def fugacity_coefficient(self, P, rho, xi, T, dy=1e-5, log_method=True):
"""
Compute fugacity coefficient.
Parameters
----------
P : float
Pressure of the system [Pa]
rho : float
Molar density of system [:math:`mol/m^3`]
T : float
Temperature of the system [K]
xi : list[float]
Mole fraction of each component, sum(xi) should equal 1.0
log_method : bool, Optional, default=False
Choose to use a log transform in central difference method. This allows easier calculations for very small numbers.
Returns
-------
fugacity_coefficient : numpy.ndarray
Array of fugacity coefficient values for each component
"""
if len(xi) != self.number_of_components:
raise ValueError(
"Number of components in mole fraction list, {}, doesn't match self.number_of_components, {}"
.format(len(xi), self.number_of_components))
if gtb.isiterable(T):
if len(T) == 1:
T = T[0]
else:
raise ValueError("Temperature must be given as a scalar.")
if gtb.isiterable(rho):
if len(rho) == 1:
rho = rho[0]
else:
raise ValueError("Density must be given as a scalar.")
if gtb.isiterable(P):
if len(P) == 1:
P = P[0]
else:
raise ValueError("Pressure must be given as a scalar.")
rho = self._check_density(rho)
logZ = np.log(P / (rho * T * constants.R))
Ares = self.residual_helmholtz_energy(rho, T, xi)
dAresdrho = tb.partial_density_central_difference(
xi,
rho,
T,
self.residual_helmholtz_energy,
step_size=dy,
log_method=True)
phi = np.exp(Ares + rho * dAresdrho - logZ)
return phi
def pressure(self, rho, T, xi):
"""
Compute pressure given system information
Parameters
----------
rho : numpy.ndarray
Number density of system [:math:`mol/m^3`]
T : float
Temperature of the system [K]
xi : list[float]
Mole fraction of each component
Returns
-------
P : numpy.ndarray
Array of pressure values [Pa] associated with each density and so equal in length
"""
if T != self.T:
self.T = T
self._calc_temp_dependent_parameters(T)
self._calc_mixed_parameters(xi, T)
if not gtb.isiterable(rho):
rho = np.array([rho])
elif not isinstance(rho, np.ndarray):
rho = np.array(rho)
P = constants.R * self.T * rho / (
1 - self.eos_dict["bij"] * rho) - rho**2 * self.eos_dict["aij"] / (
(1 + self.eos_dict["bij"] * rho) + rho * self.eos_dict["bij"] *
(1 - self.eos_dict["bij"] * rho))
return P
def reformat_output(cluster):
r"""
Takes a list of lists that contain thermo output of lists and floats and reformats it into a 2D numpy array.
Parameters
----------
cluster : list[list[list/floats]]
A list of lists, where the inner list is made up of lists and floats
Returns
-------
matrix : numpy.ndarray
A 2D matrix
len_cluster : list
a list of lengths for each of the columns (whether 1 for float, or len(list))
"""
# if input is a list or array
if len(cluster) == 1:
matrix = np.transpose(np.array(cluster[0]))
if not gtb.isiterable(cluster[0]):
len_cluster = [1]
else:
len_cluster = [len(cluster[0])]
# If list of lists or arrays
else:
# Obtain dimensions of final matrix
len_cluster = []
for i, tmp_cluster in enumerate(cluster):
if gtb.isiterable(tmp_cluster[0]):
len_cluster.append(len(tmp_cluster[0]))
else:
len_cluster.append(1)
matrix_tmp = np.zeros([len(cluster[0]), sum(len_cluster)])
# Transfer information to final matrix
ind = 0
for i, val in enumerate(cluster):
try:
matrix = np.zeros([len(val[0]), len(val)])
except Exception:
matrix = np.zeros([1, len(val)])
for j, tmp in enumerate(
val
): # yes, this is a simple transpose, but for some reason a numpy array of np arrays wouldn't transpose
matrix[:, j] = tmp
l = len_cluster[i]
if l == 1:
matrix_tmp[:, ind] = np.array(matrix)
ind += 1
else:
if len(matrix) == 1:
matrix = matrix[0]
for j in range(l):
matrix_tmp[:, ind] = matrix[j]
ind += 1
matrix = np.array(matrix_tmp)
return matrix, len_cluster
def __init__(self, data_dict):
super().__init__(data_dict)
# If required items weren't defined, set defaults
self.name = "saturation_properties"
if self.thermodict["calculation_type"] == None:
self.thermodict["calculation_type"] = "saturation_properties"
tmp = {
"min_density_fraction": (1.0 / 80000.0),
"density_increment": 10.0,
"max_volume_increment": 1.0e-4,
}
if "density_opts" in self.thermodict:
tmp.update(self.thermodict["density_opts"])
self.thermodict["density_opts"] = tmp
# Extract system data
if "xi" in data_dict:
self.thermodict["xilist"] = data_dict["xi"]
del data_dict["xi"]
if "yi" in data_dict:
self.thermodict["xilist"] = data_dict["yi"]
logger.info("Vapor mole fraction recorded as 'xi'")
del data_dict["yi"]
if "T" in data_dict:
self.thermodict["Tlist"] = data_dict["T"]
del data_dict["T"]
if "P" in data_dict:
self.thermodict["Psat"] = data_dict["P"]
del data_dict["P"]
if "P" in self.weights:
if gtb.isiterable(self.weights["P"]) and len(
self.weights["P"]) != len(self.thermodict["Psat"]):
raise ValueError(
"Array of weights for '{}' values not equal to number of experimental values given."
.format("P"))
else:
self.weights["Psat"] = self.weights.pop("P")
self.thermodict.update(data_dict)
thermo_keys = ["xilist", "Tlist"]
self.result_keys = ["rhol", "rhov", "Psat"]
key_list = list(set(thermo_keys + self.result_keys))
self.thermodict.update(gtb.check_length_dict(self.thermodict,
key_list))
for key in self.result_keys:
if key in self.thermodict:
self.npoints = np.size(self.thermodict[key])
break
if "xilist" not in self.thermodict and self.Eos.number_of_components > 1:
raise ValueError(
"Ambiguous instructions. Include xi to define intended component to obtain saturation properties"
)
thermo_defaults = [
np.array([[1.0] for x in range(self.npoints)]),
constants.standard_temperature,
]
self.thermodict.update(
gtb.set_defaults(self.thermodict,
thermo_keys,
thermo_defaults,
lx=self.npoints))
self.weights.update(
gtb.check_length_dict(self.weights,
self.result_keys,
lx=self.npoints))
self.weights.update(
gtb.set_defaults(self.weights, self.result_keys, 1.0))
if "Tlist" not in self.thermodict:
raise ImportError(
"Given saturation data, value(s) for T should have been provided."
)
tmp = ["Psat", "rhol", "rhov"]
if not any([x in self.thermodict for x in tmp]):
raise ImportError(
"Given saturation data, values for Psat, rhol, and/or rhov should have been provided."
)
logger.info(
"Data type 'saturation_properties' initiated with calculation_type, {}, and data types: {}.\nWeight data by: {}"
.format(
self.thermodict["calculation_type"],
", ".join(self.result_keys),
self.weights,
))
def fugacity_coefficient(self, P, rho, xi, T):
r"""
Compute fugacity coefficient
Parameters
----------
P : float
Pressure of the system [Pa]
rho : float
Molar density of system [:math:`mol/m^3`]
T : float
Temperature of the system [K]
xi : list[float]
Mole fraction of each component
Returns
-------
fugacity_coefficient : numpy.ndarray
:math:`\phi_i`, Array of fugacity coefficient values for each component
"""
if gtb.isiterable(T):
if len(T) == 1:
T = T[0]
else:
raise ValueError("Temperature must be given as a scalar.")
if gtb.isiterable(rho):
if len(rho) == 1:
rho = rho[0]
else:
raise ValueError("Density must be given as a scalar.")
if gtb.isiterable(P):
if len(P) == 1:
P = P[0]
else:
raise ValueError("Pressure must be given as a scalar.")
if T != self.T:
self.T = T
self._calc_temp_dependent_parameters(T)
self._calc_mixed_parameters(xi, T)
tmp_RT = constants.R * T
Z = P / (tmp_RT * rho)
Ai = self.eos_dict["ai"] * self.eos_dict["alpha"] * P / tmp_RT**2
Bi = self.eos_dict["bi"] * P / tmp_RT
B = self.eos_dict["bij"] * P / tmp_RT
A = self.eos_dict["aij"] * P / tmp_RT**2
sqrt2 = np.sqrt(2.0)
tmp1 = (A / (2.0 * sqrt2 * B) * np.log(
(Z + (1 + sqrt2) * B) / (Z + (1 - sqrt2) * B)))
tmp3 = Bi * (Z - 1) / B - np.log(Z - B)
tmp2 = np.zeros(len(xi))
index = range(len(xi))
for i in index:
Aij = np.zeros(len(xi))
for j in index:
Aij[j] = np.sqrt(
Ai[i] * Ai[j]) * (1.0 - self.eos_dict["kij"][i][j])
tmp2[i] = Bi[i] / B - 2 * np.sum(xi * Aij) / A
phi = np.exp(tmp1 * tmp2 + tmp3)
return phi
def obj_function_form(
data_test,
data0,
weights=1.0,
method="average-squared-deviation",
nan_number=1000,
nan_ratio=0.1,
):
"""
Sets objective functional form
Note that if the result is np.nan, that point is removed from the list for the purposes of averaging.
Parameters
----------
data_test : numpy.ndarray
Data that is being assessed. Array of data of the same length as ``data_test``
data0 : numpy.ndarray
Reference data for comparison
weights : (numpy.ndarray or float), Optional, default=1.0
Can be a float or array of data of the same length as ``data_test``. Allows the user to tune the importance of various data points.
method : str, Optional, default="mean-squared-relative-error"
Keyword used to choose the functional form. Can be:
- average-squared-deviation: :math:`\sum{(\\frac{data\_test-data0}{data0})^2}/N`
- sum-squared-deviation: :math:`\sum{(\\frac{data\_test-data0}{data0})^2}`
- sum-squared-deviation-boltz: :math:`\sum{(\\frac{data\_test-data0}{data0})^2 exp(\\frac{data\_test\_min-data\_test}{|data\_test\_min|})}` [DOI: 10.1063/1.2181979]
- sum-deviation-boltz: :math:`\sum{\\frac{data\_test-data0}{data0} exp(\\frac{data\_test\_min-data\_test}{|data\_test\_min|})}` [DOI: 10.1063/1.2181979]
- percent-absolute-average-deviation: :math:`\sum{(\\frac{data\_test-data0}{data0})^2}/N \\times 100`
nan_ratio : float, Optional, default=0.1
If more than "nan_ratio*100" percent of the calculated data failed to produce NaN, increase the objective value by the number of entries where data_test is NaN times ``nan_number``.
nan_number : float, Optional, default=1000
If a thermodynamic calculation produces NaN, add this quantity to the objective value. (See nan_ratio)
Returns
-------
obj_value : float
Objective value given the calculated and reference information
"""
if np.size(data0) != np.size(data_test):
raise ValueError(
"Input data of length, {}, must be the same length as reference data of length {}"
.format(len(data_test), len(data0)))
if np.size(weights) > 1 and np.size(weights) != np.size(data_test):
raise ValueError(
"Weight for data is provided as an array of length, {}, but must be length, {}."
.format(len(weights), len(data_test)))
data_tmp = np.array([(data_test[i] - data0[i]) / data0[i]
for i in range(len(data_test))
if not np.isnan((data_test[i] - data0[i]) / data0[i])
])
if gtb.isiterable(weights):
weight_tmp = np.array([
weights[i] for i in range(len(data_test))
if not np.isnan((data_test[i] - data0[i]) / data0[i])
])
else:
weight_tmp = weights
if method == "average-squared-deviation":
obj_value = np.mean(data_tmp**2 * weight_tmp)
elif method == "sum-squared-deviation":
obj_value = np.sum(data_tmp**2 * weight_tmp)
elif method == "sum-squared-deviation-boltz":
data_min = np.min(data_tmp)
obj_value = np.sum(data_tmp**2 * weight_tmp * np.exp(
(data_min - data_tmp) / np.abs(data_min)))
elif method == "sum-deviation-boltz":
data_min = np.min(data_tmp)
obj_value = np.sum(data_tmp * weight_tmp * np.exp(
(data_min - data_tmp) / np.abs(data_min)))
elif method == "percent-absolute-average-deviation":
obj_value = np.mean(np.abs(data_tmp) * weight_tmp) * 100
if len(data_tmp) == 0:
obj_value = np.nan
if len(data_test) != len(data_tmp):
tmp = 1 - len(data_tmp) / len(data_test)
if tmp > nan_ratio:
obj_value += (len(data_test) - len(data_tmp)) * nan_number
logger.debug(
"Values of NaN were removed from objective value calculation, nan_ratio {} > {}, augment obj. value"
.format(tmp, nan_ratio))
else:
logger.debug(
"Values of NaN were removed from objective value calculation, nan_ratio {} < {}"
.format(tmp, nan_ratio))
return obj_value
