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Merge pull request #78 from KingsburyLab/D_temp
D temp
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‎CHANGELOG.md

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@@ -5,24 +5,42 @@ All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [0.10.0] - 2023-11-10
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## [0.10.0] - 2023-11-12
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### Added
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- `Solution`: Revamped docstrings for `conductivity`, `get_transport_number`, `get_molar_conductivity`, and
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`get_diffusion_coefficient`.
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- `Solution`: new method `get_diffusion_coefficient` for dedicated retrieval of diffusion coefficients. This method
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implements an improved algorithm for temperature adjustment and a new algorithm for adjusting infinite dilution D values
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for ionic strengthe effects. The algorithm is identical to that implemented in PHREEQC >= 3.4.
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- Database: empirical parameters for temperature and ionic strength adjustment of diffusion coefficients for 15 solutes
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- Added tests for temperature and ionic strength adjustment and conductivity
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- Docs: new tutorial notebooks
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- Docs: remove duplicate contributing pages (Closes [#68](https://github.com/KingsburyLab/pyEQL/issues/68))
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- `Solution`: new method `to_file()` for more convenient saving Solution object to json or yaml files. (@kirill-push)
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- `Solution`: new method `from_file()` for more convenient loading Solution object from json or yaml files. (@kirill-push)
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- `Solution`: new classmethod `from_preset()` to `replace pyEQL.functions.autogenerate()` and instantiate a solution from a preset composition. (@kirill-push)
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### Changed
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- `Solution`: method af adjusting diffusion coefficients for temperature was updated (same as used in PHREEQC >= 3.4)
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- `Solution.conductvity`: improved equation (same as used in PHREEQC >= 3.4) which is more accurate at higher concentrations
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### Fixed
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- Database errors with `Cs[+1]` diffusion coefficient and `KBr` Pitzer parameters
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- Restored filter that suppresses duplicate log messages
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### Deprecated
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- `replace pyEQL.functions.autogenerate()` is now deprecated. Use `from_preset` instead.
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### Removed
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- The `activity_correction` kwarg in `get_transport_number` has been removed, because this now occurs by default and is
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handled in `get_diffusion_coefficient`.
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## [0.9.2] - 2023-11-07
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### Fixed

‎src/pyEQL/activity_correction.py

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import math
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from iapws import IAPWS95
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from pint import Quantity
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# the pint unit registry
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from pyEQL import ureg
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from pyEQL.logging_system import logger
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def _debye_parameter_B(temperature="25 degC"):
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def _debye_parameter_B(temperature: str = "25 degC") -> Quantity:
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"""
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Return the constant B used in the extended Debye-Huckel equation.
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Parameters
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----------
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temperature : str Quantity, optional
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String representing the temperature of the solution. Defaults to '25 degC' if not specified.
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Args:
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temperature: The temperature of the solution at which to calculate the constant.
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Defaults to '25 degC'.
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Notes
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-----
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The parameter B is equal to:
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Returns:
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The parameter B for use in extended Debye-Huckel equation (base e). For base 10,
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divide the resulting value by 2.303. Note that A is often given in base 10 terms
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in older textbooks and reference material (0.3281 at 25 degC).
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.. math:: B = ( {8 \\pi N_A e^2 \\over 1000 \\epsilon k T} ) ^ {1 \\over 2}
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Notes:
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The parameter B is equal to:
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References
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----------
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Bockris and Reddy. /Modern Electrochemistry/, vol 1. Plenum/Rosetta, 1977, p.210.
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.. math:: B = ( \\frac{{2 N_A \\rho_w e^2}{\\epsilon_o \\epsilon_r k T}) ^ {1 \\over 2}
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Examples:
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--------
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>>> _debye_parameter_B() #doctest: +ELLIPSIS
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0.3291...
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References:
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Bockris and Reddy. /Modern Electrochemistry/, vol 1. Plenum/Rosetta, 1977, p.210.
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Archer, Donald G. and Wang, Peiming. "The Dielectric Constant of Water \
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and Debye-Huckel Limiting Law Slopes." /J. Phys. Chem. Ref. Data/ 19(2), 1990.
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https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Physical_Chemistry_(LibreTexts)/25%3A_Solutions_II_-_Nonvolatile_Solutes/25.06%3A_The_Debye-Huckel_Theory
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https://en.wikipedia.org/wiki/Debye%E2%80%93H%C3%BCckel_equation
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"""
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water_substance = IAPWS95(
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T=ureg.Quantity(temperature).magnitude,
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T=ureg.Quantity(temperature).to("K").magnitude,
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P=ureg.Quantity("1 atm").to("MPa").magnitude,
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)
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param_B = (
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8
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* math.pi
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2
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* ureg.N_A
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* ureg.Quantity(water_substance.rho, "g/L")
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* ureg.elementary_charge**2
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/ (
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water_substance.mu
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* ureg.Quantity("1 g/L") # in g/L
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* ureg.epsilon_0
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* water_substance.epsilon
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* ureg.boltzmann_constant
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* ureg.Quantity(temperature)
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)
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/ (ureg.epsilon_0 * water_substance.epsilon * ureg.boltzmann_constant * ureg.Quantity(temperature))
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) ** 0.5
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return param_B.to_base_units()
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def _debye_parameter_activity(temperature="25 degC"):
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def _debye_parameter_activity(temperature: str = "25 degC") -> "Quantity":
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"""
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Return the constant A for use in the Debye-Huckel limiting law (base 10).
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Return the constant A for use in the Debye-Huckel limiting law (base e).
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Parameters
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----------
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temperature : str Quantity, optional
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String representing the temperature of the solution. Defaults to '25 degC' if not specified.
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Args:
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temperature: The temperature of the solution at which to calculate the constant.
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Defaults to '25 degC'.
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Returns
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-------
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Quantity The parameter A for use in the Debye-Huckel limiting law (base e)
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Returns:
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The parameter A for use in the Debye-Huckel limiting law (base e). For base 10,
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divide the resulting value by 2.303. Note that A is often given in base 10 terms
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in older textbooks and reference material (0.509 at 25 degC).
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Notes
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-----
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The parameter A is equal to:
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Notes:
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The parameter A is equal to:
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.. math::
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A^{\\gamma} = {e^3 ( 2 \\pi N_A {\\rho})^{0.5} \\over (4 \\pi \\epsilon_o \\epsilon_r k T)^{1.5}}
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.. math::
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A^{\\gamma} = {e^3 ( 2 \\pi N_A {\\rho})^{0.5} \\over (4 \\pi \\epsilon_o \\epsilon_r k T)^{1.5}}
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Note that this equation returns the parameter value that can be used to calculate
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the natural logarithm of the activity coefficient. For base 10, divide the
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value returned by 2.303. The value is often given in base 10 terms (0.509 at
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25 degC) in older textbooks.
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Note that this equation returns the parameter value that can be used to calculate
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the natural logarithm of the activity coefficient. For base 10, divide the
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value returned by 2.303.
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References
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----------
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Archer, Donald G. and Wang, Peiming. "The Dielectric Constant of Water \
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and Debye-Huckel Limiting Law Slopes." /J. Phys. Chem. Ref. Data/ 19(2), 1990.
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References:
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Archer, Donald G. and Wang, Peiming. "The Dielectric Constant of Water \
92+
and Debye-Huckel Limiting Law Slopes." /J. Phys. Chem. Ref. Data/ 19(2), 1990.
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Examples:
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--------
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>>> _debye_parameter_activity() #doctest: +ELLIPSIS
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1.17499...
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https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Physical_Chemistry_(LibreTexts)/25%3A_Solutions_II_-_Nonvolatile_Solutes/25.06%3A_The_Debye-Huckel_Theory
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https://en.wikipedia.org/wiki/Debye%E2%80%93H%C3%BCckel_equation
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See Also:
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:py:func:`_debye_parameter_osmotic`
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"""
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water_substance = IAPWS95(
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T=ureg.Quantity(temperature).magnitude,
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T=ureg.Quantity(temperature).to("K").magnitude,
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P=ureg.Quantity("1 atm").to("MPa").magnitude,
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)
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debyeparam = (
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ureg.elementary_charge**3
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* (2 * math.pi * ureg.N_A * water_substance.rho * ureg.Quantity("1 g/L")) ** 0.5
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* (2 * math.pi * ureg.N_A * ureg.Quantity(water_substance.rho, "g/L")) ** 0.5
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/ (
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4
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* math.pi

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