def __init__(self,
stoichiometry,
A=c.kb('J/K') / c.h('J s'),
EoRT=None,
BEP=None,
beta=0.,
T_ref=1.,
use_sticking_coefficient=False,
s=0.5):
self.stoichiometry = stoichiometry
self.A = A
self.EoRT = EoRT
self.BEP = BEP
self.beta = beta
self.T_ref = T_ref
self.use_sticking_coefficient = use_sticking_coefficient
self.s = s
def _get_single_CpoR(self, T):
"""
Returns the constant pressure heat capacity.
"""
if self.is_gas:
if self.IdealGasThermo.geometry == 'monatomic':
return 2.5
elif self.IdealGasThermo.geometry == 'linear':
CpoR = 2.5
elif self.IdealGasThermo.geometry == 'nonlinear':
CpoR = 3.
else:
warnings.warn(
"Gas phase species with invalid geometry. Returning 0.")
return 0.
#Correction between Cv and Cp
CpoR += 1.
else:
CpoR = 0.
for vib_f in self.vib_freq:
vib_T = vib_f * c.c('cm/s') * c.h('J s') / c.kb('J/K')
CpoR += (vib_T / (2. * T))**2 * 1. / (np.sinh(vib_T / (2. * T)))**2
return CpoR
def dft_to_thermdat(input_path,
ref_path='thermdat_ref.csv',
T_low=300.,
T_high=800.,
write_files=True,
out_path='thermdat',
verbose=False,
warn=False,
freq_cut_off=0.,
pressure=1.,
add_gas_species=True,
gas_path='thermdat_gas'):
"""
Convert DFT energies and frequencies to NASA polynomials that can be written as a thermdat file
Attributes
----------
input_path - string
Path to .csv file that contains the DFT information of all species to be written in thermdat
ref_path - string
Path to .csv file that contains the gas-phase reference information
T_low - float
Lower temperature bound for the NASA polynomials
T_high - float
Higher temperature bound for the NASA polynomials
write_files - boolean
Whether or not the thermdat file should be written
out_path - string
Path where the thermdat file will be written
verbose - boolean
Whether or not more detailed output should be given
warn - boolean
Whether or not warnings should be given
freq_cut_off - float
Cut off frequency. If vibrational frequencies (in 1/cm) are below this value, they are ignored
since they are assumed to be frustrated rotational or translational modes
pressure - float
Pressure (in atmospheres) to generate the NASA polynomials. Usually this value is left at 1 atm
add_gas_species - boolean
Whether or not gas-phase species from gas_path should be written to the thermdat file
gas_path - string
Path to thermdat file that contains the gas-phase species to add
Returns
-------
thermdat - Thermdat object
The successfully converted thermdat object
"""
T_range = np.linspace(T_low, T_high, T_high - T_low)
n_T = len(T_range)
print("Opening reference file: %s" % ref_path)
(fund_energies, fund_CHON, rm_list) = read_ref(ref_path,
verbose=verbose,
warn=warn)
print('Fundamental energies:')
print(fund_energies)
print('Fund CHON')
print(fund_CHON)
#Read the species to be processed
print("Opening input file: %s" % input_path)
thermdats_dft = read_freq(input_path,
verbose=verbose,
freq_cut_off=freq_cut_off,
warn=warn)
for i, thermdat_dft in enumerate(thermdats_dft):
print("-" * 10)
print("Processing %s..." % thermdat_dft.symbol)
thermdat_dft.nasa = Nasa(symbol=thermdat_dft.symbol,
T_low=min(T_range),
T_high=max(T_range))
print("Calculating heat capacities.")
CpoR = thermdat_dft.get_CpoR(T_range)
print("Calculating DFT enthalpy of formation")
if thermdat_dft.is_gas:
H0 = thermdat_dft.IdealGasThermo.get_enthalpy(
temperature=c.T0('K'), verbose=verbose)
thermo_parameters = thermdat_dft.IdealGasThermo.__dict__
else:
thermo_parameters = thermdat_dft.HarmonicThermo.__dict__
if np.sum(thermdat_dft.HarmonicThermo.vib_energies) == 0:
H0 = thermdat_dft.HarmonicThermo.potentialenergy
else:
H0 = thermdat_dft.HarmonicThermo.get_internal_energy(
temperature=c.T0('K'), verbose=verbose)
print("Adjusting enthalpy to reference")
CHON = np.delete(thermdat_dft.CHON, rm_list)
TransformCHON = np.dot(CHON, np.linalg.inv(fund_CHON))
HoRT0 = (H0 - np.dot(TransformCHON, fund_energies)) / (c.T0('K') *
c.kb('eV/K'))
print("Calculating DFT enthalpy of formation")
if thermdat_dft.is_gas:
S0 = thermdat_dft.IdealGasThermo.get_entropy(
temperature=c.T0('K'),
pressure=pressure * c.convert_unit(from_='atm', to='Pa'),
verbose=verbose)
else:
if np.sum(thermdat_dft.HarmonicThermo.vib_energies) == 0:
S0 = 0.
else:
S0 = thermdat_dft.HarmonicThermo.get_entropy(
temperature=c.T0('K'), verbose=verbose)
SoR0 = S0 / c.kb('eV/K')
print('Species: {}'.format(thermdat_dft.symbol))
print('thermo parameters: {}'.format(thermo_parameters))
print('HoRT0 = {}'.format(HoRT0))
print('S/R0 = {}'.format(SoR0))
print('#')
print("Calculating NASA polynomials")
thermdat_dft.nasa.fit_NASA(T_range, CpoR, HoRT0, SoR0)
#Add gas-phase species
if add_gas_species:
print("Opening gas phase file: {}".format(gas_path))
thermdats_gas = Thermdats.from_thermdat(thermdat_path=gas_path,
verbose=verbose,
warn=warn)
print("Attaching gas species")
thermdats_dft.extend(thermdats_gas)
if write_files:
print("Writing to thermdat")
thermdats_dft.write_thermdat(out_path, verbose=False)
return thermdats_dft
def test_kb(self):
self.assertEqual(c.kb('J/K'), 1.38064852e-23)
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)