pyrast 0.1.0__tar.gz

pyrast-0.1.0/LICENSE.md

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+Copyright (c) 2026 Jonah Finkelstein
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pyrast-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyrast
+Version: 0.1.0
+Author-email: Jonah Finkelstein <jonahfinkelstein2030@u.northwestern.edu>
+Keywords: adsorption,thermodynamics,isotherm
+Requires-Python: >=3.6
+Description-Content-Type: text/x-rst
+License-File: LICENSE.md
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Provides-Extra: all
+Requires-Dist: pyrast[dev,docs,test]; extra == "all"
+Provides-Extra: dev
+Requires-Dist: pyrast[docs,test]; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: ipykernel; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Provides-Extra: test
+Dynamic: license-file
+
+.. image:: https://raw.githubusercontent.com/snurr-group/pyRAST/refs/heads/main/docs/source/_static/pyrast_logo_200x200.png
+    :alt: pyRAST logo
+    :align: center
+    :width: 200px
+
+========
+Overview
+========
+
+Python Real Adsorbed Solution Theory (pyRAST) is a package for modeling adsorption
+using ideal and real adsorbed solution theories. pyRAST was designed to be user-friendly
+and flexible, allowing users to easily control the fitting and calculation process.
+
+
+.. badges
+
+|status| |docs| |license|
+
+
+.. |status| image:: https://www.repostatus.org/badges/latest/active.svg
+    :alt: Project Status: Active - The project has reached a stable, usable state and is being actively developed.
+    :target: https://www.repostatus.org/#active
+
+.. |docs| image:: https://readthedocs.org/projects/pyrast/badge/?style=flat
+    :target: https://readthedocs.org/projects/pyrast
+    :alt: Documentation Status
+
+.. |license| image:: https://img.shields.io/badge/License-MIT-yellow.svg
+    :target: https://opensource.org/licenses/MIT
+    :alt: Project License
+
+Features
+--------
+- Analytical single component isotherm fitting
+- Vacancy solution theory (VST) isotherm fitting
+- Single component interpolator isotherms
+- Activity coefficient fitting for binary adsorbed mixtures (component loading or total loading)
+- Multicomponent forward and reverse IAST calculations
+- Binary forward and reverse RAST calculations
+
+Usage
+-----
+Please see the `tutorial <https://pyrast.readthedocs.io/en/latest/tutorial/index.html>`__ for a detailed overview
+of pyRAST's functionality and usage. If you are looking for detailed documentation, please see the
+`reference <https://pyrast.readthedocs.io/en/latest/reference/index.html>`__ section. For a detailed
+description of the underlying theory, please see the manuscript (link to be added).
+
+Installation
+============
+pyRAST is available on pyPI and can be installed using pip: ::
+
+    pip install pyrast
+
+
+Citation
+========
+If you used pyRAST in your research, please cite the following paper: ::
+
+    To be added
+
+pyRAST was built on the foundation of `pyIAST <https://github.com/CorySimon/pyIAST>`__ by Cory Simon
+and pulled ideas from `pyGAPS <https://github.com/pauliacomi/pyGAPS>`__ by Paul Iacomi. Please
+check out the work of these developers, too!
+
+Acknowledgements
+================
+pyRAST was developed by Jonah Finkelstein in the Snurr Research Group at Northwestern University.
+The development of pyRAST was supported by: TBD
+
+Development
+===========
+If you wish to install pyRAST in development mode, clone the repository and run the following command in the root directory: ::
+
+    pip install -e .[dev]
+
+If you wish to contribute to the development of pyRAST, please submit a `pull request <https://github.com/snurr-group/pyRAST/pulls>`__ 
+on the GitHub Repository or contact Jonah Finkelstein.
+
+Questions?
+==========
+If you have any questions, please contact Jonah Finkelstein at jonahfinkelstein2030@u.northwestern.edu.
+Alternatively, you can open an `issue <https://github.com/snurr-group/pyRAST/issues>`__ on the GitHub repository.

pyrast-0.1.0/README.rst

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+.. image:: https://raw.githubusercontent.com/snurr-group/pyRAST/refs/heads/main/docs/source/_static/pyrast_logo_200x200.png
+    :alt: pyRAST logo
+    :align: center
+    :width: 200px
+
+========
+Overview
+========
+
+Python Real Adsorbed Solution Theory (pyRAST) is a package for modeling adsorption
+using ideal and real adsorbed solution theories. pyRAST was designed to be user-friendly
+and flexible, allowing users to easily control the fitting and calculation process.
+
+
+.. badges
+
+|status| |docs| |license|
+
+
+.. |status| image:: https://www.repostatus.org/badges/latest/active.svg
+    :alt: Project Status: Active - The project has reached a stable, usable state and is being actively developed.
+    :target: https://www.repostatus.org/#active
+
+.. |docs| image:: https://readthedocs.org/projects/pyrast/badge/?style=flat
+    :target: https://readthedocs.org/projects/pyrast
+    :alt: Documentation Status
+
+.. |license| image:: https://img.shields.io/badge/License-MIT-yellow.svg
+    :target: https://opensource.org/licenses/MIT
+    :alt: Project License
+
+Features
+--------
+- Analytical single component isotherm fitting
+- Vacancy solution theory (VST) isotherm fitting
+- Single component interpolator isotherms
+- Activity coefficient fitting for binary adsorbed mixtures (component loading or total loading)
+- Multicomponent forward and reverse IAST calculations
+- Binary forward and reverse RAST calculations
+
+Usage
+-----
+Please see the `tutorial <https://pyrast.readthedocs.io/en/latest/tutorial/index.html>`__ for a detailed overview
+of pyRAST's functionality and usage. If you are looking for detailed documentation, please see the
+`reference <https://pyrast.readthedocs.io/en/latest/reference/index.html>`__ section. For a detailed
+description of the underlying theory, please see the manuscript (link to be added).
+
+Installation
+============
+pyRAST is available on pyPI and can be installed using pip: ::
+
+    pip install pyrast
+
+
+Citation
+========
+If you used pyRAST in your research, please cite the following paper: ::
+
+    To be added
+
+pyRAST was built on the foundation of `pyIAST <https://github.com/CorySimon/pyIAST>`__ by Cory Simon
+and pulled ideas from `pyGAPS <https://github.com/pauliacomi/pyGAPS>`__ by Paul Iacomi. Please
+check out the work of these developers, too!
+
+Acknowledgements
+================
+pyRAST was developed by Jonah Finkelstein in the Snurr Research Group at Northwestern University.
+The development of pyRAST was supported by: TBD
+
+Development
+===========
+If you wish to install pyRAST in development mode, clone the repository and run the following command in the root directory: ::
+
+    pip install -e .[dev]
+
+If you wish to contribute to the development of pyRAST, please submit a `pull request <https://github.com/snurr-group/pyRAST/pulls>`__ 
+on the GitHub Repository or contact Jonah Finkelstein.
+
+Questions?
+==========
+If you have any questions, please contact Jonah Finkelstein at jonahfinkelstein2030@u.northwestern.edu.
+Alternatively, you can open an `issue <https://github.com/snurr-group/pyRAST/issues>`__ on the GitHub repository.

pyrast-0.1.0/pyproject.toml

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+[project]
+name = "pyrast"
+version = "0.1.0"
+readme = "README.rst"
+keywords = ["adsorption", "thermodynamics", "isotherm"]
+requires-python = ">=3.6"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Jonah Finkelstein", email = "jonahfinkelstein2030@u.northwestern.edu"}
+]
+dependencies = [
+    "numpy",
+    "scipy",
+    "pandas",
+    "matplotlib",
+]
+
+[project.optional-dependencies]
+all = ["pyrast[dev,docs,test]"]
+dev = [
+    "pyrast[test,docs]",
+    "ruff",
+    "ipykernel",
+]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+]
+test = [
+    
+]
+
+
+[tool.ruff]
+target-version = "py314"
+line-length = 88
+
+[tool.ruff.lint]
+extend-select = [
+    "F",        # Pyflakes rules
+    "W",        # PyCodeStyle warnings
+    "E",        # PyCodeStyle errors
+    "I",        # Sort imports properly
+    "UP",       # Warn if certain things can changed due to newer Python versions
+    "C4",       # Catch incorrect use of comprehensions, dict, list, etc
+    "FA",       # Enforce from __future__ import annotations
+    "ISC",      # Good use of string concatenation
+    "ICN",      # Use common import conventions
+    "RET",      # Good return practices
+    "SIM",      # Common simplification rules
+    "TID",      # Some good import practices
+    "TC",       # Enforce importing certain types in a TYPE_CHECKING block
+    "PTH",      # Use pathlib instead of os.path
+    "TD",       # Be diligent with TODO comments
+    "NPY",      # Some numpy-specific things
+    "COM",      # enforce trailing comma rules
+    "DTZ",      # require strict timezone manipulation with datetime
+    "FBT",      # detect boolean traps
+    "N",        # enforce naming conventions, e.g. ClassName vs function_name
+    "A",        # detect shadowed builtins
+    "BLE",      # disallow catch-all exceptions
+    "S",        # disallow things like "exec"
+]
+
+[tool.ruff.format]
+quote-style = "single"
+indent-style = "space"
+
+[build-system]
+requires=["setuptools"]
+build-backend = "setuptools.build_meta"

pyrast-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

pyrast-0.1.0/src/pyrast/activity_coefficients/__init__.py

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+# ruff: noqa: F401
+from .a_margules import AMargules
+from .a_nrtl import ANRTL
+from .activity_coefficient import ActivityCoefficient
+from .s_margules import SMargules
+from .s_nrtl import SNRTL
+from .van_laar import VanLaar
+from .wilson import Wilson

pyrast-0.1.0/src/pyrast/activity_coefficients/a_margules.py

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+"""Implementation of Asymmetric Margules Model"""
+
+import numpy as np
+
+from pyrast.activity_coefficients.activity_coefficient import ActivityCoefficient
+
+
+class AMargules(ActivityCoefficient, model_name='aMargules'):
+    r"""
+    The Asymmetric Margules model is an extension of the traditional Margules model that
+    allows for asymmetry in the activity coefficients of the components in a
+    binary mixture. It is best suited for mixtures where adsorbates differ slightly in
+    size, shape, or polarity. It is more flexible than the symmetric Margules model, but
+    is not great for highly non-ideal mixtures.
+
+    The excess Gibbs free energy in the Asymmetric Margules model is given by:
+
+    .. math:: \frac{g^E}{RT} = x_1 x_2 (A_{12} x_2 + A_{21} x_1) (1 - e^{-C \phi})
+
+    Source: Krishna, R. & van Baten, J. M. How reliable is the Real Adsorbed Solution
+    Theory (RAST) for estimating ternary mixture equilibrium in microporous host
+    materials? Fluid Phase Equilibria 589, 114260 (2025).
+    """
+    # Class variables for every instance
+    name = 'aMargules'
+    param_names = ('A12', 'A21', 'C')
+    param_default_bounds = ((-np.inf, np.inf), (-np.inf, np.inf), (0.0, np.inf))
+    param_ideal_values = (0.0, 0.0)
+
+    def ln_gamma(self, x, phi):
+        r"""Calculates the natural log of the activity coefficients for each component.
+
+        In the Asymmetric Margules model, the activity coefficients are calculated as:
+
+        .. math::
+            \ln \gamma_1 = x_2^2 (A_{12} + 2(A_{21} - A_{12}) x_1) (1 - e^{-C \phi})
+
+            \ln \gamma_2 = x_1^2 (A_{21} + 2(A_{12} - A_{21}) x_2) (1 - e^{-C \phi})
+
+        Args:
+            x (array-like): Mole fractions of the components in the mixture.
+            phi (float): Spreading pressure for the mixture.
+
+        Returns:
+            np.ndarray: Natural log of the activity coefficients for each component.
+        """
+        a12 = self.model_parameters['A12']
+        a21 = self.model_parameters['A21']
+        c = self.model_parameters['C']
+        f = 1.0 - np.exp(-c * phi)
+        ln_gamma0 = x[1]**2 * f * (a12 + 2*(a21 - a12)*x[0])
+        ln_gamma1 = x[0]**2 * f * (a21 + 2*(a12 - a21)*x[1])
+        return np.array([ln_gamma0, ln_gamma1])
+
+    def inverse_excess_loading(self, x, phi):
+        r"""Calculates the inverse of the excess loading given composition and phi.
+
+        The excess loading in the Asymmetric Margules model is calculated as:
+
+        .. math::
+            \left(\frac{1}{q}\right)^E = C x_1 x_2 (A_{12} x_2 + A_{21} x_1)
+            e^{-C \phi}
+
+        Args:
+            x (array-like): Mole fractions of the components in the mixture.
+            phi (float): Spreading pressure for the mixture.
+
+        Returns:
+            float: Inverse of the excess loading for the mixture.
+        """
+        a12 = self.model_parameters['A12']
+        a21 = self.model_parameters['A21']
+        c = self.model_parameters['C']
+
+        return c * x[0] * x[1] * np.exp(-c * phi) * (a12*x[1] + a21*x[0])

pyrast-0.1.0/src/pyrast/activity_coefficients/a_nrtl.py

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+"""Implementation of Asymmetric NRTL Model"""
+
+import numpy as np
+
+from pyrast.activity_coefficients.activity_coefficient import ActivityCoefficient
+
+
+class ANRTL(ActivityCoefficient, model_name='aNRTL'):
+    r"""
+    The Asymmetric NRTL model is analagous to the Asymmetric NRTL model for vapor liquid
+    equlibria. The Asymmetric NRTL model is best suited for: UPDATE
+
+    The excess Gibbs free energy in the Asymmetric NRTL model is given by:
+
+    .. math::
+        \frac{g^E}{RT} = \frac{x_1 x_2 \tau_{12} (G_{12} - 1)}
+            {x_1 G_{12} + x_2} (1 - e^{-C \phi})
+
+        G_{12} = \exp(-\alpha \tau_{12}), \ \tau_{12} = -\tau_{21}, \ \alpha = 0.3
+
+    Sources: Kaur, H., Tun, H., Sees, M. & Chen, C.-C. Local composition activity
+    coefficient model for mixed-gas adsorption equilibria. Adsorption 25, 951-964
+    (2019).
+
+    Kopatsis, A., Salinger, A. & Myers, A. L. Thermodynamics of solutions with solvent
+    and solute in different pure states. AIChE Journal 34, 1275-1286 (1988).
+    """
+    # Class variables for every instance
+    name = 'aNRTL'
+    param_names = ('t12', 'C')
+    param_default_bounds = ((-np.inf, np.inf), (0.0, np.inf))
+    param_ideal_values = (1.0,)
+    alpha = 0.3
+
+    def ln_gamma(self, x, phi):
+        r"""Calculates the natural log of the activity coefficients for each component.
+
+        In the Asymmetric NRTL model, the activity coefficients are calculated as:
+
+        .. math::
+            \ln \gamma_1 = \frac{x_2^2 \tau_{12} (G_{12} - 1)}{(x_1 G_{12} + x_2)^2}
+            (1 - e^{-C \phi})
+
+            \ln \gamma_2 = \frac{x_1^2 \tau_{21} (G_{21} - 1)}{(x_2 G_{21} + x_1)^2}
+            (1 - e^{-C \phi})
+
+        Args:
+            x (array-like): Mole fractions of the components in the mixture.
+            phi (float): Spreading pressure for the mixture.
+
+        Returns:
+            np.ndarray: Natural log of the activity coefficients for each component.
+        """
+        t12 = self.model_parameters['t12']
+        t21 = -t12
+        c = self.model_parameters['C']
+        f = 1.0 - np.exp(-c * phi)
+        alpha = self.alpha
+        g12 = np.exp(-alpha*t12)
+        g21 = np.exp(-alpha*t21)
+
+        ln_gamma0 = x[1]**2 * f * t12 * (g12 - 1.0) / (x[0] * g12 + x[1])**2
+        ln_gamma1 = x[0]**2 * f * t21 * (g21 - 1.0) / (x[1] * g21 + x[0])**2
+        return np.array([ln_gamma0, ln_gamma1])
+
+    def inverse_excess_loading(self, x, phi):
+        r"""Calculates the inverse of the excess loading given composition and phi.
+
+        The excess loading in the Asymmetric NRTL model is calculated as:
+
+        .. math:: \left(\frac{1}{q}\right)^E = \frac{x_1 x_2 \tau_{12} (G_{12} - 1)}
+            {x_1 G_{12} + x_2} C e^{-C \phi}
+
+        Args:
+            x (array-like): Mole fractions of the components in the mixture.
+            phi (float): Spreading pressure for the mixture.
+
+        Returns:
+            float: Inverse of the excess loading for the mixture.
+        """
+        t12 = self.model_parameters['t12']
+        g12 = np.exp(-self.alpha*t12)
+        c = self.model_parameters['C']
+
+        return c * x[0] * x[1] * t12 * (g12 - 1.0) * np.exp(-c * phi) / \
+               (x[0]*g12 + x[1])