pyEQL 0.12.2__py2.py3-none-any.whl → 0.14.0__py2.py3-none-any.whl

pyEQL/engines.py

@@ -1,7 +1,7 @@
 """
 pyEQL engines for computing aqueous equilibria (e.g., speciation, redox, etc.).
 
-:copyright: 2013-2023 by Ryan S. Kingsbury
+:copyright: 2013-2024 by Ryan S. Kingsbury
 :license: LGPL, see LICENSE for more details.
 
 """
@@ -52,8 +52,7 @@ class EOS(ABC):
             Quantity: dimensionless quantity object
 
         Raises:
-            ValueError if the calculation cannot be completed, e.g. due to insufficient number of
-            parameters.
+            ValueError if the calculation cannot be completed, e.g. due to insufficient number of parameters.
         """
 
     @abstractmethod
@@ -68,8 +67,7 @@ class EOS(ABC):
             Quantity: dimensionless molal scale osmotic coefficient
 
         Raises:
-            ValueError if the calculation cannot be completed, e.g. due to insufficient number of
-            parameters.
+            ValueError if the calculation cannot be completed, e.g. due to insufficient number of parameters.
         """
 
     @abstractmethod
@@ -84,8 +82,7 @@ class EOS(ABC):
             Quantity: solute volume in L
 
         Raises:
-            ValueError if the calculation cannot be completed, e.g. due to insufficient number of
-            parameters.
+            ValueError if the calculation cannot be completed, e.g. due to insufficient number of parameters.
         """
 
     @abstractmethod
@@ -102,8 +99,7 @@ class EOS(ABC):
             Nothing. The speciation of the Solution is modified in-place.
 
         Raises:
-            ValueError if the calculation cannot be completed, e.g. due to insufficient number of
-            parameters or lack of convergence.
+            ValueError if the calculation cannot be completed, e.g. due to insufficient number of parameters or lack of convergence.
         """
 
 
@@ -163,7 +159,15 @@ class NativeEOS(EOS):
             Path(os.path.dirname(__file__)) / "database" if self.phreeqc_db in ["llnl.dat", "geothermal.dat"] else None
         )
         # create the PhreeqcPython instance
-        self.pp = PhreeqPython(database=self.phreeqc_db, database_directory=self.db_path)
+        # try/except added to catch unsupported architectures, such as Apple Silicon
+        try:
+            self.pp = PhreeqPython(database=self.phreeqc_db, database_directory=self.db_path)
+        except OSError:
+            logger.error(
+                "OSError encountered when trying to instantiate phreeqpython. Most likely this means you"
+                " are running on an architecture that is not supported by PHREEQC, such as Apple M1/M2 chips."
+                " pyEQL will work, but equilibrate() will have no effect."
+            )
         # attributes to hold the PhreeqPython solution.
         self.ppsol = None
         # store the solution composition to see whether we need to re-instantiate the solution
@@ -238,7 +242,7 @@ class NativeEOS(EOS):
             self.ppsol = None
 
     def get_activity_coefficient(self, solution, solute):
-        """
+        r"""
         Whenever the appropriate parameters are available, the Pitzer model [may]_ is used.
         If no Pitzer parameters are available, then the appropriate equations are selected
         according to the following logic: [stumm]_.
@@ -250,17 +254,17 @@ class NativeEOS(EOS):
 
         The ionic strength, activity coefficients, and activities are all
         calculated based on the molal (mol/kg) concentration scale. If a different
-        scale is given as input, then the molal-scale activity coefficient :math:`\\gamma_\\pm` is
+        scale is given as input, then the molal-scale activity coefficient :math:`\gamma_\pm` is
         converted according to [rbs]_
 
-        .. math:: f_\\pm = \\gamma_\\pm * (1 + M_w \\sum_i \\nu_i \\m_i)
+        .. math:: f_\pm = \gamma_\pm * (1 + M_w \sum_i \nu_i m_i)
 
-        .. math:: y_\\pm = m \\rho_w / C \\gamma_\\pm
+        .. math:: y_\pm = \frac{m \rho_w}{C \gamma_\pm}
 
-        where :math:`f_\\pm` is the rational activity coefficient, :math:`M_w` is
+        where :math:`f_\pm` is the rational activity coefficient, :math:`M_w` is
         the molecular weight of water, the summation represents the total molality of
-        all solute  species, :math:`y_\\pm` is the molar activity coefficient,
-        :math:`\\rho_w` is the density of pure water, :math:`m` and :math:`C` are
+        all solute  species, :math:`y_\pm` is the molar activity coefficient,
+        :math:`\rho_w` is the density of pure water, :math:`m` and :math:`C` are
         the molal and molar concentrations of the chosen salt (not individual solute), respectively.
 
         Args:
@@ -280,11 +284,11 @@ class NativeEOS(EOS):
             molality," which is the molality that would result in a single-salt
             mixture with the same total ionic strength as the multicomponent solution.
 
-            .. math:: m_effective = 2 I \\over (\\nu_{+} z_{+}^2 + \\nu{_}- z_{-} ^2)
+            .. math:: m_{effective} = \frac{2 I}{(\nu_{+} z_{+}^2 + \nu_{-}- z_{-}^2)}
 
         References:
-        .. [may] May, P. M., Rowland, D., Hefter, G., & Königsberger, E. (2011).
-               A Generic and Updatable Pitzer Characterization of Aqueous Binary Electrolyte Solutions at 1 bar and 25 °C.
+            .. [may] May, P. M., Rowland, D., Hefter, G., & Königsberger, E. (2011).
+                A Generic and Updatable Pitzer Characterization of Aqueous Binary Electrolyte Solutions at 1 bar and 25 °C.
                *Journal of Chemical & Engineering Data*, 56(12), 5066-5077. doi:10.1021/je2009329
 
         .. [stumm] Stumm, Werner and Morgan, James J. *Aquatic Chemistry*, 3rd ed,
@@ -297,12 +301,11 @@ class NativeEOS(EOS):
                desalination calculations for mixed electrolyte solutions with comparison to seawater. Desalination 2013, 318, 34-47.
 
         See Also:
-            get_ionic_strength
-            get_salt
-            activity_correction.get_activity_coefficient_debyehuckel
-            activity_correction.get_activity_coefficient_guntelberg
-            activity_correction.get_activity_coefficient_davies
-            activity_correction.get_activity_coefficient_pitzer
+            :attr:`pyEQL.solution.Solution.ionic_strength`
+            :func:`pyEQL.activity_correction.get_activity_coefficient_debyehuckel`
+            :func:`pyEQL.activity_correction.get_activity_coefficient_guntelberg`
+            :func:`pyEQL.activity_correction.get_activity_coefficient_davies`
+            :func:`pyEQL.activity_correction.get_activity_coefficient_pitzer`
         """
         # identify the predominant salt that this ion is a member of
         salt = None
@@ -418,7 +421,7 @@ class NativeEOS(EOS):
         return molal
 
     def get_osmotic_coefficient(self, solution):
-        """
+        r"""
         Return the *molal scale* osmotic coefficient of solute, given a Solution
         object.
 
@@ -427,28 +430,27 @@ class NativeEOS(EOS):
         coefficient of 1.
 
         If the 'rational' scale is given as input, then the molal-scale osmotic
-        coefficient :math:`\\phi` is converted according to [rbs]_
+        coefficient :math:`\phi` is converted according to [rbs]_
 
-        .. math:: g = - \\phi * M_{w} \\sum_{i} \\nu_{i} \\m_{i}) / \\ln x_{w}
+        .. math:: g = - \phi M_{w} \frac{\sum_{i} \nu_{i} m_{i}}{\ln x_{w}}
 
         where :math:`g` is the rational osmotic coefficient, :math:`M_{w}` is
         the molecular weight of water, the summation represents the total molality of
         all solute  species, and :math:`x_{w}` is the mole fraction of water.
 
         Args:
-            scale:
-            The concentration scale for the returned osmotic coefficient. Valid options are "molal",
-            "rational" (i.e., mole fraction), and "fugacity".  By default, the molal scale osmotic
-            coefficient is returned.
+            scale: The concentration scale for the returned osmotic coefficient. Valid options are "molal",
+                "rational" (i.e., mole fraction), and "fugacity".  By default, the molal scale osmotic
+                coefficient is returned.
 
-        Returns
+        Returns:
             Quantity:
                 The osmotic coefficient
 
         See Also:
-            get_water_activity
-            get_ionic_strength
-            get_salt
+            :meth:`pyEQL.solution.Solution.get_water_activity`
+            :meth:`pyEQL.solution.Solution.get_salt`
+            :attr:`pyEQL.solution.Solution.ionic_strength`
 
         Notes:
             For multicomponent mixtures, pyEQL adopts the "effective Pitzer model"
@@ -469,8 +471,7 @@ class NativeEOS(EOS):
             the author confirmed that the weight factor should be the true molality, and that is what is implemented
             in pyEQL.)
 
-        References
-
+        References:
             .. [may] May, P. M., Rowland, D., Hefter, G., & Königsberger, E. (2011).
                 A Generic and Updatable Pitzer Characterization of Aqueous Binary Electrolyte Solutions at 1 bar and
                 25 °C. Journal of Chemical & Engineering Data, 56(12), 5066-5077. doi:10.1021/je2009329
@@ -482,7 +483,6 @@ class NativeEOS(EOS):
                behavior on desalination calculations for mixed electrolyte solutions with comparison to seawater. Desalination 2013, 318, 34-47.
 
         Examples:
-
             >>> s1 = pyEQL.Solution([['Na+','0.2 mol/kg'],['Cl-','0.2 mol/kg']])
             >>> s1.get_osmotic_coefficient()
             <Quantity(0.923715281, 'dimensionless')>

pyEQL/equilibrium.py

@@ -4,7 +4,7 @@ redox, complexation, etc.).
 
 NOTE: these methods are not currently used but are here for the future.
 
-:copyright: 2013-2023 by Ryan S. Kingsbury
+:copyright: 2013-2024 by Ryan S. Kingsbury
 :license: LGPL, see LICENSE for more details.
 
 """
@@ -36,23 +36,15 @@ SPECIES_ALIAISES = {
 
 def adjust_temp_pitzer(c1, c2, c3, c4, c5, temp, temp_ref=ureg.Quantity("298.15 K")):
     """
-    Calculate a parameter for the Pitzer model based on temperature-dependent
-    coefficients c1,c2,c3,c4,and c5.
-
-    Parameters
-    ----------
-    c1, c2, c3, c4, c5: float
-                Temperature-dependent coefficients for the pitzer parameter of
-                interest.
-    temp: Quantity
-                The temperature at which the Pitzer parameter is to be calculated
-    temp_ref: Quantity, optional
-                The reference temperature on which the parameters are based.
-                298.15 K if omitted.
-
-    As described in the PHREEQC documentation
+    Calculate a parameter for the Pitzer model based on temperature-dependent coefficients c1,c2,c3,c4,and c5.
 
+    Args:
+        c1, c2, c3, c4, c5 (float): Temperature-dependent coefficients for the pitzer parameter of interest.
+        temp (Quantity): The temperature at which the Pitzer parameter is to be calculated.
+        temp_ref (Quantity, optional): The reference temperature on which the parameters are based. Defaults to 298.15 K if omitted.
 
+    Note:
+        As described in the PHREEQC documentation.
     """
     return (
         c1
@@ -65,53 +57,37 @@ def adjust_temp_pitzer(c1, c2, c3, c4, c5, temp, temp_ref=ureg.Quantity("298.15
 
 
 def adjust_temp_vanthoff(equilibrium_constant, enthalpy, temperature, reference_temperature=ureg.Quantity(25, "degC")):
-    r"""(float,float,number, optional number) -> float.
-
+    r"""
     Adjust a reaction equilibrium constant from one temperature to another.
 
-    Parameters
-    ----------
-    equilibrium_constant : float
-                           The reaction equilibrium constant for the reaction
-    enthalpy : Quantity
-               The enthalpy change (delta H) for the reaction in kJ/mol. Assumed
-               independent of temperature (see Notes).
-    temperature : Quantity
-                  the desired reaction temperature in degrees Celsius
-    reference_temperature : Quantity, optional
-                      the temperature at which equilibrium_constant is valid. (25 degrees C if omitted).
-
-    Returns
-    -------
-    float
-        adjusted reaction equilibrium constant
-
-    Notes
-    -----
-    This function implements the Van't Hoff equation to adjust measured
-    equilibrium constants to other temperatures.
-
-    .. math::
-        ln(K2 / K1) = {\delta H \over R} ( {1 \over T_1} - {1 \over T_2} )
-
-    This implementation assumes that the enthalpy is independent of temperature
-    over the range of interest.
-
-    References
-    ----------
-    Stumm, Werner and Morgan, James J. Aquatic Chemistry, 3rd ed, pp 53.
-        Wiley Interscience, 1996.
+    Args:
+        equilibrium_constant (float): The reaction equilibrium constant for the reaction.
+        enthalpy (Quantity): The enthalpy change (delta H) for the reaction in kJ/mol. Assumed independent of temperature (see Notes).
+        temperature (Quantity): The desired reaction temperature in degrees Celsius.
+        reference_temperature (Quantity, optional): The temperature at which equilibrium_constant is valid. Defaults to 25 degrees C if omitted.
 
-    Examples:
-    --------
-    >>> adjust_temp_vanthoff(0.15,ureg.Quantity('-197.6 kJ/mol'),ureg.Quantity('42 degC'),ureg.Quantity(' 25degC')) #doctest: +ELLIPSIS
-    0.00203566...
+    Returns:
+        float: The adjusted reaction equilibrium constant.
+
+    Note:
+        This function implements the Van't Hoff equation to adjust measured equilibrium constants to other temperatures.
+
+        .. math::
+            ln(K2 / K1) = {\delta H \over R} ( {1 \over T_1} - {1 \over T_2} )
+
+        This implementation assumes that the enthalpy is independent of temperature over the range of interest.
+
+    References:
+        Stumm, Werner and Morgan, James J. Aquatic Chemistry, 3rd ed, pp 53. Wiley Interscience, 1996.
 
-    If the 'ref_temperature' parameter is omitted, a default of 25 C is used.
+    Examples:
+        >>> adjust_temp_vanthoff(0.15,ureg.Quantity('-197.6 kJ/mol'),ureg.Quantity('42 degC'),ureg.Quantity(' 25degC')) #doctest: +ELLIPSIS
+        0.00203566...
 
-    >>> adjust_temp_vanthoff(0.15,ureg.Quantity('-197.6 kJ/mol'),ureg.Quantity('42 degC')) #doctest: +ELLIPSIS
-    0.00203566...
+        If the 'ref_temperature' parameter is omitted, a default of 25 C is used.
 
+        >>> adjust_temp_vanthoff(0.15,ureg.Quantity('-197.6 kJ/mol'),ureg.Quantity('42 degC')) #doctest: +ELLIPSIS
+        0.00203566...
     """
     output = equilibrium_constant * math.exp(
         enthalpy / ureg.R * (1 / reference_temperature.to("K") - 1 / temperature.to("K"))
@@ -131,51 +107,31 @@ def adjust_temp_arrhenius(
     temperature,
     reference_temperature=ureg.Quantity(25, "degC"),
 ):
-    r"""(float,float,number, optional number) -> float.
-
+    r"""
     Adjust a reaction equilibrium constant from one temperature to another.
 
-    Parameters
-    ----------
-    rate_constant : Quantity
-                The parameter value (usually a rate constant) being adjusted
-    activation_energy : Quantity
-               The activation energy of the process, in kJ/mol
-    temperature : Quantity
-                  the desired reaction temperature.
-    reference_temperature : Quantity, optional
-                      the temperature at which equilibrium_constant is valid
-                      Defaults to 25 degrees C if omitted.
-
-    Returns
-    -------
-    Quantity
-        The adjusted reaction equilibrium constant
+    Args:
+        rate_constant (Quantity): The parameter value (usually a rate constant) being adjusted.
+        activation_energy (Quantity): The activation energy of the process, in kJ/mol.
+        temperature (Quantity): The desired reaction temperature.
+        reference_temperature (Quantity, optional): The temperature at which equilibrium_constant is valid. Defaults to 25 degrees C if omitted.
 
-    See Also:
-    --------
-    kelvin
+    Returns:
+        Quantity: The adjusted reaction equilibrium constant.
 
-    Notes
-    -----
-    This function implements the Arrhenius equation to adjust measured rate
-    constants to other temperatures.
-    TODO - add better reference
+    Notes:
+        This function implements the Arrhenius equation to adjust measured rate constants to other temperatures.
+        TODO - add better reference
 
-    .. math::
-        ln(\\frac{K2}{K1} = \\frac{E_a}{R} ( \\frac{1}{T_{1}} - {\\frac{1}{T_2}} )
-
-    References
-    ----------
-
-    http://chemwiki.ucdavis.edu/Physical_Chemistry/Kinetics/Reaction_Rates/Temperature_Dependence_of_Reaction_Rates/Arrhenius_Equation
+        .. math::
+            ln(\frac{K2}{K1} = \frac{E_a}{R} ( \frac{1}{T_{1}} - {\frac{1}{T_2}} )
 
+    References:
+        http://chemwiki.ucdavis.edu/Physical_Chemistry/Kinetics/Reaction_Rates/Temperature_Dependence_of_Reaction_Rates/Arrhenius_Equation
 
     Examples:
-    --------
-    >>> adjust_temp_arrhenius(7,900*ureg.Quantity('kJ/mol'),37*ureg.Quantity('degC'),97*ureg.Quantity('degC')) #doctest: +ELLIPSIS
-    1.8867225...e-24
-
+        >>> adjust_temp_arrhenius(7,900*ureg.Quantity('kJ/mol'),37*ureg.Quantity('degC'),97*ureg.Quantity('degC')) #doctest: +ELLIPSIS
+        1.8867225...e-24
     """
     output = rate_constant * math.exp(
         activation_energy / ureg.R * (1 / reference_temperature.to("K") - 1 / temperature.to("K"))
@@ -189,98 +145,76 @@ def adjust_temp_arrhenius(
 
 
 def alpha(n, pH, pKa_list):
-    """Returns the acid-base distribution coefficient (alpha) of an acid in the
-        n-deprotonated form at a given pH.
-
-    Parameters
-    ----------
-    n : int
-        The number of protons that have been lost by the desired form of the
-        acid. Also the subscript on the alpha value. E.g. for bicarbonate
-        (HCO3-), n=1 because 1 proton has been lost from the fully-protonated
-        carbonic acid (H2CO3) form.
-    pH : float or int
-            The pH of the solution.
-    pKa_list : list of floats or ints
-                The pKa values (negative log of equilibrium constants) for the acid
-                of interest. There must be a minimum of n pKa values in the list.
-
-    Returns
-    -------
-        float
-            The fraction of total acid present in the specified form.
-
-    Notes
-    -----
-        The acid-base cient is calculated as follows: [stm]_
+    r"""
+    Returns the acid-base distribution coefficient (alpha) of an acid in the n-deprotonated form at a given pH.
+
+    Args:
+        n (int): The number of protons that have been lost by the desired form of the acid. Also the subscript on the
+            alpha value. E.g. for bicarbonate (HCO3-), n=1 because 1 proton has been lost from the fully-protonated
+            carbonic acid (H2CO3) form.
+        pH (float or int): The pH of the solution.
+        pKa_list (list of floats or ints): The pKa values (negative log of equilibrium constants) for the acid of
+            interest. There must be a minimum of n pKa values in the list.
+
+    Returns:
+        float: The fraction of total acid present in the specified form.
+
+    Notes:
+        The acid-base coefficient is calculated as follows: [stm]_
 
         .. math::
 
-            \\alpha_n = \\frac{term_n}{[H+]^n + k_{a1}[H+]^{n-1} + k_{a1}k_{a2}[H+]^{n-2} ... k_{a1}k_{a2}...k_{an} }
+            \alpha_n = \frac{term_n}{[H+]^n + k_{a1}[H+]^{n-1} + k_{a1}k_{a2}[H+]^{n-2} ... k_{a1}k_{a2}...k_{an} }
 
         Where :math: '\term_n' refers to the nth term in the denominator, starting from 0
 
-    References
-    ----------
-        .. [stm] Stumm, Werner and Morgan, James J. Aquatic Chemistry, 3rd ed, pp 127-130. Wiley Interscience, 1996.
+    References:
+        Stumm, Werner and Morgan, James J. Aquatic Chemistry, 3rd ed, pp 127-130. Wiley Interscience, 1996.
 
     Examples:
-    --------
-    >>> alpha(1,8,[4.7]) #doctest: +ELLIPSIS
-    0.999...
-
-    The sum of all alpha values should equal 1
+        >>> alpha(1,8,[4.7]) #doctest: +ELLIPSIS
+        0.999...
 
-    >>> alpha(0,8,[6.35,10.33]) #doctest: +ELLIPSIS
-    0.021...
-    >>> alpha(1,8,[6.35,10.33]) #doctest: +ELLIPSIS
-    0.979...
-    >>> alpha(2,8,[6.35,10.33]) #doctest: +ELLIPSIS
-    2.043...e-09
+        The sum of all alpha values should equal 1
 
-    If pH is equal to one of the pKa values the function should return 0.5.
+        >>> alpha(0,8,[6.35,10.33]) #doctest: +ELLIPSIS
+        0.021...
+        >>> alpha(1,8,[6.35,10.33]) #doctest: +ELLIPSIS
+        0.979...
+        >>> alpha(2,8,[6.35,10.33]) #doctest: +ELLIPSIS
+        2.043...e-09
 
-    >>> alpha(1,6.35,[6.35,10.33])
-    0.5
+        If pH is equal to one of the pKa values the function should return 0.5.
 
+        >>> alpha(1,6.35,[6.35,10.33])
+        0.5
     """
     # generate an error if no pKa values are specified
     if len(pKa_list) == 0:
-        logger.error("No pKa values given. Cannot calculate distribution coeffiicent.")
-        return None
+        raise ValueError("No pKa values given. Cannot calculate distribution coefficient.")
 
     # generate an error if n > number of pKa values
     if len(pKa_list) < n:
-        logger.error("Insufficient number of pKa values given. Cannot calculate distribution coeffiicent.")
-        return None
+        raise ValueError("Insufficient number of pKa values given. Cannot calculate distribution coefficient.")
 
-    # convert pH to hydrogen ion concentration
-    Hplus = 10**-pH
+    # sort the pKa list
+    pKa_list = sorted(pKa_list)
 
     # determine how many protons the acid has
     num_protons = len(pKa_list)
 
     # build a list of terms where the term subscript corresponds to the list index
-    terms_list = []
-    k_term = 1
-
-    # the 'item' index counts from 0 to the number of protons, inclusive
-    for item in range(num_protons + 1):
-        # multiply the preceding k values together
-        for i in range(len(pKa_list[:item])):
-            k_term *= 10 ** -pKa_list[i]
-
-        # add the term to the list
-        terms_list.append(k_term * Hplus ** (num_protons - item))
-
-    # build the expression
-    numerator = terms_list[n]
-    denominator = 0
-    for item in terms_list:
-        denominator += item
+    terms_list = [10 ** (-pH * num_protons)]
+    for i in range(len(pKa_list)):
+        # multiply together all K values with
+        k_term = 1
+        for pK in pKa_list[0 : i + 1]:
+            k_term *= 10**-pK
+        terms_list.append(k_term * 10 ** (-pH * (num_protons - (i + 1))))
+    print(terms_list)
 
     # return the desired distribution factor
-    alpha = numerator / denominator
+    alpha = terms_list[n] / sum(terms_list)
     logger.info(
         "Calculated %s-deprotonated acid distribution coefficient of %s for pKa=%s at pH %s % n,alpha,pKa_list,pH"
     )

pyEQL/functions.py

@@ -1,7 +1,7 @@
 """
 pyEQL functions that take Solution objects as inputs or return Solution objects.
 
-:copyright: 2013-2023 by Ryan S. Kingsbury
+:copyright: 2013-2024 by Ryan S. Kingsbury
 :license: LGPL, see LICENSE for more details.
 
 """
@@ -19,7 +19,8 @@ def gibbs_mix(solution1: Solution, solution2: Solution):
     Return the Gibbs energy change associated with mixing two solutions.
 
     Args:
-        solution1, solution2: The two solutions to be mixed.
+        solution1: a solution to be mixed.
+        solution2: a solution to be mixed.
 
     Returns:
         The change in Gibbs energy associated with complete mixing of the
@@ -30,7 +31,7 @@ def gibbs_mix(solution1: Solution, solution2: Solution):
 
         .. math::
 
-            \\Delta_{mix} G = \\sum_i (n_c + n_d) R T \\ln a_b - \\sum_i n_c R T \\ln a_c - \\sum_i n_d R T \\ln a_d
+            \Delta_{mix} G = \sum_i {(n_c + n_d) R T \ln a_b} - \sum_i {n_c R T \ln a_c} - \sum_i {n_d R T \ln a_d}
 
         Where :math:`n` is the number of moles of substance, :math:`T` is the temperature in kelvin,
         and  subscripts :math:`b`, :math:`c`, and :math:`d` refer to the concentrated, dilute, and blended
@@ -41,8 +42,8 @@ def gibbs_mix(solution1: Solution, solution2: Solution):
         anion, and water).
 
     References:
-        Koga, Yoshikata, 2007. *Solution Thermodynamics and its Application to Aqueous Solutions:
-            A differential approach.* Elsevier, 2007, pp. 23-37.
+        Koga, Yoshikata, 2007. Solution Thermodynamics and its Application to Aqueous Solutions:
+            A differential approach. Elsevier, 2007, pp. 23-37.
 
     """
     concentrate = solution1
@@ -77,7 +78,7 @@ def entropy_mix(solution1: Solution, solution2: Solution):
 
         .. math::
 
-            \\Delta_{mix} S = \\sum_i (n_c + n_d) R T \\ln x_b - \\sum_i n_c R T \\ln x_c - \\sum_i n_d R T \\ln x_d
+            \Delta_{mix} S = \sum_i {(n_c + n_d) R T \ln x_b} - \sum_i {n_c R T \ln x_c} - \sum_i {n_d R T \ln x_d}
 
         Where :math:`n` is the number of moles of substance, :math:`T` is the temperature in kelvin,
         and  subscripts :math:`b`, :math:`c`, and :math:`d` refer to the concentrated, dilute, and blended
@@ -111,10 +112,10 @@ def entropy_mix(solution1: Solution, solution2: Solution):
 
 
 def donnan_eql(solution: Solution, fixed_charge: str):
-    """
+    r"""
     Return a solution object in equilibrium with fixed_charge.
 
-    Parameters:
+    Args:
         solution : Solution object
             The external solution to be brought into equilibrium with the fixed
             charges
@@ -133,19 +134,20 @@ def donnan_eql(solution: Solution, fixed_charge: str):
 
         .. math::
 
-            \\frac{a_{-}}{\\bar a_{-}}^{\\frac{1}{z_{-}} \\frac{\\bar a_{+}}{a_{+}}^{\\frac{1}{z_{+}} \
-            = exp(\\frac{\\Delta \\pi \\bar V}{{RT z_{+} \\nu_{+}}})
+            \big(\frac{a_{-}}{\bar a_{-}} \big)^(\frac{1}{z_{-})
+            \big(\frac{\bar a_{+}}{a_{+}}\big)^(\frac{1}{z_{+})
+            \exp(\frac{\Delta \pi \bar V}{RT z_{+} \nu_{+}})
 
         Where subscripts :math:`+` and :math:`-` indicate the cation and anion, respectively,
         the overbar indicates the membrane phase,
-        :math:`a` represents activity, :math:`z` represents charge, :math:`\\nu` represents the stoichiometric
+        :math:`a` represents activity, :math:`z` represents charge, :math:`\nu` represents the stoichiometric
         coefficient, :math:`V` represents the partial molar volume of the salt, and
-        :math:`\\Delta \\pi` is the difference in osmotic pressure between the membrane and the
+        :math:`\Delta \pi` is the difference in osmotic pressure between the membrane and the
         solution phase.
 
         In addition, electroneutrality must prevail within the membrane phase:
 
-        .. math:: \\bar C_{+} z_{+} + \\bar X + \\bar C_{-} z_{-} = 0
+        .. math:: \bar C_{+} z_{+} + \bar X + \bar C_{-} z_{-} = 0
 
         Where :math:`C` represents concentration and :math:`X` is the fixed charge concentration
         in the membrane or ion exchange phase.

pyEQL/logging_system.py

@@ -15,7 +15,7 @@ WARNING     -   assumptions or limitations of module output
 ERROR       -   Module could not complete a task due to invalid input or other problem
 CRITICAL    -   not used
 
-:copyright: 2013-2023 by Ryan S. Kingsbury
+:copyright: 2013-2024 by Ryan S. Kingsbury
 :license: LGPL, see LICENSE for more details.
 
 """