def to_dict(self):
"""Represents object as dictionary with JSON-accepted datatypes
Returns
-------
obj_dict : dict
"""
obj_dict = {
'class': str(self.__class__),
'name': self.name,
'trans_model': self.trans_model.to_dict(),
'vib_model': self.vib_model.to_dict(),
'rot_model': self.rot_model.to_dict(),
'elec_model': self.elec_model.to_dict(),
'nucl_model': self.nucl_model.to_dict(),
'smiles': self.smiles,
'notes': self.notes
}
if _is_iterable(self.mix_models):
obj_dict['mix_models'] = \
[mix_model.to_dict() for mix_model in self.mix_models]
else:
obj_dict['mix_models'] = self.mix_models
return obj_dict
def to_dict(self):
"""Represents object as dictionary with JSON-accepted datatypes
Returns
-------
obj_dict : dict
"""
obj_dict = {
'class': str(self.__class__),
'type': 'empiricalbase',
'name': self.name,
'phase': self.phase,
'elements': self.elements,
'notes': self.notes,
'smiles': self.smiles,
}
try:
obj_dict['references'] = self.references.to_dict()
except AttributeError:
obj_dict['references'] = self.references
try:
obj_dict['statmech_model'] = self.statmech_model.to_dict()
except AttributeError:
obj_dict['statmech_model'] = self.statmech_model
if _is_iterable(self.mix_models):
obj_dict['mix_models'] = \
[mix_model.to_dict() for mix_model in self.mix_models]
else:
obj_dict['mix_models'] = self.mix_models
return obj_dict
def __init__(self,
name=None,
phase=None,
elements=None,
statmech_model=None,
references=None,
mix_models=None,
smiles=None,
notes=None,
**kwargs):
self.name = name
self.phase = phase
self.elements = elements
self.references = references
self.smiles = smiles
self.notes = notes
# Assign self.statmech_model
if inspect.isclass(statmech_model):
# If you're passing a class. Note that the required
# arguments will be guessed.
self.statmech_model = statmech_model(**kwargs)
else:
# If it's an object that has already been initialized
self.statmech_model = statmech_model
# Assign mixing models
# TODO Mixing models can not be initialized by passing the class
# because all the models will have the same attributes. Figure out a
# way to pass them. Perhaps have a dictionary that contains the
# attributes separated by species
if not _is_iterable(mix_models) and mix_models is not None:
mix_models = [mix_models]
self.mix_models = mix_models
def __init__(self,
name=None,
trans_model=EmptyMode(),
vib_model=EmptyMode(),
rot_model=EmptyMode(),
elec_model=EmptyMode(),
nucl_model=EmptyMode(),
mix_models=None,
smiles=None,
notes=None,
**kwargs):
self.name = name
self.smiles = smiles
self.notes = notes
# Translational modes
if inspect.isclass(trans_model):
self.trans_model = _pass_expected_arguments(trans_model, **kwargs)
else:
self.trans_model = trans_model
# Vibrational modes
if inspect.isclass(vib_model):
self.vib_model = _pass_expected_arguments(vib_model, **kwargs)
else:
self.vib_model = vib_model
# Rotational modes
if inspect.isclass(rot_model):
self.rot_model = _pass_expected_arguments(rot_model, **kwargs)
else:
self.rot_model = rot_model
# Electronic modes
if inspect.isclass(elec_model):
self.elec_model = _pass_expected_arguments(elec_model, **kwargs)
else:
self.elec_model = elec_model
# Nuclear modes
if inspect.isclass(nucl_model):
self.nucl_model = _pass_expected_arguments(nucl_model, **kwargs)
else:
self.nucl_model = nucl_model
# Assign mixing models
# TODO Mixing models can not be initialized by passing the class
# because all the models will have the same attributes. Figure out
# a way to pass them. Perhaps have a dictionary that contains the
# attributes separated by species
if not _is_iterable(mix_models) and mix_models is not None:
mix_models = [mix_models]
self.mix_models = mix_models
def get_CpoR(self, T, raise_error=True, raise_warning=True, **kwargs):
"""Calculate the dimensionless heat capacity
Parameters
----------
T : float or (N,) `numpy.ndarray`_
Temperature(s) in K
raise_error : bool, optional
If True, raises an error if any of the modes do not have the
quantity of interest. Default is True
raise_warning : bool, optional
Only relevant if raise_error is False. Raises a warning if any
of the modes do not have the quantity of interest. Default is
True
kwargs : key-word arguments
Arguments to calculate mixture model properties, if any
Returns
-------
CpoR : float or (N,) `numpy.ndarray`_
Dimensionless heat capacity
.. _`numpy.ndarray`: https://docs.scipy.org/doc/numpy-1.14.0/reference/generated/numpy.ndarray.html
"""
# Convert T to 1D numpy format
if not _is_iterable(T):
T = [T]
T = np.array(T)
# Calculate pure properties
CpoR = get_shomate_CpoR(a=self.a, T=T)
# Calculate mixing properties
for T_i in T:
CpoR_mix = _get_mix_quantity(mix_models=self.mix_models,
method_name='get_CpoR',
raise_error=raise_error,
raise_warning=raise_warning,
default_value=0.,
T=T_i,
**kwargs)
# Add mixing quantity in appropriate format
if len(T) == 1:
CpoR += CpoR_mix[0]
else:
CpoR += CpoR_mix
return CpoR
def get_SoR(self, T, raise_error=True, raise_warning=True, **kwargs):
"""Calculate the dimensionless entropy
Parameters
----------
T : float or (N,) `numpy.ndarray`_
Temperature(s) in K
raise_error : bool, optional
If True, raises an error if any of the modes do not have the
quantity of interest. Default is True
raise_warning : bool, optional
Only relevant if raise_error is False. Raises a warning if any
of the modes do not have the quantity of interest. Default is
True
kwargs : key-word arguments
Arguments to calculate mixture model properties, if any
Returns
-------
SoR : float or (N,) `numpy.ndarray`_
Dimensionless entropy
.. _`numpy.ndarray`: https://docs.scipy.org/doc/numpy-1.14.0/reference/generated/numpy.ndarray.html
"""
if _is_iterable(T):
SoR = np.zeros_like(T)
for i, T_i in enumerate(T):
a = self.get_a(T=T_i)
SoR[i] = get_nasa_SoR(a=a, T=T_i) \
+ np.sum(_get_mix_quantity(mix_models=self.mix_models,
method_name='get_SoR',
raise_error=raise_error,
raise_warning=raise_warning,
default_value=0.,
T=T_i, **kwargs))
else:
a = self.get_a(T=T)
SoR = get_nasa_SoR(a=a, T=T) \
+ np.sum(_get_mix_quantity(mix_models=self.mix_models,
method_name='get_SoR',
raise_error=raise_error,
raise_warning=raise_warning,
default_value=0.,
T=T, **kwargs))
return SoR
def _shomate_CpoR(T, A, B, C, D, E):
"""
Helper function to fit shomate heat capacity.
Paramters
---------
T - float
Temperature in K
A, B, C, D, E - float
Shomate parameters
Returns
-------
CpoR - float
Dimensionless heat capacity
"""
a = np.array([A, B, C, D, E, 0., 0., 0.])
if not _is_iterable(T):
T = [T]
T = np.array(T)
return get_shomate_CpoR(a=a, T=T)
def _fit_CpoR(T, CpoR, T_mid=None):
"""Fit a[0]-a[4] coefficients in a_low and a_high attributes given the
dimensionless heat capacity data
Parameters
----------
T : (N,) `numpy.ndarray`_
Temperatures in K
CpoR : (N,) `numpy.ndarray`_
Dimensionless heat capacity
T_mid : float or iterable of float, optional
Guess for T_mid. If float, only uses that value for T_mid. If
list, finds the best fit for each element in the list. If None,
a range of T_mid values are screened between the lowest value
and highest value of T.
Returns
-------
a_low : (7,) `numpy.ndarray`_
Lower coefficients of NASA polynomial
a_high : (7,) `numpy.ndarray`_
Higher coefficients of NASA polynomial
T_mid : float
Temperature in K used to split the CpoR data
.. _`numpy.ndarray`: https://docs.scipy.org/doc/numpy-1.14.0/reference/generated/numpy.ndarray.html
"""
# If the Cp/R does not vary with temperature (occurs when no
# vibrational frequencies are listed), return default values
if (np.isclose(np.mean(CpoR), 0.) and np.isnan(variation(CpoR))) \
or np.isclose(variation(CpoR), 0.) \
or any([np.isnan(x) for x in CpoR]):
T_mid = T[int(len(T) / 2)]
a_low = np.zeros(7)
a_high = np.zeros(7)
return a_low, a_high, T_mid
# If T_mid not specified, generate range between 6th smallest data point
# and 6th largest data point
if T_mid is None:
T_mid = T[5:-5]
# If a single value for T_mid is chosen, convert to a tuple
if not _is_iterable(T_mid):
T_mid = (T_mid, )
# Initialize parameters for T_mid optimization
mse_list = []
prev_mse = np.inf
all_a_low = []
all_a_high = []
for T_m in T_mid:
# Generate temperature data
(mse, a_low, a_high) = _get_CpoR_MSE(T=T, CpoR=CpoR, T_mid=T_m)
mse_list.append(mse)
all_a_low.append(a_low)
all_a_high.append(a_high)
# Check if the optimum T_mid has been found by determining if the
# fit MSE value for the current T_mid is higher than the previous
# indicating that subsequent guesses will not improve the fit
if mse > prev_mse:
break
prev_mse = mse
# Select the optimum T_mid based on the highest fit R2 value
min_mse = min(mse_list)
min_i = np.where(min_mse == mse_list)[0][0]
T_mid_out = T_mid[min_i]
a_low_rev = all_a_low[min_i]
a_high_rev = all_a_high[min_i]
# Reverse array and append two zeros to end
empty_arr = np.zeros(2)
a_low_out = np.concatenate((a_low_rev[::-1], empty_arr))
a_high_out = np.concatenate((a_high_rev[::-1], empty_arr))
return a_low_out, a_high_out, T_mid_out
def from_statmech(cls,
name,
statmech_model,
T_low,
T_high,
T_mid=None,
references=None,
elements=None,
**kwargs):
"""Calculates the NASA polynomials using statistical mechanic models
Parameters
----------
name : str
Name of the species
statmech_model : `pMuTT.statmech.StatMech` object or class
Statistical Mechanics model to generate data
T_low : float
Lower limit temerature in K
T_high : float
Higher limit temperature in K
T_mid : float or iterable of float, optional
Guess for T_mid. If float, only uses that value for T_mid. If
list, finds the best fit for each element in the list. If None,
a range of T_mid values are screened between the 6th lowest
and 6th highest value of T.
references : `pMuTT.empirical.references.References` object
Reference to adjust enthalpy
elements : dict
Composition of the species.
Keys of dictionary are elements, values are stoichiometric
values in a formula unit.
e.g. CH3OH can be represented as:
{'C': 1, 'H': 4, 'O': 1,}.
kwargs : keyword arguments
Used to initalize ``statmech_model`` or ``EmpiricalBase``
attributes to be stored.
Returns
-------
Nasa : Nasa object
Nasa object with polynomial terms fitted to data.
"""
# Initialize the StatMech object
if inspect.isclass(statmech_model):
statmech_model = statmech_model(**kwargs)
# Generate data
T = np.linspace(T_low, T_high)
if T_mid is not None:
# Check to see if specified T_mid's are in T and, if not,
# insert them into T.
# If a single value for T_mid is chosen, convert to a tuple
if not _is_iterable(T_mid):
T_mid = (T_mid, )
for x in range(0, len(T_mid)):
if np.where(T == T_mid[x])[0].size == 0:
# Insert T_mid's into T and save position
Ts_index = np.where(T > T_mid[x])[0][0]
T = np.insert(T, Ts_index, T_mid[x])
CpoR = np.array([statmech_model.get_CpoR(T=T_i) for T_i in T])
T_ref = c.T0('K')
HoRT_ref = statmech_model.get_HoRT(T=T_ref)
# Add contribution of references
if references is not None:
descriptor_name = references.descriptor
if descriptor_name == 'elements':
descriptors = elements
else:
descriptors = kwargs[descriptor_name]
HoRT_ref += references.get_HoRT_offset(descriptors=descriptors,
T=T_ref)
SoR_ref = statmech_model.get_SoR(T=T_ref)
return cls.from_data(name=name,
T=T,
CpoR=CpoR,
T_ref=T_ref,
HoRT_ref=HoRT_ref,
SoR_ref=SoR_ref,
T_mid=T_mid,
statmech_model=statmech_model,
elements=elements,
references=references,
**kwargs)