pychnosz 1.1.12__cp310-cp310-macosx_15_0_x86_64.whl

pychnosz-1.1.12.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: pychnosz
+Version: 1.1.12
+Summary: Python port of the package CHNOSZ
+Author-email: Grayson Boyer <gmboyer@asu.edu>
+Maintainer-email: Grayson Boyer <gmboyer@asu.edu>
+License: MIT License
+Project-URL: Homepage, https://worm-portal.asu.edu
+Project-URL: Repository, https://github.com/worm-portal/pychnosz
+Project-URL: Documentation, https://worm-portal.asu.edu/pyCHNOSZ-docs/index.html
+Project-URL: Issues, https://github.com/worm-portal/pychnosz/issues
+Keywords: thermodynamics,geochemistry,geobiochemistry,aqueous chemistry,equilibrium,phase diagrams
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+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: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: matplotlib>=3.3.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=4.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Provides-Extra: interactive
+Requires-Dist: plotly>=5.0.0; extra == "interactive"
+Requires-Dist: ipython>=7.0.0; extra == "interactive"
+Dynamic: license-file
+
+# pyCHNOSZ
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11406142.svg)](https://doi.org/10.5281/zenodo.11406142)
+
+Author: Dr. Grayson Boyer, GEOPIG Lab, Arizona State University
+
+[CHNOSZ](https://www.chnosz.net/) is a package written by [Dr. Jeff Dick](https://chnosz.net/jeff/) for performing thermodynamic calculations in aqueous geochemistry and biogeochemistry. pyCHNOSZ is a Python conversion of CHNOSZ that allows these calculations to be carried out in Python 3 Jupyter notebooks.
+
+## Features
+
+The following CHNOSZ functions are supported in pyCHNOSZ:
+
+- [info](https://chnosz.net/manual/info.html) - Search for chemical species by name or formula and retrieve their thermodynamic parameters.
+- [add_OBIGT](https://chnosz.net/manual/add.OBIGT.html) - Add or overwrite species in the OBIGT thermodynamic database by supplying a comma separated value (csv) file with custom data.
+- [mod_OBIGT](https://chnosz.net/manual/add.OBIGT.html) - Modify species in the OBIGT thermodynamic database. Optionally, supply a Pandas dataframe containing custom data.
+- [reset](https://chnosz.net/manual/thermo.html) - reset data to default values.
+- [subcrt](https://chnosz.net/manual/subcrt.html) - Calculate standard state partial molal thermodynamic properties of reactions at elevated temperatures and pressures.
+- [basis](https://chnosz.net/manual/basis.html) - Define basis species of a chemical system.
+- [species](https://chnosz.net/manual/species.html) - Define the species of interest in a system.
+- [equilibrate](https://chnosz.net/manual/equilibrate.html) - Calculate equilibrium chemical activities of species from the affinities of formation of the species at unit activity.
+- [affinity](https://chnosz.net/manual/affinity.html) - Calculate the chemical affinities of formation reactions of species.
+- [diagram](https://chnosz.net/manual/diagram.html) - Plot equilibrium chemical activity (1-D speciation) or equal-activity (2-D predominance) diagrams as a function of chemical activities of basis species, temperature and/or pressure.
+- And more. See the [documentation for pyCHNOSZ](https://worm-portal.asu.edu/pyCHNOSZ-docs/fun.html)
+
+
+## Requirements
+
+This package must be installed into an environment with an [R](https://www.r-project.org/) installation. See [these instructions](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/) for installing R with Anaconda. Additionally, the CHNOSZ package for R must be installed (see instructions below).
+
+## Installation
+
+### Installing pyCHNOSZ
+
+Install pyCHNOSZ using pip:
+
+```
+$ pip install pychnosz
+```
+
+## Usage
+
+Import pyCHNOSZ in your python code with:
+```python
+import pychnosz
+```
+
+In the following examples, pyCHNOSZ functions are imported with:
+```python
+from pychnosz import info, add_OBIGT, mod_OBIGT, reset, subcrt
+```
+
+### Search for chemical species
+
+The `info()` function can be used to look up chemical species by name or formula. If names or formulas are provided, database index integers are returned. A list of integers will look up chemical species by index and return a table of thermodynamic properties. See the `info()` function's [original documentation](https://chnosz.net/manual/info.html) to learn more about what this function can do. A few examples are shown below.
+
+Look up the database index value of Fe+2:
+
+```python
+info("Fe+2")
+```
+
+Look up multiple chemical species:
+
+```python
+info(["HCO3-", "CH4"])
+```
+
+Define chemical states:
+
+```python
+info(["HCO3-", "CH4"], state=["aq", "gas"])
+```
+
+Search species by index values to look up their thermodynamic parameters.
+
+```python
+info([13, 872])
+```
+
+Nest `info` functions to look up thermodynamic properties directly from names or formulas:
+
+```python
+info(info("Fe+2"))
+```
+
+### Add or replace thermodynamic data in the database
+
+See the original R documentation for `add_OBIGT()` and `reset()` for basic useage. A few examples are given below.
+
+Load the SUPCRT92 database.
+
+```python
+a = add_OBIGT("SUPCRT92")
+```
+
+The variable `a` is assigned a list of integers corresponding to the indices of chemical species that are added or replaced in the OBIGT thermodynamic database used by pyCHNOSZ.
+
+It is possible to add a custom table of thermodynamic parameters.
+
+```python
+a = add_OBIGT("my_custom_entries.csv")
+info(a) # confirm new entries have been added
+```
+
+The entries of `my_custom_entries.csv` would then be available for thermodynamic calculations with `subcrt()`, for example.
+
+Reset thermodynamic database to its original configuration.
+
+```python
+reset()
+```
+
+Modify values in the thermodynamic database with `mod_OBIGT()`:
+
+```python
+mod_OBIGT("HCO3-", G = -140283.7, Cp = -9)
+info(info("HCO3-"))
+```
+
+### Calculate thermodynamic properties of reactions
+
+See the [original documentation](https://chnosz.net/manual/subcrt.html) for `subcrt()`. Useage in pyCHNOSZ is the same, except python lists are used in place of R's vectors. The function produces a dictionary of results stored in pandas dataframes. An example is shown below for the reaction H<sub>2 (aq)</sub> + 0.5 O<sub>2 (gas)</sub> = H<sub>2</sub>O<sub>(liq)</sub> at 30 and 50 degrees C and 100 bars pressure:
+
+```python
+subcrt(species=["H2", "O2", "H2O"], coeff=[-1.0, -0.5, 1.0],
+       state=["aq", "gas", "liq"], T=[30, 50], P=100)
+```
+
+Output is a python dictionary of dataframes:
+```
+subcrt: 3 species at 2 values of T (ºC) and P (bar) (wet) [energy units: cal]
+
+{'reaction':       coeff    name formula state  ispecies
+ 62     -1.0      H2      H2    aq      62.0
+ 2612   -0.5  oxygen      O2   gas    2612.0
+ 1       1.0   water     H2O   liq       1.0,
+ 'out':       T    P       rho       logK             G             H         S  \
+ 1  30.0  100  1.000017  43.855086 -60832.380282 -67420.887872 -21.89070   
+ 2  50.0  100  0.992305  40.834419 -60379.262657 -67882.530994 -23.36663   
+ 
+           V         Cp  
+ 1 -7.494052 -24.126268  
+ 2 -8.259704 -20.941879  }
+```
+
+### More examples:
+
+For more examples, check out the [pyCHNOSZ tutorial notebooks available from the WORM Library](https://github.com/worm-portal/WORM-Library/tree/master/2-Reaction-Properties).

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pychnosz-1.1.12.dist-info/WHEEL

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pychnosz-1.1.12.dist-info/licenses/LICENSE.txt

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+Copyright (c) 2025 Grayson Boyer and GEOPIG Lab. The original CHNOSZ belongs to Jeff Dick.
+
+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.

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