def test_get_A(self):
exp_sm_SoR = self.H2O_TS_sm.get_SoR(T=c.T0('K')) \
- self.H2_sm.get_SoR(T=c.T0('K')) \
- self.O2_sm.get_SoR(T=c.T0('K'))*0.5
exp_sm_A = c.kb('J/K') * c.T0('K') / c.h('J s') * np.exp(-exp_sm_SoR)
exp_sm_SoR_rev = self.H2O_TS_sm.get_SoR(T=c.T0('K')) \
- self.H2O_sm.get_SoR(T=c.T0('K'))
exp_sm_A_rev = c.kb('J/K') * c.T0('K') / c.h('J s') * np.exp(
-exp_sm_SoR_rev)
self.assertAlmostEqual(self.rxn_sm.get_A(T=c.T0('K')), exp_sm_A)
self.assertAlmostEqual(self.rxn_sm.get_A(T=c.T0('K'), rev=True),
exp_sm_A_rev)
def __init__(self,
A_st=None,
atoms=None,
symmetrynumber=None,
inertia=None,
geometry=None,
vib_energies=None,
potentialenergy=None,
**kwargs):
super().__init__(atoms=atoms,
symmetrynumber=symmetrynumber,
geometry=geometry,
vib_energies=vib_energies,
potentialenergy=potentialenergy,
**kwargs)
self.A_st = A_st
self.atoms = atoms
self.geometry = geometry
self.symmetrynumber = symmetrynumber
self.inertia = inertia
self.etotal = potentialenergy
self.vib_energies = vib_energies
self.theta = np.array(vib_energies) / c.kb('eV/K')
self.zpe = sum(np.array(vib_energies)/2.) *\
c.convert_unit(from_='eV', to='kcal')*c.Na
if np.sum(vib_energies) != 0:
self.q_vib = np.product(
np.divide(1, (1 - np.exp(-self.theta / c.T0('K')))))
if self.phase == 'G':
if self.inertia is not None:
self.I3 = self.inertia
else:
self.I3 = atoms.get_moments_of_inertia() *\
c.convert_unit(from_='A2', to='m2') *\
c.convert_unit(from_='amu', to='kg')
self.T_I = c.h('J s')**2 / (8 * np.pi**2 * c.kb('J/K'))
if self.phase == 'G':
Irot = np.max(self.I3)
if self.geometry == 'nonlinear':
self.q_rot = np.sqrt(np.pi*Irot)/self.symmetrynumber *\
(c.T0('K')/self.T_I)**(3./2.)
else:
self.q_rot = (c.T0('K') * Irot /
self.symmetrynumber) / self.T_I
else:
self.q_rot = 0.
if self.A_st is not None:
self.MW = mw(self.elements) * c.convert_unit(from_='g',
to='kg') / c.Na
self.q_trans2D = self.A_st * (2 * np.pi * self.MW * c.kb('J/K') *
c.T0('K')) / c.h('J s')**2
def get_SoR(self, T, P=c.P0('bar')):
"""Calculates the dimensionless entropy
:math:`\\frac{S^{trans}}{R}=1+\\frac{n_{degrees}}{2}+\\log\\bigg(\\big(
\\frac{2\\pi mk_bT}{h^2})^\\frac{n_{degrees}}{2}\\frac{RT}{PN_a}\\bigg)`
Parameters
----------
T : float
Temperature in K
P : float, optional
Pressure (bar) or pressure-like quantity.
Default is atmospheric pressure
Returns
-------
SoR_trans : float
Translational dimensionless entropy
"""
V = self.get_V(T=T, P=P)
unit_mass = self.molecular_weight *\
c.convert_unit(from_='g', to='kg')/c.Na
return 1. + float(self.n_degrees)/2. \
+ np.log((2.*np.pi*unit_mass*c.kb('J/K')*T/c.h('J s')**2)
** (float(self.n_degrees)/2.)*V/c.Na)
def get_GoRT(self, Ts, verbose=False):
"""Calculate dimensionless Gibbs energy at a given temperature.
Args:
Ts (float or numpy array): Temperature(s) in K
verbose (bool): Flag to print each contribution to enthalpy
Returns:
GoRT (float or numpy array): Dimensionless heat capacity (H/RT)
"""
try:
iter(Ts)
except TypeError:
GoRT = self.model.get_helmholtz_energy(Ts, verbose) / \
(c.kb('eV/K') * Ts)
else:
GoRT = np.zeros_like(Ts)
for i, T in enumerate(Ts):
GoRT[i] = self.model.get_helmholtz_energy(T, verbose) / \
(c.kb('eV/K') * T)
return GoRT
def get_ZPE(self):
"""Calculates the zero point energy
:math:`ZPE=\\frac{1}{2}h\\sum_i \\Theta_{V,i}`
Returns
-------
zpe : float
Zero point energy in eV
"""
return 0.5 * c.kb('eV/K') * np.sum(self._vib_temperatures)
def _get_single_CvoR_vib(vib_energies, T):
"""Calculate the dimensionless vibrational heat capacity
Parameters:
vib_energies (array of floats): Vibrational energies in eV
T (float): Temperatures in K
Returns:
CvoR_vib (float): Dimensionless vibrational heat capacity
"""
dimensionless_vibs = vib_energies / c.kb('eV/K') / T
CvoR_vib = np.sum((0.5 * dimensionless_vibs)**2 *
(1. / np.sinh(0.5 * dimensionless_vibs))**2)
return CvoR_vib
def get_CvoR_vib(vib_energies, temperature):
"""Calculate the dimensionless vibrational heat capacity
:math:`\\frac {Cp_{vib}}{R} = \\sum_{i=1}^{n} \\bigg(\\frac {\\Theta_{V,i}}{2T}\\bigg)^2 \\frac {1}{\\big(sinh(\\frac {\\Theta_{V,i}}{2T})\\big)^2}`
Parameters:
vib_energies (array of floats): Vibrational energies in eV
temperature (float): Temperature in K
"""
dimensionless_vibs = vib_energies / c.kb('eV/K') / temperature
CvoR_vib = np.sum((0.5 * dimensionless_vibs)**2 *
(1. / np.sinh(0.5 * dimensionless_vibs))**2)
return CvoR_vib
def get_HoRT(self, Ts, verbose=False):
"""Calculate the dimensionless enthalpy.
Parameters:
Ts : float or (N,) `numpy.ndarray`_
Temperature(s) in K
verbose : bool
Whether a table breaking down each contribution should be printed
Returns
HoRT : float or (N,) `numpy.ndarray`_
Dimensionless heat capacity (H/RT)
"""
try:
iter(Ts)
except TypeError:
HoRT = self.model.get_enthalpy(Ts, verbose=verbose) / \
(c.kb('eV/K') * Ts)
else:
HoRT = np.zeros_like(Ts)
for i, T in enumerate(Ts):
HoRT[i] = self.model.get_enthalpy(T, verbose=verbose) / \
(c.kb('eV/K') * T)
return HoRT
def get_HoRT(self, temperature, verbose=False):
"""Calculate the dimensionless enthalpy.
Parameters:
temperature (float): Temperature in K
verbose (bool): Print a table breaking down each contribution
"""
if self.specie_type == 'ideal gas':
enthalpy = self.model.get_enthalpy(temperature, verbose=verbose)
else:
enthalpy = self.model.get_internal_energy(temperature,
verbose=verbose)
return enthalpy / (c.kb('eV/K') * temperature)
def get_UoRT(self, T):
"""Calculates the imensionless internal energy
:math:`\\frac{U^{elec}}{RT}=\\frac{E}{RT}`
Parameters
----------
T : float
Temperature in K
Returns
-------
UoRT_elec : float
Electronic dimensionless internal energy
"""
return self.potentialenergy / c.kb('eV/K') / T
def get_GoRT(self, temperature, pressure=1.0, verbose=False):
"""Calculate the dimensionless Gibbs energy.
Parameters:
temperature (float): Temperature(s) in K
pressure (float, optional): Pressure in atm. Default is 1 atm.
verbose (bool): Print a table breaking down each contribution
"""
if self.specie_type == 'ideal gas':
G = self.model.get_gibbs_energy(
temperature,
pressure=pressure * c.convert_unit(from_='bar', to='Pa'),
verbose=verbose)
else:
G = self.model.get_helmholtz_energy(temperature, verbose=verbose)
return G / (c.kb('eV/K') * temperature)
def _get_SoR_RRHO(self, T, vib_inertia):
"""Calculates the dimensionless RRHO contribution to entropy
Parameters
----------
T : float
Temperature in K
vib_inertia : float
Vibrational inertia in kg m2
Returns
-------
SoR_RHHO : float
Dimensionless entropy of Rigid Rotor Harmonic Oscillator
"""
return 0.5 + np.log(
(8. * np.pi**3 * vib_inertia * c.kb('J/K') * T / c.h('J s')**2)**
0.5)
def get_A(self, T=c.T0('K'), rev=False, **kwargs):
"""Gets pre-exponential factor between reactants (or products) and
transition state in 1/s
Parameters
----------
rev : bool, optional
Reverse direction. If True, uses products as initial state
instead of reactants. Default is False
T : float, optional
Temperature in K. Default is standard temperature.
kwargs : keyword arguments
Parameters required to calculate pre-exponential factor
Returns
-------
A : float
Pre-exponential factor
"""
return c.kb('J/K')*T/c.h('J s')\
*np.exp(-self.get_SoR_act(rev=rev, T=c.T0('K'), **kwargs))
def get_q(self, T, P=c.P0('bar')):
"""Calculates the partition function
:math:`q_{trans} = \\bigg(\\frac{2\\pi \\sum_{i}^{atoms}m_ikT}{h^2}
\\bigg)^\\frac {n_{degrees}} {2}V`
Parameters
----------
T : float
Temperature in K
P : float, optional
Pressure (bar) or pressure-like quantity.
Default is atmospheric pressure
Returns
-------
q_trans : float
Translational partition function
"""
V = self.get_V(T=T, P=P)
unit_mass = self.molecular_weight *\
c.convert_unit(from_='g', to='kg')/c.Na
return V*(2*np.pi*c.kb('J/K')*T*unit_mass/c.h('J s')**2) \
** (float(self.n_degrees)/2.)
def test_get_CvoR_vib(self):
#Vibrational frequencies correspond to H2O
vib_energies = np.array([5360., 5160., 2290.]) * c.kb('eV/K')
self.assertAlmostEqual(heat_capacity._get_single_CvoR_vib(vib_energies=vib_energies, T=300.), 0.02824711469596)
self.assertAlmostEqual(heat_capacity.get_CvoR_vib(vib_energies=vib_energies, Ts=300.), 0.02824711469596)
np.testing.assert_almost_equal(heat_capacity.get_CvoR_vib(vib_energies=vib_energies, Ts=np.array([300., 400., 500.])), np.array([0.02824711469596, 0.10834772440392, 0.22564243671432]))
def test_kb(self):
self.assertEqual(c.kb('J/K'), 1.38064852e-23)
with self.assertRaises(KeyError):
c.kb('arbitrary unit')
