feat: geochemistrypi-chemical-modeling

geochemistrypi-chemical-modeling/.gitignore

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geochemistrypi-chemical-modeling/LICENSE.txt

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+MIT License
+
+Copyright (c) [2024] [Chufan Zhou]
+
+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 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.

geochemistrypi-chemical-modeling/README.md

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+# GeochemistryPi Chemical Modeling
+
+A Python package for solving geochemistry equations using different numerical methods (fsolve and root).
+
+## Features
+
+- Solve chemical equations using scipy.optimize.fsolve
+- Solve chemical equations using scipy.optimize.root
+- Compare results from both methods
+- Command-line interface for easy use
+
+## Installation
+
+```bash
+pip install geochemistrypi-chemical-modeling
+```
+
+## Usage
+
+```bash
+# Using fsolve method
+geochemistrypi solve --initial-guess 0.5 0.5 2.0
+
+# Using root method
+geochemistrypi root-method --initial-guess 0.5 0.5 2.0
+
+# Compare both methods
+geochemistrypi compare --initial-guess 0.5 0.5 2.0
+```
+
+## Requirements
+
+- Python >= 3.8
+- numpy
+- scipy
+- typer
+- rich
+
+## Development
+
+To contribute to this project:
+
+1. Clone the repository
+2. Install development dependencies:
+```bash
+pip install -e ".[dev]"
+```
+3. Run tests:
+```bash
+python -m pytest
+```
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE.txt file for details.
+
+## Author
+
+Chufan Zhou (1176733817@qq.com)

geochemistrypi-chemical-modeling/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "geochemistrypi-chemical-modeling"
+version = "0.1.0"
+authors = [
+  { name="Chufan Zhou", email="1176733817@qq.com" },
+]
+description = "A package for chemical modeling using fsolve and root methods."
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: MIT License",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Intended Audience :: Science/Research",
+]
+license = "MIT"
+license-files = ["LICENSE.txt"]
+dependencies = [
+    "numpy",
+    "scipy",
+    "typer",
+    "rich",
+]
+
+[project.urls]
+Homepage = "https://github.com/Yoko286/Geochemistrypi-chemical-modeling"
+Issues = "https://github.com/Yoko286/Geochemistrypi-chemical-modeling/issues"
+Documentation = "https://geochemistrypi.readthedocs.io/"
+
+[tool.hatch.build]
+directory = "dist"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src"]
+
+[project.scripts]
+geochemistrypi = "geochemistrypi.cli:app"

geochemistrypi-chemical-modeling/src/cli.py

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+from typing import Tuple
+import typer
+from .fsolve import solve_equations as fsolve_solve
+from .root import equations, jacobi_matrix
+from scipy.optimize import root
+
+app = typer.Typer(help="A command line tool to compare fsolve and root methods for solving equations.")
+
+@app.command()
+def fsolve(
+    phi_ref: float = typer.Option(0.5, "--phi-ref", "-p", help="Initial guess for φ_ref"),
+    beta_sple: float = typer.Option(0.5, "--beta-sple", "-b", help="Initial guess for β_sple"),
+    beta_mix: float = typer.Option(2.0, "--beta-mix", "-m", help="Initial guess for β_mix")
+) -> None:
+    """
+    Solve the system of equations using scipy.optimize.fsolve method.
+
+    Args:
+        phi_ref (float): Initial guess for φ_ref parameter
+        beta_sple (float): Initial guess for β_sple parameter
+        beta_mix (float): Initial guess for β_mix parameter
+    """
+    initial_guess = (phi_ref, beta_sple, beta_mix)
+    solution = fsolve_solve(initial_guess)
+    typer.echo(f"fsolve Solution: {solution}")
+
+
+@app.command()
+def root_method(
+    phi_ref: float = typer.Option(0.5, "--phi-ref", "-p", help="Initial guess for φ_ref"),
+    beta_sple: float = typer.Option(0.5, "--beta-sple", "-b", help="Initial guess for β_sple"),
+    beta_mix: float = typer.Option(2.0, "--beta-mix", "-m", help="Initial guess for β_mix")
+) -> None:
+    """
+    Solve the system of equations using scipy.optimize.root method.
+
+    Args:
+        phi_ref (float): Initial guess for φ_ref parameter
+        beta_sple (float): Initial guess for β_sple parameter
+        beta_mix (float): Initial guess for β_mix parameter
+    """
+    initial_guess = (phi_ref, beta_sple, beta_mix)
+    solution = root(equations, initial_guess, jac=jacobi_matrix, method='hybr')
+    typer.echo(f"root Solution: {solution.x}")
+
+
+@app.command()
+def compare(
+    phi_ref: float = typer.Option(0.5, "--phi-ref", "-p", help="Initial guess for φ_ref"),
+    beta_sple: float = typer.Option(0.5, "--beta-sple", "-b", help="Initial guess for β_sple"),
+    beta_mix: float = typer.Option(2.0, "--beta-mix", "-m", help="Initial guess for β_mix")
+) -> None:
+    """
+    Compare solutions from both fsolve and root methods.
+
+    Args:
+        phi_ref (float): Initial guess for φ_ref parameter
+        beta_sple (float): Initial guess for β_sple parameter
+        beta_mix (float): Initial guess for β_mix parameter
+    """
+    initial_guess = (phi_ref, beta_sple, beta_mix)
+
+    # Get solutions from both methods
+    fsolve_solution = fsolve_solve(initial_guess)
+    root_solution = root(equations, initial_guess, jac=jacobi_matrix, method='hybr')
+
+    # Print results
+    typer.echo("Comparison of solutions:")
+    typer.echo(f"fsolve Solution: {fsolve_solution}")
+    typer.echo(f"root Solution: {root_solution.x}")
+
+
+if __name__ == "__main__":
+    app()