pyEQL 1.1.5__py3-none-any.whl → 1.1.6__py3-none-any.whl

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 +67,10 @@ 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 +86,16 @@ 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.
 
@@ -107,8 +121,8 @@ 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"
     )
 
 
@@ -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/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

@@ -137,6 +137,12 @@ def standardize_formula(formula: str):
     elif sform == "C2I2ClO2[-1]":
         sform = "CI2ClCOO[-1]"
 
+    # 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-1.1.6.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-1.1.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyEQL
-Version: 1.1.5
+Version: 1.1.6
 Summary: A python interface for solution chemistry
 Author-email: Ryan Kingsbury <kingsbury@princeton.edu>
 Project-URL: Docs, https://pyeql.readthedocs.io/
@@ -21,13 +21,13 @@ 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: numpy <2,>1.26
+Requires-Dist: scipy >=1.12
 Requires-Dist: pymatgen ==2024.5.1
-Requires-Dist: iapws
+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'
@@ -35,14 +35,14 @@ 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/)

{pyEQL-1.1.5.dist-info → pyEQL-1.1.6.dist-info}/RECORD

@@ -2,11 +2,11 @@ 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=nc-Hc61MmW-ELBR1PByJvQnELxM7PZexMHbU_O5-Bnw,10584
+pyEQL/functions.py,sha256=BZXkiNJWuo4ZMQSVdFQkwqQmzbSkwi-vg1DFFQuFsos,11435
 pyEQL/salt_ion_match.py,sha256=0nCZXmeo67VqcyYWQpPx-81hjSvnsg8HFB3fIyfjW_k,4070
 pyEQL/solute.py,sha256=no00Rc3tRfHmyht4wm2UXA1KZhKC45tWMO5QEkZY6yg,5140
-pyEQL/solution.py,sha256=0eaPmI3bm_ipGyXtZCcQQ5kuA8Bv_0DBYZeZZ3eWXYk,115758
-pyEQL/utils.py,sha256=DWLtNm71qw5j4-jqBp5v3LssEjWgJnVvI6a_H60c5ic,6670
+pyEQL/solution.py,sha256=3hvtqeu5KzfFKzeOdKlzS_aIFPTNgUfhjIwBurfuGJw,115754
+pyEQL/utils.py,sha256=zOXqg89jTqD1mPVAtlBbRxkpP9-IdHfJpK_1VDOywIQ,6828
 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
@@ -17,10 +17,10 @@ pyEQL/presets/rainwater.yaml,sha256=S0WHZNDfCJyjSSFxNFdkypjn2s3P0jJGCiYIxvi1ibA,
 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-1.1.5.dist-info/AUTHORS.md,sha256=K9ZLhKFwZ2zLlFXwN62VuUYCpr5T6n4mOUCUHlytTUs,415
-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,,
+pyEQL-1.1.6.dist-info/AUTHORS.md,sha256=Ukdh6f3jO6jdgl2k_r_xdNOuzmjXcISMQqUTSH39QVw,506
+pyEQL-1.1.6.dist-info/COPYING,sha256=Ww2oUywfFTn242v9ksCgQdIVSpcMXJiKKePn0GFm25E,7649
+pyEQL-1.1.6.dist-info/LICENSE.txt,sha256=2Zf1F7RzbpeposgIxUydpurqNCMoMgDi2gAB65_GjwQ,969
+pyEQL-1.1.6.dist-info/METADATA,sha256=zV5ynllRkS-BEc8prG7c-e_7O7tR4MOvAgX2altqT08,6160
+pyEQL-1.1.6.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
+pyEQL-1.1.6.dist-info/top_level.txt,sha256=QMOaZjCAm_lS4Njsjh4L0B5aWnJFGQMYKhuH88CG1co,6
+pyEQL-1.1.6.dist-info/RECORD,,

{pyEQL-1.1.5.dist-info → pyEQL-1.1.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.0.0)
+Generator: setuptools (74.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any