Doxyfile Configuration and Comprehensive Documentation for TurboRVB using cursor #99
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k-yoshimi wants to merge 23 commits into
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Doxyfile Configuration and Comprehensive Documentation for TurboRVB using cursor #99k-yoshimi wants to merge 23 commits into
k-yoshimi wants to merge 23 commits into
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… comments explaining namelist parameters and their purposes - Organize variables by functionality with clear section headers - Improve code readability and maintainability
…dd comprehensive comments for matrix contraction subroutines (scontract_genj, scontract_mat_jas, scontract_mat_det) - Add detailed explanations for update_kgrid subroutine including algorithm and mathematical background - Add documentation for norm_metric function and prep_map subroutine - Improve code understanding for periodic boundary condition calculations
…iled Doxygen comments to all Fortran files in src/m_common - Document pseudopotential, memory management, file operations, Pfaffian calculations - Include algorithm descriptions, parameters, usage examples, and cross-references - Improve code maintainability and documentation quality for quantum Monte Carlo algorithms
- Add missing variable declarations (ai, aj, ak, al) in force_improper subroutine - Remove duplicate variable declarations in max_ovlp subroutine - Fix 'already has basic type' and 'no IMPLICIT type' errors - Ensure variables are properly declared as arguments or local variables
- Add logo/turborvb_logo_doxygen.png (200x55px) for Doxygen HTML output - Update Doxyfile to use resized logo - Add doc/ to .gitignore to exclude generated documentation from version control
…tailed comments to all subroutines and functions including dsygv_my, purify, checkmat, etc. - Document matrix operations, eigenvalue problems, and Jastrow matrix processing - Include parameter descriptions, algorithm explanations, and mathematical background - Improve code documentation quality for quantum Monte Carlo wave function conversion
… detailed comments to main program explaining molecular orbital conversion process - Document namelist parameters for control, mesh_info, and molec_info - Include MPI initialization, file processing, and output generation sections - Improve code documentation quality for quantum Monte Carlo molecular orbital optimization
…ailed comments to main program explaining AGP to Pfaffian conversion process - Document variable declarations, matrix transformations, and spin rotation handling - Include unpaired orbital processing and symmetry considerations - Add documentation for fill_surot subroutine with mathematical background - Improve code documentation quality for quantum Monte Carlo wave function conversion
…d detailed comments explaining physical and mathematical constants - Document SI constants, atomic units, and unit conversion factors - Include numerical precision parameters and compatibility constants - Improve code documentation quality for quantum Monte Carlo physics constants
- Add comprehensive header comment explaining program purpose and features - Include usage instructions and minimal input example - Document main features: PBC support, symmetry detection, wave function types - Provide clear guidance for users and developers
- Add or improve Doxygen headers and docstrings in cubicsym.f90, error_handler.f90, findsection.f90, intc.f90, invmat.f90, kind.f90, makeforces.f90, makelambda.f90, makepfaff.f90, orbitals.f90, symm_data.f90 - Improve code readability and maintainability for developers and users - No logic changes, documentation only
- Add detailed function documentation with @brief, @details, @param, @return tags - Document all major subroutines in convertmod.f90 including: - shift_originref: Reference origin calculation for coordinate systems - convertmol_fast: Molecular orbital conversion with DMRG support - convertmol_c: Complex molecular orbital conversion - ortho_fast: Fast orthogonalization routine - evalovers: Overlap matrix evaluation - upmuctranspip: mu_c matrix updates - update_dup_c: dup_c matrix updates with molecular orbitals - projectder/projectmat: Matrix projection routines - Document eigenvalue problem solvers in eval_molec_epsdgel.f90 and eval_molec_unpaired.f90 - Add documentation for I/O routines in fort10_io.f90 and read_datas.f90 - Include parameter descriptions, return values, and usage notes - Follow NumPy-style docstring format with proper English comments
- Added comprehensive Doxygen-style documentation to all major subroutines - Documented correlation function calculations, grid generation, and data output - Added parameter descriptions for complex subroutines - Improved code documentation for maintainability and understanding - Covered modules: compute_corr_fun, compute_dipole, compute_grid, compute_qpwf - Covered modules: compute_rho, compute_rho_assar, compute_spin2, berry_phase - Covered modules: write_corr_fun, read_corr_fun, readforward, and utility functions
- Add module-level documentation for estimator.f90 with detailed type descriptions - Add program-level documentation for all utility programs - Add function-level documentation for key subroutines - Add inline variable documentation with descriptive comments - Improve code structure and readability - Standardize documentation format across all files Files modified: - estimator.f90: Complete module documentation with type and interface docs - find_kpoints.f90: Program documentation for k-points finder - funvsa.f90: Program documentation for variable selection analysis - intc.f90: Function documentation for integer-to-string conversion - orthomol.f90: Program documentation for molecular orbital orthogonalization - plot_orbitals.f90: Program documentation for orbital plotting - plotlambda.f90: Program documentation for lambda parameter plotting - pseudo.f90: Program and function documentation for pseudopotential analysis - zerojasfort10.f90: Program documentation for Jastrow factor zeroing - Plus 22 other files with improved documentation This commit significantly improves code maintainability and developer experience.
…s for documentation clarity
…le recursive search
…URCES, and reference relations
…LOCAL_METHODS, and EXTRACT_ANON_NSPACES to YES
- Add detailed installation instructions for all platforms - Include quick start and advanced usage guides - Provide troubleshooting and performance optimization tips - Add CI/CD integration examples (GitHub Actions) - Include customization and contribution guidelines - Support for HTML, LaTeX, and source code documentation - Comprehensive coverage of TurboRVB Fortran codebase
k-yoshimi
requested review from
addman2,
kousuke-nakano and
michele-casula
as code owners
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This pull request focuses on enhancing the documentation for the TurboRVB project. It introduces comprehensive guidelines for generating, customizing, and maintaining documentation, along with automated comment generation for Fortran code. Additionally, it includes updates to the HTML and JavaScript files for improved navigation and functionality in the generated documentation.
Documentation Enhancements:
docs/README.md: Added detailed instructions for generating documentation using Doxygen, including prerequisites, quick start steps, advanced usage, continuous integration setup, and troubleshooting tips. This README serves as a central guide for developers working on TurboRVB.docs/auto_generation_note.md: Documented the automated process for generating Doxygen comments using Cursor AI, ensuring consistency and quality in the documentation of Fortran subroutines and functions.HTML Documentation Updates:
docs/html/__assembling__pseudo_8f90.html: Generated an HTML reference for the_assembling_pseudo.f90file, detailing its purpose, functions, and subroutines. Includes navigation features and links to source code for better accessibility.JavaScript Integration:
docs/html/__assembling__pseudo_8f90.js: Added JavaScript definitions for functions and subroutines in_assembling_pseudo.f90, enabling dynamic navigation and search functionality in the HTML documentation.