Fix get salt dict type

AUTHORS.md

@@ -8,14 +8,15 @@ Other contributors, listed alphabetically, are:
 - Arpit Bhardwaj (@abhardwaj73)
 - Nikhil Dhruv (@NikhilDhruv)
 - Dhruv Duseja (@DhruvDuseja)
-- Hernan Grecco (@hgrecco)
 - @githubalexliu
+- Hernan Grecco (@hgrecco)
 - @Ouriel Ndalamba (@Ouriel-N)
+- Ugo Nwosu (@ugognw)
 - Yitong Pan (@YitongPan1)
 - Jaebeom Park (@Jaebeom-P)
 - Kirill Pushkarev (@kirill-push)
 - Andrew Rosen (@arosen93)
 - Sui Xiong Tay (@SuixiongTay)
-- @ugognw
+
 
 (If you think that your name belongs here, please let the maintainer know)

CHANGELOG.md

@@ -7,13 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
-### Added
-
-- Docs/CI: sphinx linkcheck job and tox environment/command (`tox -e links`) (#255, @ugognw)
-- Docs: add carbonate system tutorial (#204, @NikhilDhruv)
-
 ### Fixed
 
+- `Solution` engine, solvent, database were not inherited by the sum of `Solution` objects (#258, ugognw)
+- Bugs where incorrect $\alpha_1$ and $\alpha_2$ parameters were used to calculate activity
+  coefficients and solute molar volumes for salts with divalent (or greater) ions (#258, ugognw)
+- calculation of salt concentrations in `Solution.get_salt_dict` for salts containing polyvalent cations (#258, ugognw)
+- `Solution.get_salt_dict` now respects the `cutoff` parameter (#258, ugognw)
+  - Note that `cutoff` is interpreted in units of moles per kilogram of solution (#258, ugognw)
+- `Solution.get_salt_dict` always returns a salt dictionary sorted in order of decreasing salt concentration (#258, ugognw)
 - `Solution.__init__`: Raise `ValueError` if a user sets inconsistent `H[+1]` in `solutes` and
   `pH` keyword arguments (#270, @gnuhpdiem, @rkingsbury). Previously, if the user set `H[+1]` in `solutes`, it's value would silently override the `pH` kwarg. Now, you will get a `ValueError`
   if the two are inconsistent, unless the `pH` kwarg is kept at the default value. In that case,
@@ -29,8 +31,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Docs: Minor fixes for private / cached methods (#197, @githubalexliu)
 - Docs: Edit documentation of `debye_parameter_B` (#196, @YitongPan1)
 
+### Added
+
+- Docs/CI: sphinx linkcheck job and tox environment/command (`tox -e links`) (#255, @ugognw)
+- Docs: add carbonate system tutorial (#204, @NikhilDhruv)
+
 ### Changed
 
+- **BREAKING** - the return value of `Solution.get_salt_dict` now includes `Salt` objects instead of keys corresponding
+  to `cation` and `anion`. See the example in the docstring for how to adapt existing code to accommodate this
+  change. (#258, @ugognw)
+- **BREAKING** - `Solution.get_salt_dict` no longer returns an entry for water (#258)
+- **BREAKING** - `Solution.get_salt` will not return water and may return `None` if no salt is present.
+  Previously, `Solution.get_salt` would have returned a `Salt` representing water. (#258)
 - Ensure more consistent column formatting in `Solution.print()` (#269, @rkingsbury)
 - Switch `math.log10` to `np.log10` in `Solution.p()` (#269, @rkingsbury)
 - update pre-commit configuration (#269, @rkingsbury)
@@ -43,12 +56,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Docs: `tox -e docs` command configured to fail on warning (#255, ugognw)
 - Docs: ReadTheDocs built with Python 3.11 (#255, ugognw)
 - Use `importlib` to locate test files (#241, @SuixiongTay)
+- Support `numpy>2.0`
+- Bump `pint` to `0.24.4` for `numpy` `v2.0` compatibility and to mitigate CI issues (#239, @SuixiongTay, @rkingsbury)
+- CI: add `python` `v3.13` to post-merge unit tests
 - bump `pymatgen` to `v2025.1.9`
 - bump `maggma` to `v0.71.4`
 
 ### Removed
 
 - Python 3.9 version classifier in pyproject.toml (#247, @ugognw)
+- `Solution.list_salts` (use `Solution.get_salt_dict()` instead) (#258)
 
 ## [1.2.0] - 2024-09-24
 

src/pyEQL/engines.py

@@ -6,6 +6,7 @@
 
 """
 
+import copy
 import logging
 import os
 import warnings
@@ -17,7 +18,6 @@
 
 import pyEQL.activity_correction as ac
 from pyEQL import ureg
-from pyEQL.salt_ion_match import Salt
 from pyEQL.utils import standardize_formula
 
 # These are the only elements that are allowed to have parenthetical oxidation states
@@ -215,7 +215,7 @@ def _setup_ppsol(self, solution: "solution.Solution") -> None:
             if bare_el in SPECIAL_ELEMENTS:
                 # PHREEQC will ignore float-formatted oxi states. Need to make sure we are
                 # passing, e.g. 'C(4)' and not 'C(4.0)'
-                key = f'{bare_el}({int(float(el.split("(")[-1].split(")")[0]))})'
+                key = f"{bare_el}({int(float(el.split('(')[-1].split(')')[0]))})"
             elif bare_el in ["H", "O"]:
                 continue
             else:
@@ -317,12 +317,9 @@ def get_activity_coefficient(self, solution: "solution.Solution", solute: str):
         # identify the predominant salt that this ion is a member of
         salt = None
         rform = standardize_formula(solute)
-        for v in solution.get_salt_dict().values():
-            if v == "HOH":
-                continue
-            if rform == v["cation"] or rform == v["anion"]:
-                del v["mol"]
-                salt = Salt.from_dict(v)
+        for d in solution.get_salt_dict().values():
+            if rform == d["salt"].cation or rform == d["salt"].anion:
+                salt = d["salt"]
                 break
 
         # show an error if no salt can be found that contains the solute
@@ -340,8 +337,8 @@ def get_activity_coefficient(self, solution: "solution.Solution", solute: str):
             # determine alpha1 and alpha2 based on the type of salt
             # see the May reference for the rules used to determine
             # alpha1 and alpha2 based on charge
-            if salt.nu_cation >= 2 and salt.nu_anion <= -2:
-                if salt.nu_cation >= 3 or salt.nu_anion <= -3:
+            if salt.z_cation >= 2 and salt.z_anion <= -2:
+                if salt.z_cation >= 3 or salt.z_anion <= -3:
                     alpha1 = 2.0
                     alpha2 = 50.0
                 else:
@@ -513,11 +510,7 @@ def get_osmotic_coefficient(self, solution: "solution.Solution") -> ureg.Quantit
         # coefficint for each, and average them into an effective osmotic
         # coefficient
         for d in solution.get_salt_dict().values():
-            item = Salt(d["cation"], d["anion"])
-            # ignore HOH in the salt list
-            if item.formula == "HOH":
-                continue
-
+            item = d["salt"]
             # determine alpha1 and alpha2 based on the type of salt
             # see the May reference for the rules used to determine
             # alpha1 and alpha2 based on charge
@@ -577,7 +570,7 @@ def get_osmotic_coefficient(self, solution: "solution.Solution") -> ureg.Quantit
             return effective_osmotic_sum / molality_sum
         except ZeroDivisionError:
             # this means the solution is empty
-            return 1
+            return ureg.Quantity(1.0)
 
     def get_solute_volume(self, solution: "solution.Solution") -> ureg.Quantity:
         """Return the volume of the solutes."""
@@ -587,8 +580,8 @@ def get_solute_volume(self, solution: "solution.Solution") -> ureg.Quantity:
 
         # use the pitzer approach if parameters are available
         pitzer_calc = False
+        param = None if salt is None else solution.get_property(salt.formula, "model_parameters.molar_volume_pitzer")
 
-        param = solution.get_property(salt.formula, "model_parameters.molar_volume_pitzer")
         if param is not None:
             # determine the average molality of the salt
             # this is necessary for solutions inside e.g. an ion exchange
@@ -599,8 +592,8 @@ def get_solute_volume(self, solution: "solution.Solution") -> ureg.Quantity:
             # determine alpha1 and alpha2 based on the type of salt
             # see the May reference for the rules used to determine
             # alpha1 and alpha2 based on charge
-            if salt.nu_cation >= 2 and salt.nu_anion >= 2:
-                if salt.nu_cation >= 3 or salt.nu_anion >= 3:
+            if salt.z_cation >= 2 and salt.z_anion <= -2:
+                if salt.z_cation >= 3 or salt.z_anion <= -3:
                     alpha1 = 2.0
                     alpha2 = 50.0
                 else:
@@ -702,7 +695,6 @@ def equilibrate(self, solution: "solution.Solution") -> None:
     def __deepcopy__(self, memo) -> "NativeEOS":
         # custom deepcopy required because the PhreeqPython instance used by the Native and Phreeqc engines
         # is not pickle-able.
-        import copy
 
         cls = self.__class__
         result = cls.__new__(cls)