pyEQL 0.15.1__py2.py3-none-any.whl → 1.0.1__py2.py3-none-any.whl

pyEQL/functions.py

@@ -5,13 +5,14 @@ pyEQL functions that take Solution objects as inputs or return Solution objects.
 :license: LGPL, see LICENSE for more details.
 
 """
-import math
-from typing import Literal
 
-from monty.dev import deprecated
+import logging
+
+import numpy as np
 
 from pyEQL import Solution, ureg
-from pyEQL.logging_system import logger
+
+logger = logging.getLogger(__name__)
 
 
 def gibbs_mix(solution1: Solution, solution2: Solution):
@@ -55,7 +56,7 @@ def gibbs_mix(solution1: Solution, solution2: Solution):
     for solution in term_list:
         for solute in solution.components:
             if solution.get_amount(solute, "fraction") != 0:
-                term_list[solution] += solution.get_amount(solute, "mol") * math.log(solution.get_activity(solute))
+                term_list[solution] += solution.get_amount(solute, "mol") * np.log(solution.get_activity(solute))
 
     return (ureg.R * blend.temperature.to("K") * (term_list[blend] - term_list[concentrate] - term_list[dilute])).to(
         "J"
@@ -102,7 +103,7 @@ def entropy_mix(solution1: Solution, solution2: Solution):
     for solution in term_list:
         for solute in solution.components:
             if solution.get_amount(solute, "fraction") != 0:
-                term_list[solution] += solution.get_amount(solute, "mol") * math.log(
+                term_list[solution] += solution.get_amount(solute, "mol") * np.log(
                     solution.get_amount(solute, "fraction")
                 )
 
@@ -242,7 +243,7 @@ def donnan_eql(solution: Solution, fixed_charge: str):
 
         return (act_cation_mem / act_cation_soln) ** (1 / z_cation) * (act_anion_soln / act_anion_mem) ** (
             1 / z_anion
-        ) - math.exp(delta_pi * exp_term)
+        ) - np.exp(delta_pi * exp_term)
 
     # solve the function above using one of scipy's nonlinear solvers
 
@@ -264,157 +265,3 @@ def donnan_eql(solution: Solution, fixed_charge: str):
 
     # return the equilibrated solution
     return donnan_soln
-
-
-@deprecated(
-    message="mix() is deprecated and will be removed in the next release! You can now mix solutions using the addition operator, e.g. s_mix = s1 + s2."
-)
-def mix(s1, s2):  # pragma: no cover
-    """
-    Mix two solutions together.
-
-    Args:
-        s1, s2: The two solutions to be mixed.
-
-    Returns:
-        A Solution object that represents the result of mixing s1 and s2.
-
-    Notes:
-        The initial volume of the mixed solution is set as the sum of the volumes of s1 and s2. The pressure and
-        temperature are volume-weighted averages. The pH and pE values are currently APPROXIMATE because they are
-        calculated assuming H+ and e- mix conservatively (i.e., the mixing process does not incorporate any
-        equilibration reactions or buffering). Such support is planned in a future release.
-    """
-    return s1 + s2
-
-
-@deprecated(
-    message="autogenerate() is deprecated and will be removed in the next release! Use Solution.from_preset() instead.)"
-)
-def autogenerate(
-    solution: Literal["seawater", "rainwater", "wastewater", "urine", "Ringers lactate", "normal saline"]
-):  # pragma: no cover
-    """
-    This method provides a quick way to create Solution objects representing
-    commonly-encountered solutions, such as seawater, rainwater, and wastewater.
-
-    Parameters
-    ----------
-    solution : str
-                String representing the desired solution
-                Valid entries are 'seawater', 'rainwater',
-                'wastewater',and 'urine'
-
-    Returns
-    -------
-    Solution
-        A pyEQL Solution object.
-
-    Notes
-    -----
-    The following sections explain the different solution options:
-
-    - '' - empty solution, equivalent to pyEQL.Solution()
-    - 'rainwater' - pure water in equilibrium with atmospheric CO2 at pH 6
-    - 'seawater' or 'SW'- Standard Seawater. See Table 4 of the Reference for Composition [1]_
-    - 'wastewater' or 'WW' - medium strength domestic wastewater. See Table 3-18 of [2]_
-    - 'urine' - typical human urine. See Table 3-15 of [2]_
-    - 'normal saline' or 'NS' - normal saline solution used in medicine [3]_
-    - 'Ringers lacatate' or 'RL' - Ringer's lactate solution used in medicine [4]_
-
-    References:
-    ----------
-        .. [1] Millero, Frank J. "The composition of Standard Seawater and the definition of
-            the Reference-Composition Salinity Scale." *Deep-sea Research. Part I* 55(1), 2008, 50-72.
-
-        .. [2] Metcalf & Eddy, Inc. et al. *Wastewater Engineering: Treatment and Resource Recovery*, 5th Ed.
-                McGraw-Hill, 2013.
-
-        .. [3] https://en.wikipedia.org/wiki/Saline_(medicine)
-
-        .. [4] https://en.wikipedia.org/wiki/Ringer%27s_lactate_solution
-
-    """
-    if solution == "":
-        temperature = "25 degC"
-        pressure = "1 atm"
-        pH = 7
-        solutes = []
-    elif solution == "seawater" or solution == "SW":
-        temperature = "25 degC"
-        pressure = "1 atm"
-        pH = 8.1
-        solutes = [
-            ["Na+", "10.78145 g/kg"],
-            ["Mg+2", "1.28372 g/kg"],
-            ["Ca+2", "0.41208 g/kg"],
-            ["K+", "0.39910 g/kg"],
-            ["Sr+2", "0.00795 g/kg"],
-            ["Cl-", "19.35271 g/kg"],
-            ["SO4-2", "2.71235 g/kg"],
-            ["HCO3-", "0.10481 g/kg"],
-            ["Br-", "0.06728 g/kg"],
-            ["CO3-2", "0.01434 g/kg"],
-            ["B(OH)4", "0.00795 g/kg"],
-            ["F-", "0.00130 g/kg"],
-            ["OH-", "0.00014 g/kg"],
-            ["B(OH)3", "0.01944 g/kg"],
-            ["CO2", "0.00042 g/kg"],
-        ]
-    elif solution == "rainwater":
-        temperature = "25 degC"
-        pressure = "1 atm"
-        pH = 6
-        solutes = [["HCO3-", "10^-5.5 mol/L"], ["CO3-2", "10^-9 mol/L"]]
-    elif solution == "wastewater" or solution == "WW":
-        temperature = "25 degC"
-        pressure = "1 atm"
-        pH = 7
-        solutes = [
-            ["NH3", "24.3 mg/L"],
-            ["PO4-3", "7.6 mg/L"],
-            ["C6H12O6", "410 mg/L"],
-            ["K+", "16 mg/L"],
-            ["Cl-", "59 mg/L"],
-            ["SO4-2", "26 mg/L"],
-        ]
-        logger.warning("Total organic carbon in wastewater is approximated as glucose")
-    elif solution == "urine":
-        temperature = "25 degC"
-        pressure = "1 atm"
-        pH = 7
-        solutes = [
-            ["CON2H4", "20,000 mg/L"],
-            ["C4H7N3O", "1,000 mg/L"],
-            ["C5H4N4O3", "300 mg/L"],
-            ["NH4+", "500 mg/L"],
-            ["HCO3-", "300 mg/L"],
-            ["NH4+", "500 mg/L"],
-            ["Mg+2", "100 mg/L"],
-            ["PO4-3", "1200 mg/L"],
-            ["Na+", "6000 mg/L"],
-            ["K+", "1500 mg/L"],
-            ["Cl-", "1900 mg/L"],
-            ["SO4-2", "1800 mg/L"],
-        ]
-    elif solution == "normal saline" or solution == "NS":
-        temperature = "25 degC"
-        pressure = "1 atm"
-        pH = 7
-        solutes = [["Na+", "154 mmol/L"], ["Cl-", "154 mmol/L"]]
-    elif solution == "Ringers lactate" or solution == "RL":
-        temperature = "25 degC"
-        pressure = "1 atm"
-        pH = 6.5
-        solutes = [
-            ["Na+", "130 mmol/L"],
-            ["Cl-", "109 mmol/L"],
-            ["K+", "4 mmol/L"],
-            ["Ca+2", "1.5 mmol/L"],
-            ["C3H5O3-", "28 mmol/L"],
-        ]
-    else:
-        logger.error("Invalid solution entered - %s" % solution)
-        return None
-
-    return Solution(solutes, temperature=temperature, pressure=pressure, pH=pH)

pyEQL/salt_ion_match.py

@@ -11,6 +11,7 @@ species (e.g. Na+)
 :license: LGPL, see LICENSE for more details.
 
 """
+
 from monty.json import MSONable
 from pymatgen.core.ion import Ion
 

pyEQL/solute.py

@@ -14,6 +14,7 @@ that do depend on compsition are accessed via Solution class methods.
 
 from __future__ import annotations
 
+import logging
 import warnings
 from dataclasses import asdict, dataclass, field
 from typing import Literal
@@ -23,6 +24,8 @@ from pymatgen.core.ion import Ion
 
 from pyEQL.utils import standardize_formula
 
+logger = logging.getLogger(__name__)
+
 
 @dataclass
 class Datum: