Fix: delete abacus_cmake.sh and some compile errors#3
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Merge pull request ESROAMER hytd
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* Refactor: Restructure tools/ directory for clarity and fix include analysis script This commit consolidates three previous commits (#1, #2, #3) into a single comprehensive refactor of the tools/ directory, addressing both organizational structure and a path-related bug in the code analysis script. 1. tools/ directory reorganization - Group all numerical atomic orbital (NAO) generation tools under 01_NAO_generation/, including: * SIAB/ (Simulated Annealing method in C++) * pytorch/ and pytorch_dpsi/ (PyTorch gradient methods) * pytorch_gradient_source/ (original PyTorch implementation) * lcao_bash/ and abfs_bash/ (bash-based orbital generators) * qo/ (quasiatomic orbital generation) * Generate_Orbital_AllInOne.sh (main entry script) * examples/ (example input files) - Move all post-processing and visualization tools under 02_postprocessing/: * rt-tddft-tools/, stm/, average_pot/, selective_dynamics/, plot-tools/ - Place source code analysis tools under 03_code_analysis/ - Rename windows/ to 04_windows_installation/ for consistency - Use numerical prefixes (01_, 02_, 03_, 04_) to define a clear order - Use git mv to preserve file history throughout the refactor 2. New tools/README.md - Add a comprehensive README with directory tree, quick start guide and tool descriptions 3. Fix generate_include_analysis.py path bug - The script computed repo_root using os.path.dirname(script_dir), assuming the script lived in tools/. After moving to tools/03_code_analysis/, this resolved to tools/ instead of the repository root, causing os.walk to find no source files. - Update to os.path.dirname(os.path.dirname(script_dir)) to correctly resolve the repository root from the new script location. Combined previous commits: 6e3b7954c add code analysis python file 546d7cd76 update tools 92094b81d update * Fix: Update path references in docs and source code after tools/ directory restructuring After the tools/ directory reorganization, several path references in documentation and source code were still pointing to the old directory structure. This commit updates all hardcoded paths to match the new organization: 1. docs/advanced/windows_installer.md - tools/windows/ → tools/04_windows_installation/ (3 occurrences) 2. docs/advanced/input_files/input-main.md - tools/average_pot/aveElecStatPot.py → tools/02_postprocessing/average_pot/aveElecStatPot.py 3. docs/parameters.yaml - tools/average_pot/aveElecStatPot.py → tools/02_postprocessing/average_pot/aveElecStatPot.py 4. source/source_io/module_qo/to_qo_kernel.cpp - /tools/qo/postprocess.py → /tools/01_NAO_generation/qo/postprocess.py 5. source/source_basis/module_nao/atomic_radials.cpp - Update SIAB/PyTorchGradient paths to 01_NAO_generation/pytorch and 01_NAO_generation/SIAB 6. source/source_io/module_parameter/read_input_item_output.cpp - tools/average_pot/aveElecStatPot.py → tools/02_postprocessing/average_pot/aveElecStatPot.py * add a threshold in 17_DS_DFTU/01_LCAO_SPIN_S2_Z --------- Co-authored-by: abacus_fixer <mohanchen@pku.eud.cn> Co-authored-by: Xiaoyang Zhang <tsfxwbbzxy@163.com>
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