Update Docs and '-time gpumd'

[zhyan0603]

This pull request introduces a series of updates to the GPUMDkit project, including feature enhancements, documentation updates, and code optimizations. The most significant changes include the addition of a real-time progress tracker in the time_consuming_gpumd.sh script, updates to the project's documentation and website, and improvements to visual assets.

Feature Enhancements:

• Real-time Progress Tracker: The Scripts/analyzer/time_consuming_gpumd.sh script now includes a real-time progress tracker with features like speed calculation, estimated time remaining, and a formatted output table. This replaces the previous static calculations for frame speed and estimated time.

Documentation Updates:

• README Update: Expanded the description of GPUMDkit to highlight its user-friendly command-line interface and additional functionalities, such as script invocation, format conversion, and NEP construction workflows.
• Website Enhancements: Updated the docs/index.html file to include a favicon, Google site verification meta tag, and additional links to resources like GPUMD-Tools and MAGUS. Also, updated descriptions and added new gallery items, such as "Self Diffusion Coefficient." [1] [2] [3] [4] [5]

Visual Assets:

• Gallery Image Updates: Adjusted paths for gallery images in multiple files (docs/index.html, docs/plot_scripts.html, and docs/tutorials/plot_scripts.md) to ensure consistency and accessibility. [1] [2] [3]
• Image Styling: Increased the height of gallery images in docs/style.css from 220px to 300px for improved visibility.

Versioning:

• Version Bump: Updated the project version from 1.2.4 to 1.2.5 in both the README and gpumdkit.sh script to reflect the new changes. [1] [2]