
surf_class=None, #type
species_name=None,
species_type=None,
traj_loc=None,
vib_loc=None,
symmetrynumber=None,
geometry=None,
spin=None,
calc_params=None,
tag='',
):
self.surf_name = surf_name
self.surf_class = surf_class
self.species_name = species_name
self.species_type = species_type
self.traj_loc = traj_loc
self.symmetrynumber = symmetrynumber
self.geometry = geometry
self.spin = spin
self.tag = tag
if calc_params != None:
self.calc_params = calc_params
if traj_loc != None:
self.atoms = read(traj_loc)
self.calc_params = self.get_calc_params()
if self.calc_params['xc'] == 'BEEF':
self.beef = self.beef_reader()
else:
self.atoms = []
self.calc_params = {}
if vib_loc != None:
self.vibs = self.vibs_reader(vib_loc)
if self.species_type == 'slab':
self.gibbs = None
elif self.species_type == 'gas':
self.gibbs = IdealGasThermo(
vib_energies=self.vibs,
potentialenergy=0,
atoms=self.atoms,
geometry=self.geometry,
symmetrynumber=self.symmetrynumber,
spin=self.spin,
)
elif self.species_type == 'adsorbate':
self.gibbs = HarmonicThermo(vib_energies=self.vibs,
potentialenergy=0)
else:
print "Warning: unrecognized species_type: ", self.species_type
self.gibbs = None
def GibbsGas(self, energy, T, p):
#Expecting T in Kelvin, p in bar
#note that frequencies should have a lower bound, e.g. 56 cm-1, in order to bound entropic contributions.
if self.gas:
cm_to_eV = 1.23981e-4
vib_energies = list(self.frequencies)
for i in range(len(vib_energies)):
vib_energies[i] = vib_energies[i] * cm_to_eV
thermo_gas = IdealGasThermo(vib_energies=vib_energies,
electronicenergy=energy,
atoms=self.atoms,
geometry=self.geometry,
symmetrynumber=self.symmetrynumber,
spin=self.spin)
bar_to_Pa = 1e5
pressure = p * bar_to_Pa
val = thermo_gas.get_gibbs_energy(temperature=T,
pressure=pressure,
verbose=False)
return val
else:
raise UserWarning('%s is no gas-phase species.' % self.name)
def get_zpe_energy(self, path_to_vib_species):
zpe_energy_dict = {}
atoms = read(path_to_vib_species)
vib_path = os.path.dirname(path_to_vib_species)
os.chdir(vib_path)
prefix, species = os.path.basename(path_to_vib_species).split(
'.')[0].split('_')
indices = [
atom.index for atom in atoms
if atom.position[2] > atoms.cell[2, 2] / 2.
]
vib = Vibrations(atoms, indices=indices)
vib_energies = vib.get_energies()
key = prefix + '_' + species
try:
thermo = IdealGasThermo(vib_energies, atoms)
zpe_energy = thermo.get_ZPE_correction()
zpe_energy_dict[key] = zpe_energy
except ValueError:
pass
return zpe_energy_dict
class TestStatMech(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
# Testing Ideal Gas Model
CO2 = molecule('CO2')
CO2_pMuTT_parameters = {
'name': 'CO2',
'trans_model': trans.IdealTrans,
'n_degrees': 3,
'molecular_weight': get_molecular_weight('CO2'),
'rot_model': rot.RigidRotor,
'rot_temperatures': rot.get_rot_temperatures_from_atoms(CO2,
geometry='linear'),
'geometry': 'linear',
'symmetrynumber': 2,
'elec_model': elec.IdealElec,
'potentialenergy': -22.994202,
'spin': 0.,
'vib_model': vib.HarmonicVib,
'vib_wavenumbers': [3360., 954., 954., 1890.],
}
CO2_ase_parameters = {
'atoms': CO2,
'potentialenergy': -22.994202,
'vib_energies': [c.wavenumber_to_energy(x)
for x in CO2_pMuTT_parameters['vib_wavenumbers']],
'geometry': 'linear',
'symmetrynumber': 2,
'spin': 0.
}
self.CO2_pMuTT = StatMech(**CO2_pMuTT_parameters)
self.CO2_ASE = IdealGasThermo(**CO2_ase_parameters)
self.T0 = c.T0('K') # K
self.P0 = c.P0('Pa')
self.V0 = c.V0('m3')
def test_get_q(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_q(T=self.T0, ignore_q_elec=True, V=self.V0),
6.083051624373337e+25)
def test_get_CvoR(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_CvoR(T=self.T0, V=self.V0),
2.9422622359004853)
def test_get_Cv(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_Cv(T=self.T0, V=self.V0, units='J/mol/K'),
2.9422622359004853*c.R('J/mol/K'))
def test_get_CpoR(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_CpoR(T=self.T0, V=self.V0),
3.9422622359004853)
def test_get_Cp(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_Cp(T=self.T0, V=self.V0, units='J/mol/K'),
3.9422622359004853*c.R('J/mol/K'))
def test_get_EoRT(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_EoRT(T=self.T0),
-894.97476277965)
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_EoRT(T=self.T0, include_ZPE=True),
-877.703643641077)
def test_get_E(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_E(T=self.T0, units='J/mol'),
-894.97476277965*c.R('J/mol/K')*self.T0)
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_E(T=self.T0, units='J/mol', include_ZPE=True),
-877.703643641077*c.R('J/mol/K')*self.T0, decimal=2)
def test_get_UoRT(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_UoRT(T=self.T0, V=self.V0),
-875.1095022368354)
def test_get_U(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_U(T=self.T0, V=self.V0, units='J/mol'),
-875.1095022368354*c.R('J/mol/K')*self.T0)
def test_get_HoRT(self):
expected_HoRT_CO2 = \
self.CO2_ASE.get_enthalpy(temperature=self.T0, verbose=False) \
/ c.R('eV/K')/self.T0
calc_HoRT_CO2 = self.CO2_pMuTT.get_HoRT(T=self.T0)
np.testing.assert_almost_equal(expected_HoRT_CO2, calc_HoRT_CO2)
def test_get_H(self):
expected_H_CO2 = \
self.CO2_ASE.get_enthalpy(temperature=self.T0, verbose=False)
calc_H_CO2 = self.CO2_pMuTT.get_H(T=self.T0, units='eV')
np.testing.assert_almost_equal(expected_H_CO2, calc_H_CO2)
def test_get_SoR(self):
expected_SoR_CO2 = \
self.CO2_ASE.get_entropy(temperature=self.T0, pressure=self.P0,
verbose=False)/c.R('eV/K')
calc_SoR_CO2 = self.CO2_pMuTT.get_SoR(T=self.T0, V=self.V0)
np.testing.assert_almost_equal(expected_SoR_CO2, calc_SoR_CO2, 3)
def test_get_S(self):
expected_S_CO2 = \
self.CO2_ASE.get_entropy(temperature=self.T0, pressure=self.P0,
verbose=False)
calc_S_CO2 = self.CO2_pMuTT.get_S(
T=self.T0,
V=self.V0,
units='eV/K')
np.testing.assert_almost_equal(expected_S_CO2, calc_S_CO2, 1)
def test_get_FoRT(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_FoRT(T=self.T0, V=self.V0),
-900.5899966269182)
def test_get_F(self):
np.testing.assert_almost_equal(
self.CO2_pMuTT.get_F(T=self.T0, V=self.V0, units='J/mol'),
-900.5899966269182*c.R('J/mol/K')*self.T0)
def test_get_GoRT(self):
expected_GoRT_CO2 = \
self.CO2_ASE.get_gibbs_energy(temperature=self.T0,
pressure=self.P0,
verbose=False)/c.R('eV/K')/self.T0
calc_GoRT_CO2 = self.CO2_pMuTT.get_GoRT(T=self.T0, V=self.V0)
np.testing.assert_almost_equal(expected_GoRT_CO2, calc_GoRT_CO2, 3)
def test_get_G(self):
expected_G_CO2 = \
self.CO2_ASE.get_gibbs_energy(temperature=self.T0,
pressure=self.P0,
verbose=False)
calc_G_CO2 = self.CO2_pMuTT.get_G(
T=self.T0,
V=self.V0,
units='eV')
np.testing.assert_almost_equal(expected_G_CO2, calc_G_CO2, 5)
#electronic energy in eV
energy = -553.610395
#vibrational energies in meV
vibenergies = [0, 0, 0, 7.6, 7.6, 299.2]
#convert from meV to eV for each mode
vibenergies[:] = [ve / 1000. for ve in vibenergies]
#list of temperatures
temperatures = [298.15, 400, 500]
#operating pressure
pressures = [101325]
f = open(name + '_free.energy', 'w')
for temperature in temperatures:
for pressure in pressures:
gibbs = IdealGasThermo(vib_energies=vibenergies,
electronicenergy=energy,
atoms=atoms,
geometry=geometry,
symmetrynumber=2,
spin=0)
freeenergy = gibbs.get_gibbs_energy(temperature, pressure)
f.write('Temperature: ' + str(temperature) + '\t' + 'Pressure: ' +
str(pressure) + '\t' + 'Free energy: ' + str(freeenergy) +
'\n')
f.close
# -*- coding: utf-8 -*-
"""
Created on Mon Jul 25 14:20:17 2016
@author: lansford
"""
from __future__ import division
from ase.thermochemistry import IdealGasThermo
from ase import Atoms
OOH = Atoms('OOH')
OOHfreqs = [.484418503,.146088952,.003153291,.002971872]
OOHThermo = IdealGasThermo(OOHfreqs,'linear',atoms=OOH,symmetrynumber=1,spin=0.5,natoms=3)
OOHgibbs = OOHThermo.get_gibbs_energy(298,101325);
OOHZPE = OOHThermo.get_enthalpy(0);
print(OOHgibbs)
print(OOHZPE)
def test_vibrations(self, testdir, n2_emt, n2_optimized):
atoms = n2_emt
vib = Vibrations(atoms)
vib.run()
freqs = vib.get_frequencies()
vib.write_mode(n=None, nimages=5)
vib.write_jmol()
vib_energies = vib.get_energies()
for image in vib.iterimages():
assert len(image) == 2
thermo = IdealGasThermo(vib_energies=vib_energies,
geometry='linear',
atoms=atoms,
symmetrynumber=2,
spin=0)
thermo.get_gibbs_energy(temperature=298.15,
pressure=2 * 101325.,
verbose=False)
vib.summary(log=self.logfile)
with open(self.logfile, 'rt') as f:
log_txt = f.read()
assert log_txt == vibrations_n2_log
mode1 = vib.get_mode(-1)
assert_array_almost_equal(mode1,
[[0., 0., -0.188935], [0., 0., 0.188935]])
assert_array_almost_equal(
vib.show_as_force(-1, show=False).get_forces(),
[[0., 0., -2.26722e-1], [0., 0., 2.26722e-1]])
for i in range(3):
assert not os.path.isfile('vib.{}.traj'.format(i))
mode_traj = ase.io.read('vib.3.traj', index=':')
assert len(mode_traj) == 5
assert_array_almost_equal(mode_traj[0].get_all_distances(),
atoms.get_all_distances())
with pytest.raises(AssertionError):
assert_array_almost_equal(mode_traj[4].get_all_distances(),
atoms.get_all_distances())
with open('vib.xyz', 'rt') as f:
jmol_txt = f.read()
assert jmol_txt == jmol_txt_ref
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] == atoms
atoms2 = n2_emt
vib2 = Vibrations(atoms2)
vib2.run()
assert_array_almost_equal(freqs, vib.get_frequencies())
# write/read the data from another working directory
atoms3 = n2_optimized.copy() # No calculator needed!
workdir = os.path.abspath(os.path.curdir)
try:
os.mkdir('run_from_here')
os.chdir('run_from_here')
vib = Vibrations(atoms3, name=os.path.join(os.pardir, 'vib'))
assert_array_almost_equal(freqs, vib.get_frequencies())
assert vib.clean() == 13
finally:
os.chdir(workdir)
if os.path.isdir('run_from_here'):
os.rmdir('run_from_here')
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()
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
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))
colors = {}
for i, atoms in enumerate(ga):
N_Sn = len([a for a in atoms if a.number == 50])
N_O = len([a for a in atoms if a.number == 8])
e = atoms.get_potential_energy()
Gs_slab[(N_Sn, N_O)] = e
colors[(N_Sn, N_O)] = color_lib[i]
cwd = os.getcwd()
os.chdir('/home/matjoerg/phd/ga/SnO2/ref_structures/O2/vib/')
O2 = read('optimisation.traj')
O2vib = InfraRed(O2)
e_O2vib = O2vib.get_energies()
thermo = IdealGasThermo(vib_energies=e_O2vib,
atoms=O2,
geometry='linear',
symmetrynumber=2,
spin=1)
os.chdir(cwd)
#mu0s = {100: -0.08, 200: -0.17, 300: -0.27, 400: -0.38, 500: -0.50, 600: -0.61, 700: -0.73, 800: -0.85, 900: -0.98, 1000: -1.10}
def free_e(mu, N_Sn, N_O):
G_slab = Gs_slab[(N_Sn, N_O)]
gamma_Opoor = 1 / A * (G_slab - 0.5 * N_O * e_SnO2 - (N_Sn - 0.5 * N_O) *
(e_Sn)) - e_surfb
gamma_Orich = gamma_Opoor - 1 / A * (N_Sn - 0.5 * N_O) * e_SnO2_formation
slope = (gamma_Orich - gamma_Opoor) / (e_O - e_SnO2_formation)
class TestStatMech(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
# Testing Ideal Gas Model
CO2 = molecule('CO2')
CO2_PyMuTT_parameters = {
'trans_model':
trans.IdealTrans,
'n_degrees':
3,
'molecular_weight':
get_molecular_weight('CO2'),
'rot_model':
rot.RigidRotor,
'rot_temperatures':
rot.get_rot_temperatures_from_atoms(CO2, geometry='linear'),
'geometry':
'linear',
'symmetrynumber':
2,
'elec_model':
elec.IdealElec,
'potentialenergy':
-22.994202,
'spin':
0.,
'vib_model':
vib.HarmonicVib,
'vib_wavenumbers': [3360., 954., 954., 1890.],
}
CO2_ase_parameters = {
'atoms': CO2,
'potentialenergy': -22.994202,
'vib_energies': [c.wavenumber_to_energy(x) \
for x in CO2_PyMuTT_parameters['vib_wavenumbers']],
'geometry':'linear',
'symmetrynumber': 2,
'spin': 0.
}
self.CO2_PyMuTT = StatMech(**CO2_PyMuTT_parameters)
self.CO2_ASE = IdealGasThermo(**CO2_ase_parameters)
self.T0 = c.T0('K') # K
self.P0 = c.P0('Pa')
self.V0 = c.V0('m3')
def test_get_q(self):
self.assertAlmostEqual(
self.CO2_PyMuTT.get_q(T=self.T0, ignore_q_elec=True, V=self.V0),
6.083051624373337e+25)
def test_get_CvoR(self):
self.assertAlmostEqual(self.CO2_PyMuTT.get_CvoR(T=self.T0, V=self.V0),
2.9422622359004853)
def test_get_CpoR(self):
self.assertAlmostEqual(self.CO2_PyMuTT.get_CpoR(T=self.T0, V=self.V0),
3.9422622359004853)
def test_get_UoRT(self):
self.assertAlmostEqual(self.CO2_PyMuTT.get_UoRT(T=self.T0, V=self.V0),
-875.1095022368354)
def test_get_HoRT(self):
expected_HoRT_CO2 = \
self.CO2_ASE.get_enthalpy(temperature=self.T0, verbose=False) \
/c.R('eV/K')/self.T0
calc_HoRT_CO2 = self.CO2_PyMuTT.get_HoRT(T=self.T0)
self.assertTrue(np.isclose(expected_HoRT_CO2, calc_HoRT_CO2))
def test_get_SoR(self):
expected_SoR_CO2 = \
self.CO2_ASE.get_entropy(temperature=self.T0, pressure=self.P0,
verbose=False)/c.R('eV/K')
calc_SoR_CO2 = self.CO2_PyMuTT.get_SoR(T=self.T0, V=self.V0)
self.assertTrue(np.isclose(expected_SoR_CO2, calc_SoR_CO2))
def test_get_AoRT(self):
self.assertAlmostEqual(self.CO2_PyMuTT.get_AoRT(T=self.T0, V=self.V0),
-900.5899966269182)
def test_get_GoRT(self):
expected_GoRT_CO2 = \
self.CO2_ASE.get_gibbs_energy(temperature=self.T0, pressure=self.P0,
verbose=False)/c.R('eV/K')/self.T0
calc_GoRT_CO2 = self.CO2_PyMuTT.get_GoRT(T=self.T0, V=self.V0)
self.assertTrue(np.isclose(expected_GoRT_CO2, calc_GoRT_CO2))
calc = Vasp('molecules/wgs/CO-vib')
vib_freq = calc.get_vibrational_frequencies()
CO_vib_energies = [h * c * nu for nu in vib_freq]
calc = Vasp('molecules/wgs/CO2-vib')
vib_freq = calc.get_vibrational_frequencies()
CO2_vib_energies = [h * c * nu for nu in vib_freq]
calc = Vasp('molecules/wgs/H2-vib')
vib_freq = calc.get_vibrational_frequencies()
H2_vib_energies = [h * c * nu for nu in vib_freq]
calc = Vasp('molecules/wgs/H2O-vib')
vib_freq = calc.get_vibrational_frequencies()
H2O_vib_energies = [h * c * nu for nu in vib_freq]
# now we make a thermo object for each molecule
CO_t = IdealGasThermo(vib_energies=CO_vib_energies[0:0],
potentialenergy=E_CO,
atoms=CO,
geometry='linear',
symmetrynumber=1,
spin=0)
CO2_t = IdealGasThermo(vib_energies=CO2_vib_energies[0:4],
potentialenergy=E_CO2,
atoms=CO2,
geometry='linear',
symmetrynumber=2,
spin=0)
H2_t = IdealGasThermo(vib_energies=H2_vib_energies[0:0],
potentialenergy=E_H2,
atoms=H2,
geometry='linear',
symmetrynumber=2,
spin=0)
H2O_t = IdealGasThermo(vib_energies=H2O_vib_energies[0:3],
atoms = read('N2.traj')
#electronic energy in eV
energy = -553.610395
#vibrational energies in meV
vibenergies = [0, 0, 0, 7.6, 7.6, 299.2]
#convert from meV to eV for each mode
vibenergies[:] = [ve/1000. for ve in vibenergies]
#list of temperatures
temperatures = [298.15, 400, 500]
#operating pressure
pressures = [101325]
f=open(name+'_free.energy','w')
for temperature in temperatures:
for pressure in pressures:
gibbs = IdealGasThermo(vib_energies=vibenergies,
electronicenergy=energy,
atoms=atoms,
geometry=geometry,
symmetrynumber=2, spin=0)
freeenergy = gibbs.get_gibbs_energy(temperature,pressure)
f.write('Temperature: '+str(temperature)+'\t'+'Pressure: '+str(pressure)+'\t'+'Free energy: '+str(freeenergy)+'\n')
f.close
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']))
QuasiNewton(atoms).run(fmax=0.01)
vib = Vibrations(atoms,
name='harmonicthermo-vib',
indices=[atom.index for atom in atoms if atom.symbol != 'Cu'])
encut=300,
ibrion=2,
nsw=5,
atoms=atoms) as calc:
electronicenergy = atoms.get_potential_energy()
# next, we get vibrational modes
with jasp('molecules/n2-vib',
xc='PBE',
encut=300,
ibrion=6,
nfree=2,
potim=0.15,
nsw=1,
atoms=atoms) as calc:
calc.calculate()
vib_freq = calc.get_vibrational_frequencies() # in cm^1
#convert wavenumbers to energy
h = 4.1356675e-15 # eV*s
c = 3.0e10 #cm/s
vib_energies = [h*c*nu for nu in vib_freq]
print('vibrational energies\n====================')
for i,e in enumerate(vib_energies):
print('{0:02d}: {1} eV'.format(i,e))
# # now we can get some properties. Note we only need one vibrational
# energy since there is only one mode. This example does not work if
# you give all the energies because one energy is zero.
thermo = IdealGasThermo(vib_energies=vib_energies[0:0],
electronicenergy=electronicenergy, atoms=atoms,
geometry='linear', symmetrynumber=2, spin=0)
# temperature in K, pressure in Pa, G in eV
G = thermo.get_free_energy(temperature=298.15, pressure=101325.)
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)
# At 300K and 101325 Pa
# change for your operating conditions
freeenergy = thermo.get_gibbs_energy(temperature=300, pressure=101325)
f = open(name + '.energy', 'w')
f.write('Potential energy: ' + str(energy) + '\n' +
'Free energy: ' + str(freeenergy) + '\n')
f.close
ens = BEEF_Ensemble(calc)
ens_e = ens.get_ensemble_energies()
ens.write('ensemble.bee')
MetalLabels = list(Data.Substrate[Data.index.isin(idx111) & (Data.Adsorbate=='O')])
EO = np.array(Data.Eads[Data.index.isin(idx111) & (Data.Adsorbate=='O')])
ECO = np.array(Data.Eads[Data.index.isin(idx111) & (Data.Adsorbate=='CO')])
GO = np.array(Data.vibGibbs[Data.index.isin(idx111) & (Data.Adsorbate=='O')])
GCO = np.array(Data.vibGibbs[Data.index.isin(idx111) & (Data.Adsorbate=='CO')])
O2r = (0.5149910055-0.4850089945)*41.3427602451982
O2freq = 0.1904905 #eV
COr = (0.51388868234-0.486111317659)*41.3427602451982
COfreq = 0.260119879
O2 = Atoms('O2')
O2[1].z = O2r
CO = Atoms('CO')
CO[1].z = COr
Temp = 400
O2Thermo = IdealGasThermo([O2freq],'linear',atoms=O2,symmetrynumber=2,spin=1,natoms=2)
O2gibbs = O2Thermo.get_gibbs_energy(Temp,1*101325);
COThermo = IdealGasThermo([COfreq],'linear',atoms=CO,symmetrynumber=1,spin=0,natoms=2)
COgibbs = COThermo.get_gibbs_energy(Temp,1*101325);
PtI = MetalLabels.index('Pt')
AgI = MetalLabels.index('Ag')
CuI = MetalLabels.index('Cu')
PdI = MetalLabels.index('Pd')
#redefining O2 eenergy change from molecular oxygen
EO = EO+9.5884297/2-1.9555224
delGCOPt = GCO[PtI]+ECO[PtI]-COgibbs
delGCOAg = GCO[AgI]+ECO[AgI]-COgibbs
delGCOPtAg = GCO[PtI]+ECO[AgI]-COgibbs
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']))
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()
encut=300,
ibrion=2,
nsw=5,
atoms=atoms)
electronicenergy = atoms.get_potential_energy()
# next, we get vibrational modes
calc2 = Vasp('molecules/n2-vib',
xc='PBE',
encut=300,
ibrion=6,
nfree=2,
potim=0.15,
nsw=1,
atoms=atoms)
calc2.wait()
vib_freq = calc2.get_vibrational_frequencies() # in cm^1
#convert wavenumbers to energy
h = 4.1356675e-15 # eV*s
c = 3.0e10 #cm/s
vib_energies = [h*c*nu for nu in vib_freq]
print('vibrational energies\n====================')
for i,e in enumerate(vib_energies):
print('{0:02d}: {1} eV'.format(i,e))
# # now we can get some properties. Note we only need one vibrational
# energy since there is only one mode. This example does not work if
# you give all the energies because one energy is zero.
thermo = IdealGasThermo(vib_energies=vib_energies[0:0],
potentialenergy=electronicenergy, atoms=atoms,
geometry='linear', symmetrynumber=2, spin=0)
# temperature in K, pressure in Pa, G in eV
G = thermo.get_gibbs_energy(temperature=298.15, pressure=101325.)
atoms=atoms)
electronicenergy = atoms.get_potential_energy()
# next, we get vibrational modes
calc2 = Vasp('molecules/n2-vib',
xc='PBE',
encut=300,
ibrion=6,
nfree=2,
potim=0.15,
nsw=1,
atoms=atoms)
calc2.wait()
vib_freq = calc2.get_vibrational_frequencies() # in cm^1
#convert wavenumbers to energy
h = 4.1356675e-15 # eV*s
c = 3.0e10 #cm/s
vib_energies = [h * c * nu for nu in vib_freq]
print('vibrational energies\n====================')
for i, e in enumerate(vib_energies):
print('{0:02d}: {1} eV'.format(i, e))
# # now we can get some properties. Note we only need one vibrational
# energy since there is only one mode. This example does not work if
# you give all the energies because one energy is zero.
thermo = IdealGasThermo(vib_energies=vib_energies[0:0],
potentialenergy=electronicenergy,
atoms=atoms,
geometry='linear',
symmetrynumber=2,
spin=0)
# temperature in K, pressure in Pa, G in eV
G = thermo.get_gibbs_energy(temperature=298.15, pressure=101325.)
freq_remove = []
if RMFREQ_KbT == "True":
for i in Freq:
if i <= freq_kbt_cutoff:
freq_remove.append(i)
for i in freq_remove:
if i in Freq:
Freq.remove(i)
## get the strucuter from the output file
struc = read(log_file,format='gaussian-out')
## get the ideal gas limit thermodynamic values
thermo = IdealGasThermo(vib_energies=Freq, potentialenergy=scf_energy_eV,
atoms=struc, geometry=shape,
symmetrynumber=symnum, spin=spin)
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"
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)
# At 300K and 101325 Pa
# change for your operating conditions
freeenergy = thermo.get_gibbs_energy(temperature=300, pressure=101325)
f = open(name + '.energy', 'w')
f.write('Potential energy: ' + str(energy) + '\n' + 'Free energy: ' +
str(freeenergy) + '\n')
f.close
ens = BEEF_Ensemble(calc)
ens_e = ens.get_ensemble_energies()
ens.write('ensemble.bee')
vO2N = np.concatenate((Data2['v(M-O2)'][idx1],Data2['v(M-N)'][idx2]))
for x, y, s in zip(vOO, vO2N, M3):
texts.append(plt.text(x, y, s, bbox={'pad':0, 'alpha':0}, size=22, fontweight='bold',style='normal',name ='Calibri'))
adjustText.adjust_text(texts,autoalign=True,only_move={'points':'y','text':'y'},
arrowprops=dict(arrowstyle="-", color='k', lw=2))
plt.show()
O2r = (0.5149910055-0.4850089945)*41.3427602451982
O2freq = 0.1904905 #eV
COr = (0.51388868234-0.486111317659)*41.3427602451982
COfreq = 0.260119879
O2 = Atoms('O2')
O2[1].z = O2r
CO = Atoms('CO')
CO[1].z = COr
O2Thermo = IdealGasThermo([O2freq],'linear',atoms=O2,symmetrynumber=2,spin=1,natoms=2)
O2gibbs = O2Thermo.get_gibbs_energy(298,101325);
COThermo = IdealGasThermo([COfreq],'linear',atoms=CO,symmetrynumber=1,spin=0,natoms=2)
COgibbs = COThermo.get_gibbs_energy(298,101325);
PtI = MetalLabels.index('Pt')
AgI = MetalLabels.index('Ag')
delGCOPt = G3[PtI]+E3[PtI]-COgibbs
delGCOAg = G3[AgI]+E3[AgI]-COgibbs
delGCOPtAg = G3[PtI]+E3[AgI]-COgibbs
delGOPt = G1[PtI]+E1[PtI]-O2gibbs/2
delGOAg = G1[AgI]+E1[AgI]-O2gibbs/2
delGOPtAg = G1[PtI]+E1[AgI]-O2gibbs/2
c = 3.0e10 # cm / s
calc = Vasp('molecules/wgs/CO-vib')
vib_freq = calc.get_vibrational_frequencies()
CO_vib_energies = [h * c * nu for nu in vib_freq]
calc = Vasp('molecules/wgs/CO2-vib')
vib_freq = calc.get_vibrational_frequencies()
CO2_vib_energies = [h * c * nu for nu in vib_freq]
calc = Vasp('molecules/wgs/H2-vib')
vib_freq = calc.get_vibrational_frequencies()
H2_vib_energies = [h * c * nu for nu in vib_freq]
calc = Vasp('molecules/wgs/H2O-vib')
vib_freq = calc.get_vibrational_frequencies()
H2O_vib_energies = [h * c * nu for nu in vib_freq]
# now we make a thermo object for each molecule
CO_t = IdealGasThermo(vib_energies=CO_vib_energies[0:0],
potentialenergy=E_CO, atoms=CO,
geometry='linear', symmetrynumber=1,
spin=0)
CO2_t = IdealGasThermo(vib_energies=CO2_vib_energies[0:4],
potentialenergy=E_CO2, atoms=CO2,
geometry='linear', symmetrynumber=2,
spin=0)
H2_t = IdealGasThermo(vib_energies=H2_vib_energies[0:0],
potentialenergy=E_H2, atoms=H2,
geometry='linear', symmetrynumber=2,
spin=0)
H2O_t = IdealGasThermo(vib_energies=H2O_vib_energies[0:3],
potentialenergy=E_H2O, atoms=H2O,
geometry='nonlinear', symmetrynumber=2,
spin=0)
# now we can compute G_rxn for a range of temperatures from 298 to 1000 K
Trange = np.linspace(298, 1000, 20) # K
import statmech
from ase.thermochemistry import IdealGasThermo
from ase import Atoms
mat.rcParams['mathtext.default'] = 'regular'
mat.rcParams['legend.numpoints'] = 1
mat.rcParams['lines.linewidth'] = 3
mat.rcParams['lines.markersize'] = 20
c = 29979245800 #cm/s
h = 6.6260693*10**(-34) #planks constant
kB = 1.3806505*10**(-23) #boltzman's constant
JeV = 1.60217653*10**(-19) #eV to Joules
COr = (0.51388868234-0.486111317659)*41.3427602451982
COfreq = 0.260119879
CO = Atoms('CO')
CO[1].z = COr
COThermo = IdealGasThermo([COfreq],'linear',atoms=CO,symmetrynumber=1,spin=0,natoms=2)
COh100 = COThermo.get_enthalpy(100)
COh100 = COThermo.get_enthalpy(145)
COh100 = COThermo.get_enthalpy(130)
COh100 = COThermo.get_enthalpy(420)
COh100 = COThermo.get_enthalpy(350)
COh100 = COThermo.get_enthalpy(450)
COh100 = COThermo.get_enthalpy(340)
COh100 = COThermo.get_enthalpy(500)
H_Ag=np.array([234.060289,22.823011,16.915597,16.786227,3.576371,2.197334])*8.06573
vibAg = statmech.vibenergy(H_Ag,100)
print(vibAg)
H_Cu=np.array([223.437829,31.524364,27.338489,27.112873,13.374554,12.939494])*8.06573
vibCu = statmech.vibenergy(H_Cu,130)
print(vibCu)
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
outdir='calcdir',
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))
c = 3.0e10 # cm / s
with jasp('molecules/wgs/CO-vib') as calc:
vib_freq = calc.get_vibrational_frequencies()
CO_vib_energies = [h * c * nu for nu in vib_freq]
with jasp('molecules/wgs/CO2-vib') as calc:
vib_freq = calc.get_vibrational_frequencies()
CO2_vib_energies = [h * c * nu for nu in vib_freq]
with jasp('molecules/wgs/H2-vib') as calc:
vib_freq = calc.get_vibrational_frequencies()
H2_vib_energies = [h * c * nu for nu in vib_freq]
with jasp('molecules/wgs/H2O-vib') as calc:
vib_freq = calc.get_vibrational_frequencies()
H2O_vib_energies = [h * c * nu for nu in vib_freq]
# now we make a thermo object for each molecule
CO_t = IdealGasThermo(vib_energies=CO_vib_energies[0:0],
electronicenergy=E_CO, atoms=CO,
geometry='linear', symmetrynumber=1,
spin=0)
CO2_t = IdealGasThermo(vib_energies=CO2_vib_energies[0:4],
electronicenergy=E_CO2, atoms=CO2,
geometry='linear', symmetrynumber=2,
spin=0)
H2_t = IdealGasThermo(vib_energies=H2_vib_energies[0:0],
electronicenergy=E_H2, atoms=H2,
geometry='linear', symmetrynumber=2,
spin=0)
H2O_t = IdealGasThermo(vib_energies=H2O_vib_energies[0:3],
electronicenergy=E_H2O, atoms=H2O,
geometry='nonlinear', symmetrynumber=2,
spin=0)
# now we can compute G_rxn for a range of temperatures from 298 to 1000 K
Trange = np.linspace(298, 1000, 20) # K
def get_chemical_potential(atoms,
freq,
geometry,
potentialenergy,
symmetrynumber,
spin,
T,
nasa_liq=None,
H_gas=None,
S_gas=None,
x=None,
gas_phase=False,
verbose=False):
"""
Calculates the chemical potential of the toluene-phase species
atoms - ASE Atoms object
freq - Numpy array of floats
Frequencies of the species in 1/cm
geometry - string
Geometry of the species (monatomic, linear, nonlinear)
potentialenergy - float
DFT Energy of the species in eV
symmetrynumber - float
Symmetry number of the species
spin - int
Number of unpaired electrons in the species
nasa_liq - NASA object
NASA polynomial of the species in the liquid phase
H_gas - float
Enthalpy of the gas in kJ/mol/K
S_gas - float
Entropy of the gas in J/mol/K
T - float
Temperature to perform analysis
x - float
Mole fraction of species in liquid
"""
#DFT Delta G
DFT_thermo = IdealGasThermo(vib_energies=freq * c.h('eV s') * c.c('cm/s'),
geometry=geometry,
potentialenergy=potentialenergy,
natoms=len(atoms),
atoms=atoms,
symmetrynumber=symmetrynumber,
spin=spin)
G_DFT = DFT_thermo.get_gibbs_energy(temperature=298.,
pressure=1.e5,
verbose=verbose)
if gas_phase:
return np.array([
DFT_thermo.get_gibbs_energy(temperature=T_i,
pressure=1.e5,
verbose=verbose) for T_i in T
])
else:
#ASPEN Liquid Data
G_liq = nasa_liq.get_GoRT(T=T, verbose=False) * c.kb('eV/K') * T
#NIST Gas Phase Data
G_gas = H_gas * c.convert_unit(
from_='kJ/mol', to='eV/molecule') - T * S_gas * c.convert_unit(
from_='J/mol', to='eV/molecule')
return G_DFT + G_liq - G_gas + c.kb('eV/K') * T * np.log(x)