pyEQL 1.1.0__py3-none-any.whl → 1.1.2__py3-none-any.whl

pyEQL/__init__.py

@@ -37,11 +37,8 @@ ureg = UnitRegistry(cache_folder=":auto:")
 # convert "offset units" so that, e.g. Quantity('25 degC') works without error
 # see https://pint.readthedocs.io/en/0.22/user/nonmult.html?highlight=offset#temperature-conversion
 ureg.autoconvert_offset_to_baseunit = True
-# append custom unit definitions and contexts
-fname = files("pyEQL") / "pint_custom_units.txt"
-ureg.load_definitions(fname)
 # activate the "chemistry" context globally
-ureg.enable_contexts("chem")
+ureg.enable_contexts("chemistry")
 # set the default string formatting for pint quantities
 ureg.default_format = "P~"
 

pyEQL/database/pyeql_db.json

@@ -6698,7 +6698,7 @@
         "n_elements": 1,
         "size": {
             "radius_ionic": {
-                "value": "0.755",
+                "value": "0.755 Å",
                 "reference": "pymatgen",
                 "data_type": "experimental"
             },
@@ -24663,7 +24663,7 @@
         "n_elements": 1,
         "size": {
             "radius_ionic": {
-                "value": "0.83",
+                "value": "0.83 Å",
                 "reference": "pymatgen",
                 "data_type": "experimental"
             },

pyEQL/engines.py

@@ -11,7 +11,7 @@ import os
 import warnings
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Literal
+from typing import TYPE_CHECKING, Literal
 
 from phreeqpython import PhreeqPython
 
@@ -26,6 +26,9 @@ SPECIAL_ELEMENTS = ["S", "C", "N", "Cu", "Fe", "Mn"]
 
 logger = logging.getLogger(__name__)
 
+if TYPE_CHECKING:
+    from pyEQL import Solution
+
 
 class EOS(ABC):
     """
@@ -38,7 +41,7 @@ class EOS(ABC):
     """
 
     @abstractmethod
-    def get_activity_coefficient(self, solution, solute):
+    def get_activity_coefficient(self, solution: "Solution", solute: str) -> ureg.Quantity:
         """
         Return the *molal scale* activity coefficient of solute, given a Solution
         object.
@@ -55,7 +58,7 @@ class EOS(ABC):
         """
 
     @abstractmethod
-    def get_osmotic_coefficient(self, solution):
+    def get_osmotic_coefficient(self, solution: "Solution") -> ureg.Quantity:
         """
         Return the *molal scale* osmotic coefficient of a Solution.
 
@@ -70,7 +73,7 @@ class EOS(ABC):
         """
 
     @abstractmethod
-    def get_solute_volume(self):
+    def get_solute_volume(self, solution: "Solution") -> ureg.Quantity:
         """
         Return the volume of only the solutes.
 
@@ -85,7 +88,7 @@ class EOS(ABC):
         """
 
     @abstractmethod
-    def equilibrate(self, solution):
+    def equilibrate(self, solution: "Solution") -> None:
         """
         Adjust the speciation and pH of a Solution object to achieve chemical equilibrium.
 
@@ -105,25 +108,25 @@ class EOS(ABC):
 class IdealEOS(EOS):
     """Ideal solution equation of state engine."""
 
-    def get_activity_coefficient(self, solution, solute):
+    def get_activity_coefficient(self, solution: "Solution", solute: str) -> ureg.Quantity:
         """
         Return the *molal scale* activity coefficient of solute, given a Solution
         object.
         """
         return ureg.Quantity(1, "dimensionless")
 
-    def get_osmotic_coefficient(self, solution):
+    def get_osmotic_coefficient(self, solution: "Solution") -> ureg.Quantity:
         """
         Return the *molal scale* osmotic coefficient of solute, given a Solution
         object.
         """
         return ureg.Quantity(1, "dimensionless")
 
-    def get_solute_volume(self, solution):
+    def get_solute_volume(self, solution: "Solution") -> ureg.Quantity:
         """Return the volume of the solutes."""
         return ureg.Quantity(0, "L")
 
-    def equilibrate(self, solution):
+    def equilibrate(self, solution: "Solution") -> None:
         """Adjust the speciation of a Solution object to achieve chemical equilibrium."""
         warnings.warn("equilibrate() has no effect in IdealEOS!")
         return
@@ -138,7 +141,9 @@ class NativeEOS(EOS):
 
     def __init__(
         self,
-        phreeqc_db: Literal["vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"] = "llnl.dat",
+        phreeqc_db: Literal[
+            "phreeqc.dat", "vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"
+        ] = "llnl.dat",
     ) -> None:
         """
         Args:
@@ -172,7 +177,7 @@ class NativeEOS(EOS):
         # store the solution composition to see whether we need to re-instantiate the solution
         self._stored_comp = None
 
-    def _setup_ppsol(self, solution):
+    def _setup_ppsol(self, solution: "Solution") -> None:
         """Helper method to set up a PhreeqPython solution for subsequent analysis."""
         self._stored_comp = solution.components.copy()
         solv_mass = solution.solvent_mass.to("kg").magnitude
@@ -224,10 +229,7 @@ class NativeEOS(EOS):
                 d[key] = str(mol / solv_mass)
 
             # tell PHREEQC which species to use for charge balance
-            if (
-                solution.balance_charge is not None
-                and solution.balance_charge in solution.get_components_by_element()[el]
-            ):
+            if solution.balance_charge is not None and solution._cb_species in solution.get_components_by_element()[el]:
                 d[key] += " charge"
 
         # create the PHREEQC solution object
@@ -244,13 +246,13 @@ class NativeEOS(EOS):
 
         self.ppsol = ppsol
 
-    def _destroy_ppsol(self):
-        """Remove the PhreeqPython solution from memory"""
+    def _destroy_ppsol(self) -> None:
+        """Remove the PhreeqPython solution from memory."""
         if self.ppsol is not None:
             self.ppsol.forget()
             self.ppsol = None
 
-    def get_activity_coefficient(self, solution, solute):
+    def get_activity_coefficient(self, solution: "Solution", solute: str):
         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
@@ -329,7 +331,7 @@ class NativeEOS(EOS):
 
         # show an error if no salt can be found that contains the solute
         if salt is None:
-            logger.error("No salts found that contain solute %s. Returning unit activity coefficient." % solute)
+            logger.error(f"No salts found that contain solute {solute}. Returning unit activity coefficient.")
             return ureg.Quantity(1, "dimensionless")
 
         # use the Pitzer model for higher ionic strength, if the parameters are available
@@ -344,14 +346,14 @@ class NativeEOS(EOS):
             # 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:
-                    alpha1 = 2
-                    alpha2 = 50
+                    alpha1 = 2.0
+                    alpha2 = 50.0
                 else:
                     alpha1 = 1.4
                     alpha2 = 12
             else:
-                alpha1 = 2
-                alpha2 = 0
+                alpha1 = 2.0
+                alpha2 = 0.0
 
             # determine the average molality of the salt
             # this is necessary for solutions inside e.g. an ion exchange
@@ -427,7 +429,7 @@ class NativeEOS(EOS):
 
         return molal
 
-    def get_osmotic_coefficient(self, solution):
+    def get_osmotic_coefficient(self, solution: "Solution") -> ureg.Quantity:
         r"""
         Return the *molal scale* osmotic coefficient of solute, given a Solution
         object.
@@ -574,7 +576,7 @@ class NativeEOS(EOS):
             # this means the solution is empty
             return 1
 
-    def get_solute_volume(self, solution):
+    def get_solute_volume(self, solution: "Solution") -> ureg.Quantity:
         """Return the volume of the solutes."""
         # identify the predominant salt in the solution
         salt = solution.get_salt()
@@ -596,14 +598,14 @@ class NativeEOS(EOS):
             # 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:
-                    alpha1 = 2
-                    alpha2 = 50
+                    alpha1 = 2.0
+                    alpha2 = 50.0
                 else:
                     alpha1 = 1.4
                     alpha2 = 12
             else:
-                alpha1 = 2
-                alpha2 = 0
+                alpha1 = 2.0
+                alpha2 = 0.0
 
             apparent_vol = ac.get_apparent_volume_pitzer(
                 solution.ionic_strength,
@@ -633,7 +635,7 @@ class NativeEOS(EOS):
 
             pitzer_calc = True
 
-            logger.debug("Updated solution volume using Pitzer model for solute %s" % salt.formula)
+            logger.debug(f"Updated solution volume using Pitzer model for solute {salt.formula}")
 
         # add the partial molar volume of any other solutes, except for water
         # or the parent salt, which is already accounted for by the Pitzer parameters
@@ -649,7 +651,7 @@ class NativeEOS(EOS):
             part_vol = solution.get_property(solute, "size.molar_volume")
             if part_vol is not None:
                 solute_vol += part_vol * ureg.Quantity(mol, "mol")
-                logger.debug("Updated solution volume using direct partial molar volume for solute %s" % solute)
+                logger.debug(f"Updated solution volume using direct partial molar volume for solute {solute}")
 
             else:
                 logger.warning(
@@ -658,7 +660,7 @@ class NativeEOS(EOS):
 
         return solute_vol.to("L")
 
-    def equilibrate(self, solution):
+    def equilibrate(self, solution: "Solution") -> None:
         """Adjust the speciation of a Solution object to achieve chemical equilibrium."""
         if self.ppsol is not None:
             self.ppsol.forget()
@@ -693,18 +695,12 @@ class NativeEOS(EOS):
         if charge_adjust != 0:
             logger.warning(
                 "After equilibration, the charge balance of the solution was not electroneutral."
-                f" {charge_adjust} eq of charge were added via {solution.balance_charge}"
+                f" {charge_adjust} eq of charge were added via {solution._cb_species}"
             )
 
-            if solution.balance_charge is None:
-                pass
-            elif solution.balance_charge == "pH":
-                solution.components["H+"] += charge_adjust.magnitude
-            elif solution.balance_charge == "pE":
-                raise NotImplementedError
-            else:
-                z = solution.get_property(solution.balance_charge, "charge")
-                solution.add_amount(solution.balance_charge, f"{charge_adjust/z} mol")
+            if solution.balance_charge is not None:
+                z = solution.get_property(solution._cb_species, "charge")
+                solution.add_amount(solution._cb_species, f"{charge_adjust/z} mol")
 
         # rescale the solvent mass to ensure the total mass of solution does not change
         # this is important because PHREEQC and the pyEQL database may use slightly different molecular
@@ -734,7 +730,7 @@ class PhreeqcEOS(NativeEOS):
     def __init__(
         self,
         phreeqc_db: Literal[
-            "vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"
+            "phreeqc.dat", "vitens.dat", "wateq4f_PWN.dat", "pitzer.dat", "llnl.dat", "geothermal.dat"
         ] = "phreeqc.dat",
     ) -> None:
         """
@@ -751,12 +747,12 @@ class PhreeqcEOS(NativeEOS):
         """
         super().__init__(phreeqc_db=phreeqc_db)
 
-    def get_activity_coefficient(self, solution, solute):
+    def get_activity_coefficient(self, solution: "Solution", solute: str) -> ureg.Quantity:
         """
         Return the *molal scale* activity coefficient of solute, given a Solution
         object.
         """
-        if self.ppsol is None or solution.components != self._stored_comp:
+        if (self.ppsol is None) or (solution.components != self._stored_comp):
             self._destroy_ppsol()
             self._setup_ppsol(solution)
 
@@ -775,7 +771,7 @@ class PhreeqcEOS(NativeEOS):
 
         return ureg.Quantity(act, "dimensionless")
 
-    def get_osmotic_coefficient(self, solution):
+    def get_osmotic_coefficient(self, solution: "Solution") -> ureg.Quantity:
         """
         Return the *molal scale* osmotic coefficient of solute, given a Solution
         object.
@@ -787,7 +783,7 @@ class PhreeqcEOS(NativeEOS):
         # TODO - find a way to access or calculate osmotic coefficient
         return ureg.Quantity(1, "dimensionless")
 
-    def get_solute_volume(self, solution):
+    def get_solute_volume(self, solution: "Solution") -> ureg.Quantity:
         """Return the volume of the solutes."""
         # TODO - phreeqc seems to have no concept of volume, but it does calculate density
         return ureg.Quantity(0, "L")

pyEQL/solution.py

@@ -92,11 +92,15 @@ class Solution(MSONable):
                 -7 to +14. The default value corresponds to a pE value typical of natural
                 waters in equilibrium with the atmosphere.
             balance_charge: The strategy for balancing charge during init and equilibrium calculations. Valid options
-                are 'pH', which will adjust the solution pH to balance charge, 'pE' which will adjust the
-                redox equilibrium to balance charge, or the name of a dissolved species e.g. 'Ca+2' or 'Cl-'
-                that will be added/subtracted to balance charge. If set to None, no charge balancing will be
-                performed either on init or when equilibrate() is called. Note that in this case, equilibrate()
-                can distort the charge balance!
+                are
+                    - 'pH', which will adjust the solution pH to balance charge,
+                    - 'auto' which will use the majority cation or anion (i.e., that with the largest concentration)
+                    as needed,
+                    - 'pE' (not currently implemented) which will adjust the redox equilibrium to balance charge, or
+                    the name of a dissolved species e.g. 'Ca+2' or 'Cl-' that will be added/subtracted to balance
+                    charge.
+                    - None (default), in which case no charge balancing will be performed either on init or when
+                    equilibrate() is called. Note that in this case, equilibrate() can distort the charge balance!
             solvent: Formula of the solvent. Solvents other than water are not supported at this time.
             engine: Electrolyte modeling engine to use. See documentation for details on the available engines.
             database: path to a .json file (str or Path) or maggma Store instance that
@@ -171,7 +175,7 @@ class Solution(MSONable):
         self._pE = pE
         self._pH = pH
         self.pE = self._pE
-        if isinstance(balance_charge, str) and balance_charge not in ["pH", "pE"]:
+        if isinstance(balance_charge, str) and balance_charge not in ["pH", "pE", "auto"]:
             self.balance_charge = standardize_formula(balance_charge)
         else:
             self.balance_charge = balance_charge  #: Standardized formula of the species used for charge balancing.
@@ -257,33 +261,44 @@ class Solution(MSONable):
             for item in self._solutes:
                 self.add_solute(*item)
 
-        # adjust the charge balance, if necessary
+        # determine the species that will be used for charge balancing, when needed.
+        # this is necessary to do even if the composition is already electroneutral,
+        # because the appropriate species also needs to be passed to equilibrate
+        # to keep from distorting the charge balance.
         cb = self.charge_balance
+        if self.balance_charge is None:
+            self._cb_species = None
+        elif self.balance_charge == "pH":
+            self._cb_species = "H[+1]"
+        elif self.balance_charge == "pE":
+            raise NotImplementedError("Balancing charge via redox (pE) is not yet implemented!")
+        elif self.balance_charge == "auto":
+            # add the most abundant ion of the opposite charge
+            if cb <= 0:
+                self._cb_species = max(self.cations, key=self.cations.get)
+            elif cb > 0:
+                self._cb_species = max(self.anions, key=self.anions.get)
+        else:
+            ions = set().union(*[self.cations, self.anions])  # all ions
+            self._cb_species = self.balance_charge
+            if self._cb_species not in ions:
+                raise ValueError(
+                    f"Charge balancing species {self._cb_species} was not found in the solution!. "
+                    f"Species {ions} were found."
+                )
+
+        # adjust charge balance, if necessary
         if not np.isclose(cb, 0, atol=1e-8) and self.balance_charge is not None:
             balanced = False
             self.logger.info(
-                f"Solution is not electroneutral (C.B. = {cb} eq/L). Adding {balance_charge} to compensate."
+                f"Solution is not electroneutral (C.B. = {cb} eq/L). Adding {self._cb_species} to compensate."
             )
-            if self.balance_charge == "pH":
-                self.components["H+"] += (
-                    -1 * cb * self.volume.to("L").magnitude
-                )  # if C.B. is negative, we need to add cations. H+ is 1 eq/mol
+            z = self.get_property(self._cb_species, "charge")
+            self.components[self._cb_species] += -1 * cb / z * self.volume.to("L").magnitude
+            if np.isclose(self.charge_balance, 0, atol=1e-8):
                 balanced = True
-            elif self.balance_charge == "pE":
-                raise NotImplementedError("Balancing charge via redox (pE) is not yet implemented!")
-            else:
-                ions = set().union(*[self.cations, self.anions])  # all ions
-                if self.balance_charge not in ions:
-                    raise ValueError(
-                        f"Charge balancing species {self.balance_charge} was not found in the solution!. "
-                        f"Species {ions} were found."
-                    )
-                z = self.get_property(balance_charge, "charge")
-                self.components[balance_charge] += -1 * cb / z * self.volume.to("L").magnitude
-                balanced = True
-
             if not balanced:
-                warnings.warn(f"Unable to balance charge using species {self.balance_charge}")
+                warnings.warn(f"Unable to balance charge using species {self._cb_species}")
 
     @property
     def mass(self) -> Quantity:
@@ -1282,81 +1297,12 @@ class Solution(MSONable):
         Returns:
             Nothing. The concentration of solute is modified.
         """
-        # if units are given on a per-volume basis,
-        # iteratively solve for the amount of solute that will preserve the
-        # original volume and result in the desired concentration
-        if ureg.Quantity(amount).dimensionality in (
-            "[substance]/[length]**3",
-            "[mass]/[length]**3",
-        ):
-            # store the original volume for later
-            orig_volume = self.volume
-
-            # change the amount of the solute present to match the desired amount
-            self.components[solute] += (
-                ureg.Quantity(amount)
-                .to(
-                    "moles",
-                    "chem",
-                    mw=self.get_property(solute, "molecular_weight"),
-                    volume=self.volume,
-                    solvent_mass=self.solvent_mass,
-                )
-                .magnitude
-            )
-
-            # set the amount to zero and log a warning if the desired amount
-            # change would result in a negative concentration
-            if self.get_amount(solute, "mol").magnitude < 0:
-                self.logger.error(
-                    "Attempted to set a negative concentration for solute %s. Concentration set to 0" % solute
-                )
-                self.set_amount(solute, "0 mol")
-
-            # calculate the volume occupied by all the solutes
-            solute_vol = self._get_solute_volume()
-
-            # determine the volume of solvent that will preserve the original volume
-            target_vol = orig_volume - solute_vol
-
-            # adjust the amount of solvent
-            # volume in L, density in kg/m3 = g/L
-            target_mass = target_vol * ureg.Quantity(self.water_substance.rho, "g/L")
-
-            mw = self.get_property(self.solvent, "molecular_weight")
-            target_mol = target_mass / mw
-            self.components[self.solvent] = target_mol.magnitude
-
-        else:
-            # change the amount of the solute present
-            self.components[solute] += (
-                ureg.Quantity(amount)
-                .to(
-                    "moles",
-                    "chem",
-                    mw=self.get_property(solute, "molecular_weight"),
-                    volume=self.volume,
-                    solvent_mass=self.solvent_mass,
-                )
-                .magnitude
-            )
-
-            # set the amount to zero and log a warning if the desired amount
-            # change would result in a negative concentration
-            if self.get_amount(solute, "mol").magnitude < 0:
-                self.logger.error(
-                    "Attempted to set a negative concentration for solute %s. Concentration set to 0" % solute
-                )
-                self.set_amount(solute, "0 mol")
-
-            # update the volume to account for the space occupied by all the solutes
-            # make sure that there is still solvent present in the first place
-            if self.solvent_mass <= ureg.Quantity(0, "kg"):
-                self.logger.error("All solvent has been depleted from the solution")
-                return
-
-            # set the volume recalculation flag
-            self.volume_update_required = True
+        # Get the current amount of the solute
+        current_amt = self.get_amount(solute, amount.split(" ")[1])
+        if current_amt.magnitude == 0:
+            self.logger.warning(f"Add new solute {solute} to the solution")
+        new_amt = ureg.Quantity(amount) + current_amt
+        self.set_amount(solute, new_amt)
 
     def set_amount(self, solute: str, amount: str):
         """
@@ -2465,7 +2411,7 @@ class Solution(MSONable):
         """
         str_filename = str(filename)
         if not ("yaml" in str_filename.lower() or "json" in str_filename.lower()):
-            self.logger.error("Invalid file extension entered - %s" % str_filename)
+            self.logger.error("Invalid file extension entered - {str_filename}")
             raise ValueError("File extension must be .json or .yaml")
         if "yaml" in str_filename.lower():
             solution_dict = self.as_dict()

pyEQL/utils.py

@@ -60,6 +60,18 @@ def standardize_formula(formula: str):
         be enclosed in square brackets to remove any ambiguity in the meaning of the formula. For example, 'Na+',
         '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"]):
+        formula = formula.replace(str, rep)
+
+    # replace superscripts with non superscripts
+    for char, rep in zip("⁻⁺⁰¹²³⁴⁵⁶⁷⁸⁹", "-+0123456789"):
+        formula = formula.replace(char, rep)
+
+    # replace subscripts with non subscripts
+    for char, rep in zip("₀₁₂₃₄₅₆₇₈₉", "0123456789"):
+        formula = formula.replace(char, rep)
+
     sform = Ion.from_formula(formula).reduced_formula
 
     # TODO - manual formula adjustments. May be implemented upstream in pymatgen in the future
@@ -81,15 +93,49 @@ def standardize_formula(formula: str):
     # thiocyanate
     elif sform == "CSN[-1]":
         sform = "SCN[-1]"
-    # triiodide
+    # triiodide, nitride, an phosphide
     elif sform == "I[-0.33333333]":
         sform = "I3[-1]"
+    elif sform == "N[-0.33333333]":
+        sform = "N3[-1]"
+    elif sform == "P[-0.33333333]":
+        sform = "P3[-1]"
     # formate
     elif sform == "HCOO[-1]":
         sform = "HCO2[-1]"
     # oxalate
     elif sform == "CO2[-1]":
         sform = "C2O4[-2]"
+    # triflate
+    elif sform == "CS(OF)3[-1]":
+        sform = "CF3SO3[-1]"
+    # haloacetic acids of F, Cl, Br, I
+    elif sform == "C2Cl3O2[-1]":
+        sform = "CCl3COO[-1]"
+    elif sform == "C2O2F3[-1]":
+        sform = "CF3COO[-1]"
+    elif sform == "C2I3O2[-1]":
+        sform = "CI3COO[-1]"
+    elif sform == "C2Br3O2[-1]":
+        sform = "CBr3COO[-1]"
+
+    # Cl+F
+    elif sform == "C2Cl2O2F[-1]":
+        sform = "CFCl2COO[-1]"
+    elif sform == "C2Cl(OF)2[-1]":
+        sform = "CF2ClCOO[-1]"
+
+    # Cl+Br
+    elif sform == "C2Br(ClO)2[-1]":
+        sform = "CBrCl2COO[-1]"
+    elif sform == "C2Br2ClO2[-1]":
+        sform = "CBr2ClCOO[-1]"
+
+    # Cl+I
+    elif sform == "C2I(ClO)2[-1]":
+        sform = "CICl2COO[-1]"
+    elif sform == "C2I2ClO2[-1]":
+        sform = "CI2ClCOO[-1]"
 
     # TODO - consider adding recognition of special formulas like MeOH for methanol or Cit for citrate
     return sform

{pyEQL-1.1.0.dist-info → pyEQL-1.1.2.dist-info}/METADATA

@@ -1,20 +1,22 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 1.1.0
-Summary: Python tools for solution chemistry
-Home-page: https://github.com/KingsburyLab/pyEQL
-Author: Ryan Kingsbury
-Author-email: kingsbury@princeton.edu
-License: LGPL3
-Project-URL: Documentation, https://pyeql.readthedocs.io/
-Platform: any
+Version: 1.1.2
+Summary: A python interface for solution chemistry
+Author-email: Ryan Kingsbury <kingsbury@princeton.edu>
+Project-URL: Docs, https://pyeql.readthedocs.io/
+Project-URL: Repo, https://github.com/KingsburyLab/pyEQL
+Project-URL: Package, https://pypi.org/project/pyEQL
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Development Status :: 4 - Beta
-Classifier: Programming Language :: Python
 Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
 Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Software Development :: Libraries
 Requires-Python: >=3.9
-Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 License-File: COPYING
 License-File: AUTHORS.md
@@ -23,7 +25,7 @@ Requires-Dist: numpy <2
 Requires-Dist: scipy
 Requires-Dist: pymatgen ==2024.5.1
 Requires-Dist: iapws
-Requires-Dist: monty
+Requires-Dist: monty >=2024.7.12
 Requires-Dist: maggma >=0.67.0
 Requires-Dist: phreeqpython
 Provides-Extra: docs

{pyEQL-1.1.0.dist-info → pyEQL-1.1.2.dist-info}/RECORD

@@ -1,27 +1,26 @@
-pyEQL/__init__.py,sha256=JErflmaJVP373dm3-YGHUomFu05dgX0iXWS-Z5AgSTU,2118
+pyEQL/__init__.py,sha256=OCp_PiQEPyVoi1VX0ursBzHJWN6nDS1Id6bTBOgqCYs,1999
 pyEQL/activity_correction.py,sha256=eOixjgTd5hTrTRD5s6aPCCG12lAIH7-lRN0Z1qHu678,37151
-pyEQL/engines.py,sha256=b9ay7FYqmnINmhSMyNpVmENAtZVW-gyBfXUPf1PEUoY,34946
+pyEQL/engines.py,sha256=kE4ZtV2Z-zhOwtkH0cbv95oG1CETJmqMOoT0UfDuJeo,35221
 pyEQL/equilibrium.py,sha256=YCtoAJSgn1WC9NJnc3H4FTJdKQvogsvCuj7HqlKMtww,8307
 pyEQL/functions.py,sha256=nc-Hc61MmW-ELBR1PByJvQnELxM7PZexMHbU_O5-Bnw,10584
-pyEQL/pint_custom_units.txt,sha256=XHmcMlwVvqF9nEW7_e9Xgyq-xWEr-cDYqieas11T3eY,2882
 pyEQL/salt_ion_match.py,sha256=0nCZXmeo67VqcyYWQpPx-81hjSvnsg8HFB3fIyfjW_k,4070
 pyEQL/solute.py,sha256=no00Rc3tRfHmyht4wm2UXA1KZhKC45tWMO5QEkZY6yg,5140
-pyEQL/solution.py,sha256=XwtQmll3gPwdnnkXpQsnO7QebwTjplmlfhbEIU8rHDo,115940
-pyEQL/utils.py,sha256=unsY7zrrhl_1mOmt9_kumSKmLE5N5Hvh4bOErfS3nws,5168
+pyEQL/solution.py,sha256=vtC2xRUt1y2wTv_L1o7Qs3wr8b_X7wvkUsp56499baQ,113898
+pyEQL/utils.py,sha256=DWLtNm71qw5j4-jqBp5v3LssEjWgJnVvI6a_H60c5ic,6670
 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=TQKKofds7QBNd-Hw5QQuPwP6rQ8YWh_hHlRAtoQX0m8,1080793
+pyEQL/database/pyeql_db.json,sha256=-7Z8tpAddXhPlvpxms7cFQKL_DSSbemzOzxm6L5vaVk,1080801
 pyEQL/presets/Ringers lactate.yaml,sha256=vtSnuvgALHR27XEjpDzC0xyw5-E6b2FSsF1EUEBiWpw,413
 pyEQL/presets/normal saline.yaml,sha256=i2znhnIeXfNx1iMFFSif7crMRCFRP6xN1m7Wp7USduM,318
 pyEQL/presets/rainwater.yaml,sha256=S0WHZNDfCJyjSSFxNFdkypjn2s3P0jJGCiYIxvi1ibA,337
 pyEQL/presets/seawater.yaml,sha256=oryc1CkhRz20RpWE6uiGiT93HoZnqlB0s-0PmBWr3-U,843
 pyEQL/presets/urine.yaml,sha256=0Njtc-H1fFRo7UhquHdiSTT4z-8VZJ1utDCk02qk28M,679
 pyEQL/presets/wastewater.yaml,sha256=jTTFBpmKxczaEtkCZb0xUULIPZt7wfC8eAJ6rthGnmw,502
-pyEQL-1.1.0.dist-info/AUTHORS.md,sha256=K9ZLhKFwZ2zLlFXwN62VuUYCpr5T6n4mOUCUHlytTUs,415
-pyEQL-1.1.0.dist-info/COPYING,sha256=Ww2oUywfFTn242v9ksCgQdIVSpcMXJiKKePn0GFm25E,7649
-pyEQL-1.1.0.dist-info/LICENSE.txt,sha256=2Zf1F7RzbpeposgIxUydpurqNCMoMgDi2gAB65_GjwQ,969
-pyEQL-1.1.0.dist-info/METADATA,sha256=1KbuGQ1gjYRWA-8cq2cb_OmZgW8DTpKoCZ6_6DpQ9jo,5889
-pyEQL-1.1.0.dist-info/WHEEL,sha256=0XQbNV6JE5ziJsWjIU8TRRv0N6SohNonLWgP86g5fiI,109
-pyEQL-1.1.0.dist-info/top_level.txt,sha256=QMOaZjCAm_lS4Njsjh4L0B5aWnJFGQMYKhuH88CG1co,6
-pyEQL-1.1.0.dist-info/RECORD,,
+pyEQL-1.1.2.dist-info/AUTHORS.md,sha256=K9ZLhKFwZ2zLlFXwN62VuUYCpr5T6n4mOUCUHlytTUs,415
+pyEQL-1.1.2.dist-info/COPYING,sha256=Ww2oUywfFTn242v9ksCgQdIVSpcMXJiKKePn0GFm25E,7649
+pyEQL-1.1.2.dist-info/LICENSE.txt,sha256=2Zf1F7RzbpeposgIxUydpurqNCMoMgDi2gAB65_GjwQ,969
+pyEQL-1.1.2.dist-info/METADATA,sha256=1mxAOqZ5yuBRO4iDo2RZN7gpAcJMXYOfY_KKFPFMzQQ,6096
+pyEQL-1.1.2.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
+pyEQL-1.1.2.dist-info/top_level.txt,sha256=QMOaZjCAm_lS4Njsjh4L0B5aWnJFGQMYKhuH88CG1co,6
+pyEQL-1.1.2.dist-info/RECORD,,

{pyEQL-1.1.0.dist-info → pyEQL-1.1.2.dist-info}/WHEEL

@@ -1,6 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.2.0)
+Generator: setuptools (71.1.0)
 Root-Is-Purelib: true
-Tag: py2-none-any
 Tag: py3-none-any
 

pyEQL/pint_custom_units.txt

@@ -1,52 +0,0 @@
-#    Units definition file for pint library
-
-#    This file defines additional units and contexts to enable the pint
-#    library to process solution chemistry units such as mol/L and mol/kg.
-
-@context(mw=0,volume=0,solvent_mass=0) chemistry = chem
-    # mw is the molecular weight of the species
-    # volume is the volume of the solution
-    # solvent_mass is the mass of solvent in the solution
-
-    # moles -> mass require the molecular weight
-    [substance] -> [mass]: value * mw
-    [mass] -> [substance]: value / mw
-
-    # moles/volume -> mass/volume and moles/mass -> mass / mass
-    # require the  molecular weight
-    [substance] / [volume] -> [mass] / [volume]: value * mw
-    [mass] / [volume] -> [substance] / [volume]: value / mw
-    [substance] / [mass] -> [mass] / [mass]: value * mw
-    [mass] / [mass] -> [substance] / [mass]: value / mw
-
-    # moles/volume -> moles requires the solution volume
-    [substance] / [volume] -> [substance]: value * volume
-    [substance] -> [substance] / [volume]: value / volume
-
-    # moles/mass -> moles requires the solvent (usually water) mass
-    [substance] / [mass] -> [substance]: value * solvent_mass
-    [substance] -> [substance] / [mass]: value / solvent_mass
-
-    # moles/mass -> moles/volume require the solvent mass and the volume
-    [substance] / [mass] -> [substance]/[volume]: value * solvent_mass / volume
-    [substance] / [volume] -> [substance] / [mass]: value / solvent_mass * volume
-
-@end
-
-@context electricity = elec
-    [length] ** 2 * [mass] / [current] ** 2 / [time] ** 3 <-> [length] ** -2 * [mass] **-1 / [current] ** -2 / [time] ** -3: 1 / value
-@end
-
-
-#From the pint documentation:
-
-#@context(n=1) spectroscopy = sp
-#    # n index of refraction of the medium.
-#    [length] <-> [frequency]: speed_of_light / n / value
-#    [frequency] -> [energy]: planck_constant * value
-#    [energy] -> [frequency]: value / planck_constant
-#@end
-
-# The @context directive indicates the beginning of the transformations which are finished by the @end statement. You can optionally specify parameters for the context in parenthesis. All parameters are named and default values are mandatory. Multiple parameters are separated by commas (like in a python function definition). Finally, you provide the name of the context (e.g. spectroscopy) and, optionally, a short version of the name (e.g. sp) separated by an equal sign.
-# Conversions rules are specified by providing source and destination dimensions separated using a colon (:) from the equation. A special variable named value will be replaced by the source quantity. Other names will be looked first in the context arguments and then in registry.
-# A single forward arrow (->) indicates that the equations is used to transform from the first dimension to the second one. A double arrow (<->) is used to indicate that the transformation operates both ways.