pyEQL 1.1.5__py3-none-any.whl → 1.2.0__py3-none-any.whl

pyEQL/database/pyeql_db.json

@@ -3366,92 +3366,6 @@
             }
         }
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-            "@version": null
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-        "formula_html": "CO<sub>32</sub><sup>-1</sup>",
-        "formula_latex": "CO$_{32}$$^{-1}$",
-        "formula_hill": "C O32",
-        "formula_pretty": "CO32^-1",
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@@ -3545,14 +3459,26 @@
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             "diffusion_temp_smolyakov": {
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-                "a2": null,
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+                "a1": {
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+                    "reference": "https://doi.org/10.1016/j.cemconres.2017.08.030",
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+                    "reference": "https://doi.org/10.1016/j.cemconres.2017.08.030",
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+                    "reference": "https://doi.org/10.1016/j.cemconres.2017.08.030",
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+        "formula": "SCN[-1]",
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@@ -3570,10 +3496,10 @@
             "@class": "Ion",
             "@version": null
         },
-        "formula_html": "CSN<sup>-1</sup>",
-        "formula_latex": "CSN$^{-1}$",
+        "formula_html": "SCN<sup>-1</sup>",
+        "formula_latex": "SCN$^{-1}$",
         "formula_hill": "C N S",
-        "formula_pretty": "CSN^-1",
+        "formula_pretty": "SCN^-1",
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@@ -4364,9 +4290,21 @@
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             "diffusion_temp_smolyakov": {
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+                "a1": {
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+                    "reference": "https://doi.org/10.1016/j.cemconres.2017.08.030",
+                    "data_type": "fitted"
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+                "a2": {
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+                    "reference": "https://doi.org/10.1016/j.cemconres.2017.08.030",
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+                    "reference": "https://doi.org/10.1016/j.cemconres.2017.08.030",
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@@ -11394,7 +11332,7 @@
         }
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-        "formula": "H4N2O3(aq)",
+        "formula": "NH4NO3(aq)",
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@@ -11413,9 +11351,9 @@
             "@version": null
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         "formula_html": "H<sub>4</sub>N<sub>2</sub>O<sub>3</sub>",
-        "formula_latex": "H$_{4}$N$_{2}$O$_{3}$",
+        "formula_latex": "NH$_{4}$NO$_{3}$",
         "formula_hill": "H4 N2 O3",
-        "formula_pretty": "H4N2O3",
+        "formula_pretty": "NH4NO3",
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             "H": 1,
@@ -11515,7 +11453,7 @@
         }
     },
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-        "formula": "H4NCl(aq)",
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@@ -11533,10 +11471,10 @@
             "@class": "Ion",
             "@version": null
         },
-        "formula_html": "H<sub>4</sub>NCl",
-        "formula_latex": "H$_{4}$NCl",
+        "formula_html": "NH<sub>4</sub>Cl",
+        "formula_latex": "NH$_{4}$Cl",
         "formula_hill": "Cl H4 N",
-        "formula_pretty": "H4NCl",
+        "formula_pretty": "NH4Cl",
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             "N": -3,
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@@ -11636,7 +11574,7 @@
         }
     },
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+        "formula": "NH4ClO4(aq)",
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@@ -11656,14 +11594,14 @@
             "@class": "Ion",
             "@version": null
         },
-        "formula_html": "H<sub>4</sub>NClO<sub>4</sub>",
-        "formula_latex": "H$_{4}$NClO$_{4}$",
+        "formula_html": "NH<sub>4</sub>ClO<sub>4</sub>",
+        "formula_latex": "NH$_{4}$ClO$_{4}$",
         "formula_hill": "Cl H4 N O4",
-        "formula_pretty": "H4NClO4",
+        "formula_pretty": "NH4ClO4",
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+            "Cl": 7,
             "O": -2
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@@ -11760,7 +11698,7 @@
         }
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     {
-        "formula": "H4N[+1]",
+        "formula": "NH4[+1]",
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@@ -11779,7 +11717,7 @@
         "formula_html": "H<sub>4</sub>N<sup>+1</sup>",
         "formula_latex": "H$_{4}$N$^{+1}$",
         "formula_hill": "H4 N",
-        "formula_pretty": "H4N^+1",
+        "formula_pretty": "NH4^+1",
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             "H": 1
@@ -12134,7 +12072,7 @@
         }
     },
     {
-        "formula": "H8S(NO2)2(aq)",
+        "formula": "(NH4)2SO4(aq)",
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@@ -12157,7 +12095,7 @@
         "formula_html": "H<sub>8</sub>S(NO<sub>2</sub>)<sub>2</sub>",
         "formula_latex": "H$_{8}$S(NO$_{2}$)$_{2}$",
         "formula_hill": "H8 N2 O4 S",
-        "formula_pretty": "H8S(NO2)2",
+        "formula_pretty": "(NH4)2SO4",
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@@ -14744,7 +14682,7 @@
         }
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-        "formula": "K2PHO4(aq)",
+        "formula": "K2HPO4(aq)",
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@@ -14764,10 +14702,10 @@
             "@class": "Ion",
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         },
-        "formula_html": "K<sub>2</sub>PHO<sub>4</sub>",
-        "formula_latex": "K$_{2}$PHO$_{4}$",
+        "formula_html": "K<sub>2</sub>HPO<sub>4</sub>",
+        "formula_latex": "K$_{2}$HPO$_{4}$",
         "formula_hill": "H K2 O4 P",
-        "formula_pretty": "K2PHO4",
+        "formula_pretty": "K2HPO4",
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@@ -15658,7 +15596,7 @@
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@@ -15678,10 +15616,10 @@
             "@class": "Ion",
             "@version": null
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-        "formula_html": "KCSN",
-        "formula_latex": "KCSN",
+        "formula_html": "KSCN",
+        "formula_latex": "KSCN",
         "formula_hill": "C K N S",
-        "formula_pretty": "KCSN",
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@@ -17042,7 +16980,7 @@
         }
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@@ -17065,7 +17003,7 @@
         "formula_html": "KP(HO<sub>2</sub>)<sub>2</sub>",
         "formula_latex": "KP(HO$_{2}$)$_{2}$",
         "formula_hill": "H2 K O4 P",
-        "formula_pretty": "KP(HO2)2",
+        "formula_pretty": "KH2PO4",
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@@ -19849,9 +19787,21 @@
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+                    "reference": "https://doi.org/10.1016/j.cemconres.2017.08.030",
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+                    "reference": "https://doi.org/10.1016/j.cemconres.2017.08.030",
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@@ -20831,7 +20781,7 @@
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@@ -20846,9 +20796,9 @@
             "@version": null
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         "formula_html": "N<sup>-1</sup>",
-        "formula_latex": "N$^{-1}$",
+        "formula_latex": "N$_3^{-1}$",
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-        "formula_pretty": "N^-1",
+        "formula_pretty": "N_3^-1",
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@@ -21031,7 +20981,7 @@
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@@ -21051,10 +21001,10 @@
             "@class": "Ion",
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         },
-        "formula_html": "Na<sub>2</sub>PHO<sub>4</sub>",
-        "formula_latex": "Na$_{2}$PHO$_{4}$",
+        "formula_html": "Na<sub>2</sub>HPO<sub>4</sub>",
+        "formula_latex": "Na$_{2}$HPO$_{4}$",
         "formula_hill": "H Na2 O4 P",
-        "formula_pretty": "Na2PHO4",
+        "formula_pretty": "Na2HPO4",
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@@ -21846,7 +21796,7 @@
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@@ -21866,10 +21816,10 @@
             "@class": "Ion",
             "@version": null
         },
-        "formula_html": "NaCSN",
-        "formula_latex": "NaCSN",
+        "formula_html": "NaSCN",
+        "formula_latex": "NaSCN",
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-        "formula_pretty": "NaCSN",
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@@ -23499,7 +23449,7 @@
         }
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-        "formula": "NaP(HO2)2(aq)",
+        "formula": "NaH2PO4(aq)",
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@@ -23522,7 +23472,7 @@
         "formula_html": "NaP(HO<sub>2</sub>)<sub>2</sub>",
         "formula_latex": "NaP(HO$_{2}$)$_{2}$",
         "formula_hill": "H2 Na O4 P",
-        "formula_pretty": "NaP(HO2)2",
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@@ -25151,7 +25101,7 @@
         }
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-        "formula": "P(HO2)2[-1]",
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@@ -25172,7 +25122,7 @@
         "formula_html": "P(HO<sub>2</sub>)<sub>2</sub><sup>-1</sup>",
         "formula_latex": "P(HO$_{2}$)$_{2}$$^{-1}$",
         "formula_hill": "H2 O4 P",
-        "formula_pretty": "P(HO2)2^-1",
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@@ -25236,7 +25186,7 @@
         }
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-        "formula": "P(HO2)2[-1]",
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@@ -25257,7 +25207,7 @@
         "formula_html": "P(HO<sub>2</sub>)<sub>2</sub><sup>-1</sup>",
         "formula_latex": "P(HO$_{2}$)$_{2}$$^{-1}$",
         "formula_hill": "H2 O4 P",
-        "formula_pretty": "P(HO2)2^-1",
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@@ -25737,7 +25687,7 @@
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@@ -25755,10 +25705,10 @@
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-        "formula_html": "PHO<sub>4</sub><sup>-2</sup>",
-        "formula_latex": "PHO$_{4}$$^{-2}$",
+        "formula_html": "HPO<sub>4</sub><sup>-2</sup>",
+        "formula_latex": "HPO$_{4}$$^{-2}$",
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@@ -29250,9 +29200,9 @@
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-        "formula": "SO3[-1]",
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@@ -29266,10 +29216,10 @@
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-        "formula_html": "SO<sub>3</sub><sup>-2</sup>",
-        "formula_latex": "SO$_{3}$$^{-2}$",
+        "formula_html": "S<sub>2</sub>O<sub>6</sub><sup>-2</sup>",
+        "formula_latex": "S$_{2}$O$_{6}$$^{-2}$",
         "formula_hill": "O6 S2",
-        "formula_pretty": "SO3^-2",
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@@ -29419,95 +29369,9 @@
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-        "formula_html": "SO<sub>42</sub><sup>-1</sup>",
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@@ -29521,10 +29385,10 @@
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-        "formula_html": "SO<sub>4</sub><sup>-2</sup>",
-        "formula_latex": "SO$_{4}$$^{-2}$",
+        "formula_html": "S<sub>2</sub>O<sub>8</sub><sup>-2</sup>",
+        "formula_latex": "S$_{2}$O$_{8}$$^{-2}$",
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@@ -29675,9 +29539,21 @@
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@@ -34281,8 +34157,8 @@
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@@ -34292,18 +34168,18 @@
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-            "charge": -1,
+            "charge": -2,
             "@module": "pymatgen.core.ion",
             "@class": "Ion",
             "@version": null
         },
-        "formula_html": "WO<sub>4</sub><sup>-1</sup>",
-        "formula_latex": "WO$_{4}$$^{-1}$",
+        "formula_html": "WO<sub>4</sub><sup>-2</sup>",
+        "formula_latex": "WO$_{4}$$^{-2}$",
         "formula_hill": "O4 W",
-        "formula_pretty": "WO4^-1",
+        "formula_pretty": "WO4^-2",
         "oxi_state_guesses": {
             "W": 6,
-            "O": -1.75
+            "O": -2
         },
         "n_atoms": 5,
         "n_elements": 2,
@@ -34330,80 +34206,6 @@
                 "data_type": "experimental"
             }
         },
-        "thermo": {
-            "ΔG_hydration": null,
-            "ΔG_formation": null
-        },
-        "transport": {
-            "diffusion_coefficient": null
-        },
-        "model_parameters": {
-            "activity_pitzer": {
-                "Beta0": null,
-                "Beta1": null,
-                "Beta2": null,
-                "Cphi": null,
-                "Max_C": null
-            },
-            "molar_volume_pitzer": {
-                "Beta0": null,
-                "Beta1": null,
-                "Beta2": null,
-                "Cphi": null,
-                "V_o": null,
-                "Max_C": null
-            },
-            "viscosity_jones_dole": {
-                "B": null
-            },
-            "diffusion_temp_smolyakov": {
-                "a1": null,
-                "a2": null,
-                "d": null
-            }
-        }
-    },
-    {
-        "formula": "WO4[-2]",
-        "charge": -2,
-        "molecular_weight": "247.8376 g/mol",
-        "elements": [
-            "W",
-            "O"
-        ],
-        "chemsys": "O-W",
-        "pmg_ion": {
-            "W": 1,
-            "O": 4,
-            "charge": -2,
-            "@module": "pymatgen.core.ion",
-            "@class": "Ion",
-            "@version": null
-        },
-        "formula_html": "WO<sub>4</sub><sup>-2</sup>",
-        "formula_latex": "WO$_{4}$$^{-2}$",
-        "formula_hill": "O4 W",
-        "formula_pretty": "WO4^-2",
-        "oxi_state_guesses": {
-            "W": 6,
-            "O": -2
-        },
-        "n_atoms": 5,
-        "n_elements": 2,
-        "size": {
-            "radius_ionic": {
-                "value": "None",
-                "reference": "pymatgen",
-                "data_type": "experimental"
-            },
-            "radius_hydrated": null,
-            "radius_vdw": {
-                "value": "2.18 Å",
-                "reference": "pymatgen",
-                "data_type": "experimental"
-            },
-            "molar_volume": null
-        },
         "thermo": {
             "ΔG_hydration": {
                 "value": "-1318.0 ± 30 kJ/mol",

pyEQL/functions.py

@@ -15,13 +15,17 @@ from pyEQL import Solution, ureg
 logger = logging.getLogger(__name__)
 
 
-def gibbs_mix(solution1: Solution, solution2: Solution):
+def gibbs_mix(solution1: Solution, solution2: Solution, activity_correction: bool = True):
     r"""
     Return the Gibbs energy change associated with mixing two solutions.
 
     Args:
         solution1: a solution to be mixed.
         solution2: a solution to be mixed.
+        activity_correction : bool, optional
+            If True, activities will be used to calculate the true energy of
+            mixing. If False, mole fraction will be used, resulting in a
+            calculation of the ideal energy of mixing (i.e., :math:`\Delta_{mix} S \times T` )
 
     Returns:
         The change in Gibbs energy associated with complete mixing of the
@@ -32,10 +36,17 @@ 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_{true} = \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
+        or
+
+        .. math::
+
+            \Delta_{mix} G_{ideal} = \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, :math:`a` is the activity of solute :math:`i`,
+        :math:`x` is the mole fraction of solute :math:`i`, and  subscripts :math:`b`, :math:`c`, and :math:`d` refer to the concentrated, dilute, and blended
         Solutions, respectively.
 
         Note that dissociated ions must be counted as separate components,
@@ -56,7 +67,12 @@ 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") * np.log(solution.get_activity(solute))
+                if activity_correction is True:
+                    term_list[solution] += solution.get_amount(solute, "mol") * np.log(solution.get_activity(solute))
+                else:
+                    term_list[solution] += solution.get_amount(solute, "mol") * np.log(
+                        solution.get_amount(solute, "fraction")
+                    )
 
     return (ureg.R * blend.temperature.to("K") * (term_list[blend] - term_list[concentrate] - term_list[dilute])).to(
         "J"
@@ -72,16 +88,16 @@ def entropy_mix(solution1: Solution, solution2: Solution):
 
     Returns:
         The ideal mixing entropy associated with complete mixing of the
-        Solutions, in Joules.
+        Solutions, in Joules per Kelvin.
 
     Notes:
         The ideal entropy of mixing is calculated as follows
 
         .. 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 \ln x_b} - \sum_i {n_c R \ln x_c} - \sum_i {n_d R \ln x_d}
 
-        Where :math:`n` is the number of moles of substance, :math:`T` is the temperature in kelvin,
+        Where :math:`n` is the number of moles of substance, :math:`T` is the temperature in kelvin, :math:`x` is the mole fraction of solute :math:`i`,
         and  subscripts :math:`b`, :math:`c`, and :math:`d` refer to the concentrated, dilute, and blended
         Solutions, respectively.
 
@@ -107,9 +123,7 @@ def entropy_mix(solution1: Solution, solution2: Solution):
                     solution.get_amount(solute, "fraction")
                 )
 
-    return (ureg.R * blend.temperature.to("K") * (term_list[blend] - term_list[concentrate] - term_list[dilute])).to(
-        "J"
-    )
+    return (ureg.R * (term_list[blend] - term_list[concentrate] - term_list[dilute])).to("J/K")
 
 
 def donnan_eql(solution: Solution, fixed_charge: str):
@@ -135,9 +149,9 @@ def donnan_eql(solution: Solution, fixed_charge: str):
 
         .. math::
 
-            \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_{+}})
+            \big(\frac{a_{-}}{\bar a_{-}} \big)^{(\frac{1}{z_{-}})}
+            \big(\frac{\bar a_{+}}{a_{+}}\big)^{(\frac{1}{z_{+}})}
+            =\exp \big(\frac{\Delta \pi \bar V}{RT z_{+} \nu_{+}}\big)
 
         Where subscripts :math:`+` and :math:`-` indicate the cation and anion, respectively,
         the overbar indicates the membrane phase,

pyEQL/presets/Ringers lactate.yaml

@@ -1,6 +1,6 @@
-'@module': pyEQL.solution
-'@class': Solution
-'@version': 0.0.post1.dev699+g0764b1c
+"@module": pyEQL.solution
+"@class": Solution
+"@version": 0.0.post1.dev699+g0764b1c
 solutes:
   H2O(aq): 55.2313771443148 mol
   Na[+1]: 0.13 mol

pyEQL/presets/normal saline.yaml

@@ -1,6 +1,6 @@
-'@module': pyEQL.solution
-'@class': Solution
-'@version': 0.0.post1.dev699+g0764b1c
+"@module": pyEQL.solution
+"@class": Solution
+"@version": 0.0.post1.dev699+g0764b1c
 solutes:
   H2O(aq): 55.19703719794332 mol
   Na[+1]: 0.154 mol

pyEQL/presets/rainwater.yaml

@@ -1,6 +1,6 @@
-'@module': pyEQL.solution
-'@class': Solution
-'@version': 0.0.post1.dev699+g0764b1c
+"@module": pyEQL.solution
+"@class": Solution
+"@version": 0.0.post1.dev699+g0764b1c
 solutes:
   H2O(aq): 55.34454944845822 mol
   HCO3[-1]: 3.162277660168379e-06 mol

pyEQL/presets/seawater.yaml

@@ -1,6 +1,6 @@
-'@module': pyEQL.solution
-'@class': Solution
-'@version': 0.0.post1.dev699+g0764b1c
+"@module": pyEQL.solution
+"@class": Solution
+"@version": 0.0.post1.dev699+g0764b1c
 solutes:
   H2O(aq): 55.34455401423017 mol
   Cl[-1]: 0.54425785619973 mol

pyEQL/presets/urine.yaml

@@ -1,6 +1,6 @@
-'@module': pyEQL.solution
-'@class': Solution
-'@version': 0.0.post1.dev699+g0764b1c
+"@module": pyEQL.solution
+"@class": Solution
+"@version": 0.0.post1.dev699+g0764b1c
 solutes:
   H2O(aq): 55.135679438263864 mol
   H4CN2O(aq): 0.333026615820163 mol

pyEQL/presets/wastewater.yaml

@@ -1,6 +1,6 @@
-'@module': pyEQL.solution
-'@class': Solution
-'@version': 0.0.post1.dev699+g0764b1c
+"@module": pyEQL.solution
+"@class": Solution
+"@version": 0.0.post1.dev699+g0764b1c
 solutes:
   H2O(aq): 55.342123269143364 mol
   CH3COOH(aq): 0.006827420786931851 mol

pyEQL/solution.py

@@ -1161,7 +1161,8 @@ class Solution(MSONable):
             :meth:`get_amount`
             :func:`pyEQL.utils.interpret_units`
         """
-        TOT: Quantity = 0
+        _units = interpret_units(units)
+        TOT: Quantity = ureg.Quantity(0, _units)
 
         # standardize the element formula and units
         el = str(Element(element.split("(")[0]))
@@ -1178,7 +1179,7 @@ class Solution(MSONable):
         else:
             species = []
             for k, v in comp_by_element.items():
-                if el in k:
+                if k.split("(")[0] == el:
                     species.extend(v)
 
         # loop through the species of interest, adding moles of element
@@ -2294,9 +2295,7 @@ class Solution(MSONable):
                 self.logger.info("balance_charge is None, so no charge balancing will be performed.")
                 return
 
-            self.logger.info(
-                f"Solution is not electroneutral (C.B. = {cb} eq/L). Adjusting {self._cb_species} to compensate."
-            )
+            self.logger.info(f"Adjusting {self._cb_species} to compensate.")
 
             if self.balance_charge == "pH":
                 # the charge imbalance associated with the H+ / OH- system can be expressed

pyEQL/utils.py

@@ -61,15 +61,15 @@ def standardize_formula(formula: str):
         'Na+1', and 'Na[+]' will all standardize to "Na[+1]"
     """
     # fix permuted sign and charge number (e.g. Co2+)
-    for str, rep in zip(["²⁺", "³⁺", "⁴⁺", "²⁻", "³⁻", "⁴⁻"], ["+2", "+3", "+4", "-2", "-3", "-4"]):
+    for str, rep in zip(["²⁺", "³⁺", "⁴⁺", "²⁻", "³⁻", "⁴⁻"], ["+2", "+3", "+4", "-2", "-3", "-4"], strict=False):
         formula = formula.replace(str, rep)
 
     # replace superscripts with non superscripts
-    for char, rep in zip("⁻⁺⁰¹²³⁴⁵⁶⁷⁸⁹", "-+0123456789"):
+    for char, rep in zip("⁻⁺⁰¹²³⁴⁵⁶⁷⁸⁹", "-+0123456789", strict=False):
         formula = formula.replace(char, rep)
 
     # replace subscripts with non subscripts
-    for char, rep in zip("₀₁₂₃₄₅₆₇₈₉", "0123456789"):
+    for char, rep in zip("₀₁₂₃₄₅₆₇₈₉", "0123456789", strict=False):
         formula = formula.replace(char, rep)
 
     sform = Ion.from_formula(formula).reduced_formula
@@ -81,18 +81,24 @@ def standardize_formula(formula: str):
     # ammonia
     if sform == "H4N[+1]":
         sform = "NH4[+1]"
+    elif "H4NCl" in sform:
+        sform = sform.replace("H4NCl", "NH4Cl")
+    elif sform == "SO3[-1]":
+        sform = "S2O6[-2]"
+    elif sform == "SO4[-1]":
+        sform = "S2O8[-2]"
     elif sform == "H3N(aq)":
         sform = "NH3(aq)"
     # phosphoric acid system
     elif sform == "PH3O4(aq)":
         sform = "H3PO4(aq)"
-    elif sform == "PHO4[-2]":
-        sform = "HPO4[-2]"
-    elif sform == "P(HO2)2[-1]":
-        sform = "H2PO4[-1]"
+    elif "PHO4" in sform:
+        sform = sform.replace("PHO4", "HPO4")
+    elif "P(HO2)2" in sform:
+        sform = sform.replace("P(HO2)2", "H2PO4")
     # thiocyanate
-    elif sform == "CSN[-1]":
-        sform = "SCN[-1]"
+    elif "CSN" in sform:
+        sform = sform.replace("CSN", "SCN")
     # triiodide, nitride, an phosphide
     elif sform == "I[-0.33333333]":
         sform = "I3[-1]"
@@ -137,6 +143,15 @@ def standardize_formula(formula: str):
     elif sform == "C2I2ClO2[-1]":
         sform = "CI2ClCOO[-1]"
 
+    # ammonium nitrate salts
+    elif sform == "H4N2O3(aq)":
+        sform = "NH4NO3(aq)"
+    # ammonium sulfate salts
+    elif sform == "H8S(NO2)2(aq)":
+        sform = "(NH4)2SO4(aq)"
+    elif sform == "H4SNO4[-1]":
+        sform = "NH4SO4[-1]"
+
     # TODO - consider adding recognition of special formulas like MeOH for methanol or Cit for citrate
     return sform
 

{pyEQL-1.1.5.dist-info → pyEQL-1.2.0.dist-info}/AUTHORS.md

@@ -5,9 +5,12 @@ developed and maintained by the Kingsbury Lab at Princeton University.
 
 Other contributors, listed alphabetically, are:
 
-* Kirill Pushkarev (@kirill-push)
-* Dhruv Duseja (@DhruvDuseja)
-* Andrew Rosen (@arosen93)
-* Hernan Grecco (@hgrecco)
+- Arpit Bhardwaj (@abhardwaj73)
+- Dhruv Duseja (@DhruvDuseja)
+- Hernan Grecco (@hgrecco)
+- Jaebeom Park (@Jaebeom-P)
+- Kirill Pushkarev (@kirill-push)
+- Andrew Rosen (@arosen93)
+- Sui Xiong Tay (@SuixiongTay)
 
 (If you think that your name belongs here, please let the maintainer know)

{pyEQL-1.1.5.dist-info → pyEQL-1.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 1.1.5
+Version: 1.2.0
 Summary: A python interface for solution chemistry
 Author-email: Ryan Kingsbury <kingsbury@princeton.edu>
 Project-URL: Docs, https://pyeql.readthedocs.io/
@@ -15,19 +15,19 @@ Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 License-File: COPYING
 License-File: AUTHORS.md
 Requires-Dist: pint >=0.19
-Requires-Dist: numpy <2
-Requires-Dist: scipy
-Requires-Dist: pymatgen ==2024.5.1
-Requires-Dist: iapws
+Requires-Dist: numpy <2,>1.26
+Requires-Dist: scipy >=1.12
+Requires-Dist: pymatgen >=2024.9.10
+Requires-Dist: iapws >=1.5.3
 Requires-Dist: monty >=2024.7.12
 Requires-Dist: maggma >=0.67.0
-Requires-Dist: phreeqpython
+Requires-Dist: phreeqpython >=1.5.2
 Provides-Extra: docs
 Requires-Dist: sphinx >=3.2.1 ; extra == 'docs'
 Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
@@ -35,20 +35,20 @@ Requires-Dist: myst-parser[linkify] ; extra == 'docs'
 Provides-Extra: full
 Requires-Dist: rich ; extra == 'full'
 Provides-Extra: testing
-Requires-Dist: setuptools ; extra == 'testing'
-Requires-Dist: pre-commit ; extra == 'testing'
-Requires-Dist: pytest ; extra == 'testing'
-Requires-Dist: pytest-cov ; extra == 'testing'
-Requires-Dist: pytest-xdist ; extra == 'testing'
+Requires-Dist: setuptools >=68 ; extra == 'testing'
+Requires-Dist: pre-commit >=2 ; extra == 'testing'
+Requires-Dist: pytest >=7 ; extra == 'testing'
+Requires-Dist: pytest-cov >=2.11 ; extra == 'testing'
+Requires-Dist: pytest-xdist >2 ; extra == 'testing'
 Requires-Dist: black ; extra == 'testing'
-Requires-Dist: mypy ; extra == 'testing'
-Requires-Dist: ruff ; extra == 'testing'
+Requires-Dist: mypy >1 ; extra == 'testing'
+Requires-Dist: ruff >0.0.100 ; extra == 'testing'
 Requires-Dist: tox <4 ; extra == 'testing'
 
 [![Read the Docs](https://img.shields.io/readthedocs/pyeql)](https://pyeql.readthedocs.io/en/latest/)
 [![testing](https://github.com/KingsburyLab/pyeql/workflows/testing/badge.svg)](https://github.com/KingsburyLab/pyeql/actions?query=workflow%3Atesting)
 [![codecov](https://codecov.io/gh/KingsburyLab/pyeql/branch/main/graph/badge.svg?token=I7RP0QML6S)](https://codecov.io/gh/KingsburyLab/pyeql)
-![Supported python versions](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12-blue)
+![Supported python versions](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12-blue)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8332915.svg)](https://doi.org/10.5281/zenodo.8332915)
 [![PyPI version](https://badge.fury.io/py/pyEQL.svg)](https://badge.fury.io/py/pyEQL)
 [![status](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6/status.svg)](https://joss.theoj.org/papers/bdd9e247ea9736a0fdbbd5fe12bef7a6)
@@ -112,7 +112,7 @@ Detailed documentation is available at [https://pyeql.readthedocs.io/](https://p
 
 ### Dependencies
 
-- Python 3.9+. This project will attempt to adhere to NumPy's
+- Python 3.10+. This project will attempt to adhere to NumPy's
   [NEP 29](https://numpy.org/neps/nep-0029-deprecation_policy.html) deprecation policy
   for older version of Python.
 - [pint](https://github.com/hgrecco/pint) - for units-aware calculations

pyEQL-1.2.0.dist-info/RECORD

@@ -0,0 +1,26 @@
+pyEQL/__init__.py,sha256=OCp_PiQEPyVoi1VX0ursBzHJWN6nDS1Id6bTBOgqCYs,1999
+pyEQL/activity_correction.py,sha256=eOixjgTd5hTrTRD5s6aPCCG12lAIH7-lRN0Z1qHu678,37151
+pyEQL/engines.py,sha256=VbdQSPKlNehW96U1XxWYwjTy6k6WDpZZEx_Y4l3qZv4,34686
+pyEQL/equilibrium.py,sha256=YCtoAJSgn1WC9NJnc3H4FTJdKQvogsvCuj7HqlKMtww,8307
+pyEQL/functions.py,sha256=8TePRHfOWsDnFsmBA-twv5XZyhrkMQI6VroDLouckho,11452
+pyEQL/salt_ion_match.py,sha256=0nCZXmeo67VqcyYWQpPx-81hjSvnsg8HFB3fIyfjW_k,4070
+pyEQL/solute.py,sha256=no00Rc3tRfHmyht4wm2UXA1KZhKC45tWMO5QEkZY6yg,5140
+pyEQL/solution.py,sha256=3hvtqeu5KzfFKzeOdKlzS_aIFPTNgUfhjIwBurfuGJw,115754
+pyEQL/utils.py,sha256=dXXM7_Mv0-8MWDjoPfNl9qoFmRgV0eVt_iSEhu1JYSc,7194
+pyEQL/database/geothermal.dat,sha256=kksnfcBtWdOTpNn4CLXU1Mz16cwas2WuVKpuMU8CaVI,234230
+pyEQL/database/llnl.dat,sha256=jN-a0kfUFbQlYMn2shTVRg1JX_ZhLa-tJ0lLw2YSpLU,751462
+pyEQL/database/phreeqc_license.txt,sha256=8W1r8VxC2kVptIMSU9sDFNASYqN7MdwKEtIWWfjTQuM,2906
+pyEQL/database/pyeql_db.json,sha256=OFUwq3KjbSzmpUE9kkn17TXF4aszs-2ki5N0VKX8E0o,1075941
+pyEQL/presets/Ringers lactate.yaml,sha256=kaGiBbg_JFrmOm8xZqb_EMVqeQYxll7pOOvXcmxAJ5I,413
+pyEQL/presets/normal saline.yaml,sha256=eT5MZKgc0uW-TrQOiX87ZoTwlMO-OEhTvQyQAXoIa80,318
+pyEQL/presets/rainwater.yaml,sha256=QG3aol2Z5HwLj-s6frN7hYNQr01qw_HR2h5f4BdAvVc,337
+pyEQL/presets/seawater.yaml,sha256=Kts0vAmXSPvPzy_PJpx0RR2uSt40izxp-687Qi02oro,843
+pyEQL/presets/urine.yaml,sha256=Zpcr2Dp7xZrlLqzYk4UcMyWXlNrd2AFUexWpb8k9FEg,679
+pyEQL/presets/wastewater.yaml,sha256=zJcpp9Ye4hIw6iInsdV5bgjTNuJ8oAUVimsUgZXlG-w,502
+pyEQL-1.2.0.dist-info/AUTHORS.md,sha256=Ukdh6f3jO6jdgl2k_r_xdNOuzmjXcISMQqUTSH39QVw,506
+pyEQL-1.2.0.dist-info/COPYING,sha256=Ww2oUywfFTn242v9ksCgQdIVSpcMXJiKKePn0GFm25E,7649
+pyEQL-1.2.0.dist-info/LICENSE.txt,sha256=2Zf1F7RzbpeposgIxUydpurqNCMoMgDi2gAB65_GjwQ,969
+pyEQL-1.2.0.dist-info/METADATA,sha256=okvLJvrb90RHE5Y3GoTDeXbvY0i_b4oP9MPa6TgIn5A,6151
+pyEQL-1.2.0.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+pyEQL-1.2.0.dist-info/top_level.txt,sha256=QMOaZjCAm_lS4Njsjh4L0B5aWnJFGQMYKhuH88CG1co,6
+pyEQL-1.2.0.dist-info/RECORD,,

{pyEQL-1.1.5.dist-info → pyEQL-1.2.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.0.0)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pyEQL-1.1.5.dist-info/RECORD

@@ -1,26 +0,0 @@
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-pyEQL/functions.py,sha256=nc-Hc61MmW-ELBR1PByJvQnELxM7PZexMHbU_O5-Bnw,10584
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-pyEQL/utils.py,sha256=DWLtNm71qw5j4-jqBp5v3LssEjWgJnVvI6a_H60c5ic,6670
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-pyEQL/database/llnl.dat,sha256=jN-a0kfUFbQlYMn2shTVRg1JX_ZhLa-tJ0lLw2YSpLU,751462
-pyEQL/database/phreeqc_license.txt,sha256=8W1r8VxC2kVptIMSU9sDFNASYqN7MdwKEtIWWfjTQuM,2906
-pyEQL/database/pyeql_db.json,sha256=-7Z8tpAddXhPlvpxms7cFQKL_DSSbemzOzxm6L5vaVk,1080801
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-pyEQL/presets/urine.yaml,sha256=0Njtc-H1fFRo7UhquHdiSTT4z-8VZJ1utDCk02qk28M,679
-pyEQL/presets/wastewater.yaml,sha256=jTTFBpmKxczaEtkCZb0xUULIPZt7wfC8eAJ6rthGnmw,502
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-pyEQL-1.1.5.dist-info/COPYING,sha256=Ww2oUywfFTn242v9ksCgQdIVSpcMXJiKKePn0GFm25E,7649
-pyEQL-1.1.5.dist-info/LICENSE.txt,sha256=2Zf1F7RzbpeposgIxUydpurqNCMoMgDi2gAB65_GjwQ,969
-pyEQL-1.1.5.dist-info/METADATA,sha256=TXDkdGyqFqh4LJfyOFtcqlbRnNh87kySnIPAKzUE1k8,6096
-pyEQL-1.1.5.dist-info/WHEEL,sha256=Rp8gFpivVLXx-k3U95ozHnQw8yDcPxmhOpn_Gx8d5nc,91
-pyEQL-1.1.5.dist-info/top_level.txt,sha256=QMOaZjCAm_lS4Njsjh4L0B5aWnJFGQMYKhuH88CG1co,6
-pyEQL-1.1.5.dist-info/RECORD,,