Merge with deepmodeling/abacus-develop:develop#1
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Merge with deepmodeling/abacus-develop:develop#1Flying-dragon-boxing wants to merge 390 commits into
Flying-dragon-boxing wants to merge 390 commits into
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* move multiplication by rr to spherical bessel transform * slight modification * fix unit test * Added spline and splint; some basics of paw_cell * modify unit test * Add list of projector info to paw_cell * fix unit test * fix unit test * add lmax in paw_element * Added spherical harmonics * added input files for unit test * Added unit test for set_paw_k --------- Co-authored-by: wenfei-li <liwenfei@gmail.com>
… simplify deepks interfaces (#2697) * fix a titile * rename index mapping arrays * add getters global2local, local2global * fix deepks test * fix tests
* implement new Gaunt table * cleaner real_gaunt_lookup * minor fix
…2710) * minor interface change to radtab * cache jl in direct SBT * change iteration behavior to prioritize l * add two center table class * better cached SBT & clean up
Co-authored-by: wenfei-li <liwenfei@gmail.com>
…-relax (#2736) * new algorithm to adjust symmetry_prec * remove outputs * fix a condition narrowing symmetryprec
* fix a too-strict assert * add #ifdef __DEBUG
* fix: bug of scf's executing relax_step
update Makefile of module_pw
* update Makefile
* fix: bug when using scan with kpar > 1
performance: optimize rho_mpi
* add 'mpirun -np 4' for charge_mpi_test
* add __MPI in stress_func_mgga.cpp
* add title and timer for reduce_diff_pools
* add annotations for init_rho; update rho_mpi
* add annotations for rho_mpi
* Added interface for calculation of rhoij * Added new test case * finished accumulate_rhoij, added test --------- Co-authored-by: wenfei-li <liwenfei@gmail.com>
* add some details of UnitTest and Converge * Update docs/CONTRIBUTING.md Co-authored-by: Chun Cai <amoycaic@gmail.com> --------- Co-authored-by: Chun Cai <amoycaic@gmail.com>
* update code for S(t+dt/2) and fix restart * update autotest * update autotest
… the output Hexx(R) errors for few k-points (#2749) Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
…nto an independent class `DMgamma_2dtoGrid` (#2748) * separate 2d-to-grid operation from Local_Orbital_Charge into an independent class * separate into new file --------- Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
* refactor sparse_matrix class to use map * update output_hcontainer using new sparse matrix * add csr file reader * try to fix error * fix error --------- Co-authored-by: root <hongriTianqi>
Co-authored-by: wenfei-li <liwenfei@gmail.com>
* improved implementation of kerker preconditioner * fix bug in charge_mixing_test * make corresponding changes in Documentation after PR#3133 * extra add * correct 'scalapack-gvx' into 'scalapack_gvx'
* Update dipole.py * Update dipole.py
* Update install_elpa.sh update elpa version to 2023.05.001 * Update cmake version to 3.27.6 * Update gcc version to 13.2.0 * Update install_openblas.sh - update OpenBLAS version to 0.3.24 - update NUM_THREADS to 128 in compiling * Set default intel compiler to `icpx` * update build.sh scripts * Update README.md * Update README.md * modified toolchain*.sh * Update toolchain_intel-mpich.sh * remove error message in build*.sh when do install * Update README.md * minor update * Update README.md * version 2023.5 tag * Update README for GPU version * update optional message in README
* modify symmetry_autoclose to true * modify value of symmetry_prec to 1e-6 in source/module_io/test/support/INPUT * fix ut of write input test
Co-authored-by: Zhao Tianqi <hongriTianqi@users.noreply.github.com>
* Refactor: delete memory_type in BaseMatrix * Feature: add wrapper mode for HContainer * Fix: allocate() bug in DeePKS * Fix: allocate in AtomPair * Feature: gather 2D-block parallelized HContainer to empty serial objects --------- Co-authored-by: dyzheng <zhengdy@bjaisi.com>
Co-authored-by: Qianrui Liu <76200646+Qianruipku@users.noreply.github.com>
* doc: add doc introductions for input/precision flag * add default value
* Feature : enable cg diagonalization with PAW * Feature : added mixing of dij (not used yet) * not mixing dij yet * update libpaw_interface * update reading of STRU file --------- Co-authored-by: wenfei-li <liwenfei@gmail.com>
* Feature: add coulomb potential calculation It can only be used for tests since it need large Ecut. * add UT for Coulomb
* Refactor: PW_Basis_Big inherits from PW_Basis_Sup * Test: update unittest
* Build: enable address sanitizer for Intel oneAPI compiler * Update easy_install.md * Update CONTRIBUTING.md --------- Co-authored-by: Qianrui Liu <76200646+Qianruipku@users.noreply.github.com>
* update version of libpaw * Fix : paw bug when compiled serial --------- Co-authored-by: wenfei-li <liwenfei@gmail.com>
* Build: update MKL version * Update Dockerfile with new ELPA version and configure options * remove intel classic cpp compilers
Co-authored-by: wenfei-li <liwenfei@gmail.com>
…3231) * skip elpa compiling in Dockerfile.intel * Fix Dockerfile.intel * try avx512 * try avx512 for fortran compiler * try avx512 * tryagain * try old version elpa * fix ln to cp * unuse elpa in CI, update elpa intel image daily * try disable elpa test * try enable avx512 for elpa * try full configure command * try full configure command * try another flags to disable avx512 * change machine of image and container tests * Fix: build error with intel image * Fix: build error with intel image * reset the paths in Dockerfile.intel * remove test commands * Fix: run build_test_cmake on self-hosted * only test PAW with GNU toolchain --------- Co-authored-by: dyzheng <zhengdy@bjaisi.com> Co-authored-by: Chun Cai <amoycaic@gmail.com>
Flying-dragon-boxing
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Feb 19, 2025
) * Link mtblas library * Add mtblas gemm kernel usage * Finish memory_op on dsp * Update CMakeLists * Add compilation script * Fix warnings * Fix install script * Initialize DSP hardware * Replace gemm in math_kernel * Fix CMakeLists Bug * Fix bugs #1 * Fix bug 2 * Fix link to shared library error * Stop use gemm_mt globally * Modify op usage * Fix bug * Fix template usage * Fix compilation * Replace all dav_subspace gemm kernels --------- Co-authored-by: Mohan Chen <mohanchen@pku.edu.cn>
Flying-dragon-boxing
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Jun 25, 2026
* 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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