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… passed by reference
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…to updatebfgstrad
…#5767) * udpate ucell cell-relax * change funcion setup ucell after vc * [pre-commit.ci lite] apply automatic fixes * fix bug in relax test * [pre-commit.ci lite] apply automatic fixes * add namespace for unitcell * add unittest for the setcell_after_vc --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
…modeling#5778) * Move cal_o_delta from GlobalC::ld to DeePKS_domain and remove variable o_delta in ld. * Remove F_delta in ld and lessen the tedious dimension in orbital related variables in DeePKS.
… leaks in abacus (deepmodeling#5755) * init variable and fix memory leak bug in module_base * fix uninit member var in module_basis * chang logic bug and uninit memeber value in the module cell * chang logic bug and uninit memeber value in the module_elecstate * chang logic bug and uninit memeber value in the module_eslover * chang memory leak risk and uninit memeber value in the module_hamilt_general * chang uninit memeber value in the module_hamilt_lcao * chang uninit memeber value in the module_hamilt_pwdft * fix in klist * [pre-commit.ci lite] apply automatic fixes * fix useless assert * revert change in read_pp_upf100.cpp * change uninit memeber value in module_hamilt_pw * change uninit memeber value in module_hsolver * change uninit memeber value in module_io * change uninit memeber value in module_md and module_relax * [pre-commit.ci lite] apply automatic fixes * update nnr init data * fix uninit member value * update value in elecstate_energy.cpp * add init parameter for construct in sto_func * add value in the construct file * [pre-commit.ci lite] apply automatic fixes * change magnetism.cpp * [pre-commit.ci lite] apply automatic fixes * modify logic of elecstate_energy.cpp --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
* Feature: binary format of backup charge density * Tests: update tests * move backup charge density output to esolver_fp
…ePKS. (deepmodeling#5791) * Remove cal_orbital_precalc() and corresponding temporary variables from LCAO_Deepks; Partially change cal_gevdm() for future refactor; Remove the double pointer pdm and use tensor vector for replacement. * clang-format adjustment.
* Feature: enable init_chg=file for metagga * Tests: decrease the size of charge file
* modify periodic_boundary_adjustment * modify update_pos_tau * update compile * delete ucell referenc in update_pos_tau * add unittest for update_pos_tau * move back test file * use EXPECT_THAT instead of EXPECT_EQ in relax_old and use regex to remove the title * remove the bug in the relax_old for it didn't run update_pos * [pre-commit.ci lite] apply automatic fixes --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
* delete test print * change the boundry condition
…ull size of Hamiltonian in multi-k case (deepmodeling#5785) * renew deepks unit test * renew deepks unit test * reduce deepks-unitest's dependence on other modules * fix the bug of "Couldn't find orbital files for descriptor" * fix bugs of read orbitals and init orb&ParaO * fix the bug of DMR ; change the names of files being compared * fix: calculate H_V_delta * fix : cal_H_V_delta for check_e_deltabands * fix : Add pointer for GridD in deepks operator. use Test_Deepks::GridD in deepks unit test instead of GlobalC::GridD * fix : modify deepks operator to support insert_pair in initilize_HR in multi-k * fix : undefined reference of test_hsolver_sdft when using mpiicpx and icpx * update intergrate test result. Note modification in deepks operator for complete atom_pairs will cause time increase in multi-k cases. * remove some useless code * remove nnr in deepks unittest * fix: cutoff for overlap_orb_alpha_ in deepks test * fix : psialpha ref of gamma only case , just change the order of neighour atoms * fix uninitilized nmax_total in unitcell; simplize cal_descriptor * restore deepks unit test in gamma-only case * modify STRU of SiO2 in deepks test to reduce the number of neighbor atoms, thus reducing much time * fix a bug when merge * fix : setup nonlocal for ucell * rename phialpha_ref.dat for multi-k * modify STRU of H2O_multik in deepks test to reduce the number of neighbor atoms, thus reducing much time * fix : add module paw dependence in deepks unittest * fix : rename descriptor file * fix : modify result.ref for SiO2. The privious modification don't change totaldes wrongly. * update CMakeLists.txt
* update the broadening function in lr_spectrum * optimize transition analysis and fix norm bug
* modify the cal_tau in lcao * add template for cal_tau * updatea func for cal_tau
* Initial commit * Modify CMakeLists * Complete CMakeLists in module_base * Add blas_connector.cpp definition * Fix module_base tests * Fix tests failure * fix opt_test * OPTFIX2 * Return all changes * Fix global_func_text * Fix MPI Bug * return base_math_chebyshev * Fix MPI bug * Finish * [pre-commit.ci lite] apply automatic fixes --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
* update the update_pos_taud * change func with vector3 update_pos_taud * modify the input format * add unittest for the update_pos_tau * update test for relax_new * add update_vel for ucell * [pre-commit.ci lite] apply automatic fixes --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
* remove Psi(const Psi& psi_in, const int nk_in, int nband_in); * fix bug * fix bug * [pre-commit.ci lite] apply automatic fixes * remove device value in psi * update Psi(const Psi& psi_in, const int nk_in, int nband_in) * update get_ngk usage * fix bug about ngk * [pre-commit.ci lite] apply automatic fixes * fix bug * format operator * [pre-commit.ci lite] apply automatic fixes * fix bug * fix bug * fix bug * fix bug * add get_cur_effective_basis func * fix bug * update get_cur_effective_basis * check bugs * update Constructor 8-1 * fix bug * fix bug * fix bug * fix bug maybe * fix bug * check correct * check 1 * fix unit test * fix unit bug * update get_ngk func * remove get-ngk in velocity-pw * fix bug * [pre-commit.ci lite] apply automatic fixes * fix 186_PW_SKG_ALL bug * format source/module_io/unk_overlap_pw.cpp * update Constructor in psi * [pre-commit.ci lite] apply automatic fixes * debug unit test * fix ri test bug * [pre-commit.ci lite] apply automatic fixes * fix psi-ut bug * remove Psi<T, Device>::Psi(T* psi_pointer, const Psi& psi_in, const int nk_in, int nband_in) * remove useless code * update Psi(const Psi& psi_in, const int nk_in, const int nband_in); * remove Psi(const Psi& psi_in, const int nk_in, const int nband_in); * refactor psi code * fix sdft bug * change to get_current_ngk --------- Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
* Remove my_math.hpp * Remove the file
* update cmake * add aocc support * update mpich * update VERSION * update openmpi, allow user to switch version easily * update elpa * create aocl script * aocc install setup * bug fix and update readme * fix openmpi switch * modification * add openmpi configure option * update elpa setting (gpu setting for 2070s) * update libxc version and download * minor update * update README * minor update * minor checkout * deepmd-v3 add-in test note * AMD-AOCC-AOCL update and minor fixed * fix bug in aocl.sh
* Add GPU tests for outWfcPW & outWfcR * Update jd * Update integrate TEST CASES for new GPU tests * Update correct result.ref for test 107_PW_outWfcPw_GPU * Remove 107_PW_outWfcR_GPU from CASES GPU temporarily to wait for refactor
…pw works (deepmodeling#5994) * feat pexsi * fix : diag not completed * feat * feat: pexsi hsolver * CMake building implemented * Works * adapt to the new container * Turn off USE_PEXSI * Update LibRI to 553c91c * modify include files * namespace-ize * new inputs added * Configure Makefile Compiling, fix typos * Fix Makefile Intel toolchains compile errors * Fix even more PEXSI related Makefile compiling issues * Modify inputs and update to latest version (deepmodeling#2) * run INPUT.Default() in every process in InputParaTest (deepmodeling#3490) Co-authored-by: kirk0830 <[email protected]> * add blas support for FindLAPACK.cmake (deepmodeling#3497) * more unittest of QO: towards orbital selection (deepmodeling#3499) * Fix: fix bug in mulliken charge calculation (deepmodeling#3503) * fix phase * fix case test * Refactor: namespace Conv_Coulomb_Pot_K (deepmodeling#3446) * Refactor: namespace Conv_Coulomb_Pot_K * Refactor: namespace Conv_Coulomb_Pot_K --------- Co-authored-by: wqzhou <[email protected]> * enable the computation of all zeros in one function call (deepmodeling#3449) Co-authored-by: wqzhou <[email protected]> * replace ios.eof() by ios.good() to avoid meeting badbit and failbit in reading STRU (deepmodeling#3506) * Build: add ccache to accelerate the testing process (deepmodeling#3509) * Build: add ccache to accelerate the testing process * Update test.yml * Update test.yml * Update test.yml * Docs: to avoid the misunderstanding in docs (deepmodeling#3518) * to avoid the misunderstanding in docs * Update docs/quick_start/hands_on.md Co-authored-by: Chun Cai <[email protected]> --------- Co-authored-by: Chun Cai <[email protected]> * Docs: fix a missing depencency in conda build env (deepmodeling#3508) * Feature: Add ENABLE_RAPIDJSON option to control the output of abacus.json (deepmodeling#3519) Add ENABLE_RAPIDJSON option to control the output of abacus.json * Feature: add python wrapper for math sphbes (deepmodeling#3475) * recommit for review * add python wrapper * remove timer since performace tests add * Feature: support segment split in kline mode in KPT file and `out_band` band output precision control, `8` as default (deepmodeling#3493) * add precision control * correct serial version of nscf_band function * fix issue 3482 * update unit and integrated test * update document * correct unittest and make compatible with false and true * fix: bug in Autotest.sh when result.ref has no totaltimeref (deepmodeling#3523) * Fix : unit test of module_xc (deepmodeling#3524) * Fix: omit small magnetic moments to avoid numerical instability (deepmodeling#3530) * update deltalambda * avoid numerical error in orbMulP * add constrain on Mi * change case reference value * Fix: fix multiple compiler warnings (deepmodeling#3515) * Fix: add noreturn attribute to warning_quit * Add type conversion * fix string literal * fix small number trunctuation * Fix system call returned value not checked * fix missing braket * Refactor parameter_pool.cpp and parameter_pool.h * remove duplicated return statements * Change WARNING_QUIT occurances in tests * Add warning message to help debug UT * output the default precision flag (deepmodeling#3496) Co-authored-by: kirk0830 <[email protected]> * Build: Improving CMake performance for finding LibXC and ELPA (deepmodeling#3478) * Fix for finding LibXC and ELPA * For compatibility to previous routines * syntax fix for FindELPA.cmake * Update cmake/FindELPA.cmake Co-authored-by: Chun Cai <[email protected]> * Using CMake interface as default for finding LibXC * update docs * fix for FindLibxc: changing imcompatible if statement * fix for FindLibxc: changing imcompatible if statement * fix for FindLibxc: changing imcompatible if statement * update docs for installing pkg-config * Update FindLibxc.cmake * Update FindLibxc.cmake * remove previous LibXC routine in CMakeLists.txt Co-authored-by: Chun Cai <[email protected]> * Update easy_install.md with Makefile-built LibXC supported * Update easy_install.md to include different behavior in different version on finding ELPA --------- Co-authored-by: Chun Cai <[email protected]> * Docs: correct some docs about mp2 smearing method (deepmodeling#3533) * correct some docs about mp2 smearing method * add docs about mv method * Feature : printing band density (deepmodeling#3501) Co-authored-by: wenfei-li <[email protected]> Co-authored-by: wqzhou <[email protected]> * add some docs for PR#3501 (deepmodeling#3537) * Feature: enable restart charge density mixing during SCF (deepmodeling#3542) * add a new parameter mixing_restart * do not update rho if iter==mixing_restart * do not update rho if iter==mixing_restart-1 * reset mix and rho_mdata if iter==mixing_restart * fix SCF exit directly since drho=0 if iter=GlobalV::MIXING_RESTART * re-set_mixing in eachiterinit for PW and LCAO * enable SCF restarts in esolver_ks::RUN * add some UnitTests * add some Docs * new inputs added * Update input-main.md (deepmodeling#3551) Solve the format problem mentioned in issue 3543 * Build: fix compatibility issue against toolchain install (deepmodeling#3540) * Fix for finding LibXC and ELPA * For compatibility to previous routines * syntax fix for FindELPA.cmake * Update cmake/FindELPA.cmake Co-authored-by: Chun Cai <[email protected]> * Using CMake interface as default for finding LibXC * update docs * fix for FindLibxc: changing imcompatible if statement * fix for FindLibxc: changing imcompatible if statement * fix for FindLibxc: changing imcompatible if statement * update docs for installing pkg-config * Update FindLibxc.cmake * Update FindLibxc.cmake * remove previous LibXC routine in CMakeLists.txt Co-authored-by: Chun Cai <[email protected]> * Update easy_install.md with Makefile-built LibXC supported * Update easy_install.md to include different behavior in different version on finding ELPA * fix compatibility issue against toolchain * Change default ELPA install routine to old one --------- Co-authored-by: Chun Cai <[email protected]> * Test: Configure performance tests for math libraries (deepmodeling#3511) * add performace test of sphbes functions. * fix benchmark cmake errors * add dependencies for docker * update docs * add performance tests for sphbes * add google benchmark * rewrite benchmark tests in fixtures * disable internal testing in benchmark * merge benchmark into integration test --------- Co-authored-by: StarGrys <[email protected]> * Configure Makefile Compiling, fix typos * Fix Makefile Intel toolchains compile errors * Fix even more PEXSI related Makefile compiling issues * Update hsolver_pw.cpp (deepmodeling#3556) when use_uspp==false, overlap matrix should be E. * Fix: cuda build target (deepmodeling#3276) * Fix: cuda buid target * Update CMakeLists.txt --------- Co-authored-by: Denghui Lu <[email protected]> --------- Co-authored-by: wqzhou <[email protected]> Co-authored-by: kirk0830 <[email protected]> Co-authored-by: Haozhi Han <[email protected]> Co-authored-by: Zhao Tianqi <[email protected]> Co-authored-by: PeizeLin <[email protected]> Co-authored-by: jinzx10 <[email protected]> Co-authored-by: Chun Cai <[email protected]> Co-authored-by: Peng Xingliang <[email protected]> Co-authored-by: Jie Li <[email protected]> Co-authored-by: Wenfei Li <[email protected]> Co-authored-by: Denghui Lu <[email protected]> Co-authored-by: YI Zeping <[email protected]> Co-authored-by: wenfei-li <[email protected]> Co-authored-by: jingan-181 <[email protected]> Co-authored-by: StarGrys <[email protected]> Co-authored-by: Haozhi Han <[email protected]> * Revert "Modify inputs and update to latest version" * Update FindPEXSI.cmake to fix Comments * Fix CI errors * Fix CI Errors and Merge with Upstream * Resolve Pull Request Reviews * Fix parallel communication related issue * Fix vars in Makefile.vars, add input tests and comments for pexsi vars * Fix nspin > 1 cases * Improvement: take calculated mu as new initial guess, may slightly improve performance * Fix mistakes in the last commit * Fix: params and features - set default pexsi_temp - fix md in pexsi * fix empty lines * Fix: move params to pexsi_solver, rename USE_PEXSI to ENABLE_PEXSI * Tests: Modify Dockerfile and GitHub Workflows * Fix: wrong abacus link for dockerfile * Docs: added docs for pexsi inputs * Tests: three tests added for pexsi * Fix unit test issues in input_conv * Very good unit test, making my laptop fan spin * Change default pexsi_npole from 80 to 40 * Place pexsi_EDM in DensityMatrix, set size of pexsi_dm = 1 when GlobalV::NSPIN==4, and add comments for dmToRho * An unit test added for DiagoPexsi * modify for changed gint interface * correct nspin related behaviors * add efermi passthrough * Revert "add efermi passthrough" This reverts commit d7b402d. * commits to resolve conversations related to codes * DM and EDM pointers in pexsi now handled by diagopexsi, and copying h s matrices no longer needed * add pexsi examples * fix pexsi unit test (original version shouldn't run) * add building docs for pexsi * set cxx standard to c++14, which is required in make_unique * Fix: Fix typo related to pexsi * update to PPEXSIDFTDriver2 * default npoints to 1, so single core pexsi will work * Feature: exx operator for pw basis, single kpt * apply pexsi changes(?) * q-e style exx_div * Correct exxdiv * Fix Compile errors * refactor to abandon `pdiagh` * Fix mu_buffer and nspin * HSE examples * Feature: Multi-K exx * Feature: Multi-K exx * Updates with latest * Remove redundant global vars * Update to v3.9.0 * Update to v3.9.0, now code works * Remove Redundant cal_exx_energy in esolver_ks_pw.cpp * Some mess * Minor Fixes * Fix separate loop and screening * Add EXX stress * EXX Energy??? * Multi-K is broken??? * Fix: Multi-K and stress * Feature: ACE for single-K * Feature: ACE should work for multi-K, but not for sure * Feature: ACE works. Next step is ACE energy. * Fix: adapt to the latest instruction for variable `conv_esolver` * Reconstruct: move exx_helper to hamilt_pwdft * Fix: Now EXX PW doesn't depend on LibRI * Fix: Add input constraints for EXX PW * Fix: Remove redundant mpi barrier * Fix: Clean irrelevant files * Fix: Clean irrelevant files * Feature: add ace flag, exit on using gpu * Refactor: Phase 1 for refactoring exx energy * Feature: now ace calculates energy * Feature: enable exx energy * Fix: fix makefile compilation error * Fix: One minor fix for a segmentation fault * Tests: one integrate test for exx pw, only for verifying whether exx pw works * Tests: one integrate test for exx pw, only for verifying whether exx pw works * Tests: one integrate test for exx pw, only for verifying whether exx pw works --------- Co-authored-by: zhangzhihao <[email protected]> Co-authored-by: zhangzh-pku <[email protected]> Co-authored-by: wqzhou <[email protected]> Co-authored-by: kirk0830 <[email protected]> Co-authored-by: Haozhi Han <[email protected]> Co-authored-by: Zhao Tianqi <[email protected]> Co-authored-by: PeizeLin <[email protected]> Co-authored-by: jinzx10 <[email protected]> Co-authored-by: Chun Cai <[email protected]> Co-authored-by: Peng Xingliang <[email protected]> Co-authored-by: Jie Li <[email protected]> Co-authored-by: Wenfei Li <[email protected]> Co-authored-by: Denghui Lu <[email protected]> Co-authored-by: YI Zeping <[email protected]> Co-authored-by: wenfei-li <[email protected]> Co-authored-by: jingan-181 <[email protected]> Co-authored-by: StarGrys <[email protected]> Co-authored-by: Haozhi Han <[email protected]> Co-authored-by: Mohan Chen <[email protected]>
* Test: add test and output for dry run * test: update CASES_CPU.txt * Update relax_driver.cpp --------- Co-authored-by: Mohan Chen <[email protected]>
Co-authored-by: root <pxlxingliang>
* Fix dcu compilation error * Fix another part
* make KG support GPU * fix bug add tests for KG-GPU * add tests * modify reference Onsager.txt
* make KG support GPU * fix bug add tests for KG-GPU * add tests * modify reference Onsager.txt * Refactor: math_kernel_op split op files re-order ops * fix compile * fix compile * fix bug * update results
…6022) * Remove my_math.hpp * Add warning quit for failed decomposeRightMatrix in genelpa * Remove blas.h in genelpa
* Update latest Intel oneAPI default compiler for cxx * Update elpa version to newest in demo cmake script
…eepmodeling#6014) * Add optional LCAO base GPU versions supported by cusolvermp * Add optional LCAO base GPU versions supported by elpa * Add optional LCAO base GPU versions supported by elpa * Add L40S as GPUVER value for sm_89 architecture * Delete a few lines of content to enable Nvidia to compile * Add a specified Fortran mpi compiler for elpa to use * Add CUDA path for use by ELPA-GPU * Add optional LCAO base GPU versions supported by elpa * Modify a small issue * Change to manually specifying the link libraries for CAL and cusolverMp * Add the use of 'cusolvermp' or 'elpa' methods to compile ABACUS GPU-LCAO * Add the use of 'cusolvermp' or 'elpa' methods to compile ABACUS GPU-LCAO * Add the use of 'cusolvermp' or 'elpa' methods to compile ABACUS GPU-LCAO * Add modification - ELPA compiler flags modification - GPU_VER setting modification: user should specify the GPU compability number, but not the GPU name - Modify toolchain_[gnu,intel].sh and build_abacus_[gnu,intel].sh to use the above modification * minor adjustment * update README * give back cmake default option * update README and cusolvermp * Update README.md --------- Co-authored-by: JamesMisaka <[email protected]>
…ile (deepmodeling#6027) * Fix the angular momentum quantum number check in reading SOC pseudopot file * Fix related unit test problem and add an SOC pseudopot file * Refactor SOC check logic for improved readability
…odeling#6033) * exclude toolchain/install/ to avoid accidental push after toolchain run * also exclude toolchain/abacus_env.sh
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