Some updates #80
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Some updates #80
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Debug on Jan. 06, 2026
update plt_pdos
Add CP2K log converter to format conversion tools
Updated script usage instructions for clarity.
Update cp2k_log2xyz.py
Refactor atom and lattice extraction to handle mixed file types and improve error handling.
Updated extract_energy and extract_forces functions to support both old and new log formats. Improved logging and removed unnecessary disclaimer about unsupported formats.
Enhance CP2K-to-extended-XYZ converter with mixed structure support and CP2K 2025+ compatibility
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This pull request introduces several updates and improvements across documentation and scripts, focusing on enhanced file format support, improved plotting consistency, and bug fixes for analysis scripts. The most significant change is the addition of a new script for converting CP2K outputs to an extended XYZ format. Additionally, the documentation and plotting scripts have been updated for clarity and consistency, and minor bugs have been addressed in analysis scripts.
New Features
cp2k_log2xyz.pyfor converting CP2K output files (.log) together with structure files (.xyzor.inp) into extended XYZ format, including energy, forces, and virial tensor. The script also generates a detailed log file with conversion statistics and diagnostics.Documentation Updates
README.mdto reflect version bump to 1.5.0, revised usage instructions, updated tool and option names, and clarified supported features in the help sections. [1] [2] [3] [4] [5]Plotting and Output Consistency
plt_dimer.pyoutput files and plots from "Å" and "eV/Å" to "Angstrom" and "eV/Angstrom", and improved plot labeling and file naming conventions. [1] [2] [3]plt_force_errors.pyto use LaTeX-style formatting for Angstrom units, ensuring consistency across all plots. [1] [2] [3]Bug Fixes and Analysis Improvements
plt_hnemd.pyandplt_nemd.py, ensuring correct grouping behavior and error handling. [1] [2] [3] [4] [5]time_stepinplt_hnemd.pyto support floating-point values, improving compatibility with different simulation outputs.