Enhance interactive format conversion and menu functionalities

[zhyan0603]

This pull request introduces several documentation and functionality improvements across the project, including major updates to the documentation for plotting, analyzer, calculator, and format conversion tools, as well as the addition of a new structure minimization script. Several plotting and data selection scripts have also been corrected or enhanced for accuracy and usability.

Key changes include:

New Features

• Added a new script calc_minimize.py for structure relaxation using calorine, supporting both POSCAR and extxyz input, with customizable force convergence and step limits. The script saves the optimization trajectory and provides clear command-line usage instructions.
• Expanded the analyzer and calculator tool menus in the documentation to include new functionalities such as chemical species analysis, charge balance checking, energy/force/virial analysis, structure filtering by distance, and more, with detailed prompts and usage examples for each function. [1] [2] [3] [4]
• Updated the format conversion tool documentation to present a comprehensive, categorized menu, including new conversion utilities and clearer instructions.

Documentation Improvements

• Overhauled the plotting tool documentation in README.md to provide a categorized, versioned, and more descriptive command menu, reflecting the latest available plot types and their usage.
• Clarified usage and input file requirements for MSD plotting scripts, ensuring users understand the expected arguments and file formats. [1] [2]
• Corrected the description for the arrhenius_sigma plot type in the summary table.

Bug Fixes and Data Output

• Fixed axis order and data assignment bugs in plt_train_density.py to ensure correct plotting of energy, force, and stress data in parity plots. [1] [2] [3]
• Enhanced the structure selection script (neptrain_select_structs.py) to output PCA projection data for sampled, training, and selected structures, facilitating further analysis and reproducibility.

Other Updates

• Added a new publication to publications.json to keep the project’s publication record up to date.

These changes collectively improve the usability, transparency, and accuracy of the toolkit, making it easier for users to access, understand, and utilize the available features.