update to the newest version 2025-04-29 #345
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* 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>
* 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 (#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. (#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 (#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>
…delta_precalc in DeePKS. (#5812) * Remove functions related to v_delta in LCAO_Deepks; Remove some redundent variables. * Remove some temporary variables for force/stress calculation in DeePKS and separate force&stress calculations. Remove global dependence of descriptor. * Use accessor to accelerate the manipulation of torch::Tensor variables in DeePKS. * Remove LCAO_deepks_mpi.cpp. * Update Unittest for DeePKS. * Clang-format change. * Update cal_gdmx and cal_gdmepsl. * Fix check_gvx() bug when using mpirun. * Move functions for calculating descriptor from LCAO_deepks to DeePKS_domain. * Add UT for cal_gdmepsl and modify the ref files to suit the new data structure.
* Refactor: modify decimal digit of wfc to 8 * [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>
* feature: parallel solve subspace diagonalization in dav_subspace * [pre-commit.ci lite] apply automatic fixes * fix Makefile * fix ut * fix * fix * fix test * fix * fix pyabacus * [pre-commit.ci lite] apply automatic fixes * fix doc * update the doc --------- Co-authored-by: root <pxlxingliang> Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
…onal for OFDFT (#5777) * refactor: Remove the global variable 'global_pseudo_type' and the input variable 'pseudo_type'. Now the type of pseudopotential is assigned in STRU, not INPUT, and different type of pseudopotentials can be assigned for different elements in one calculation. Following are the supported format of STRU: Al 26.98 Al_ONCV_PBE-1.2.upf Al 26.98 Al_ONCV_PBE-1.2.upf auto Al 26.98 Al_ONCV_PBE-1.2.upf upf201 Al 26.98 Al_ONCV_PBE-1.2.upf upf201 # annotations... If no pseudo_type is assigned in STRU, the default value is 'auto', and ABACUS will recongnize the pp by itself. * test: Remove `pseudo_type` from INPUT of all integrate tests, and add them into STRU. Add two integrate tests, `101_PW_upf201_blps_pseudopots` and `101_PW_upf201_upf100_pseudopots`, which contain two elements (Mg3Al), and different types of pseudopotentials are specified for different elements. * <Feature> Add input parameters about ML_KE * <Feature> Add files about ML_KE into module_hamilt_pw/hamilt_ofdft * <Feature> Link MPN KEDF to ABACUS * <Test> Add a unittest of MPN KEDF: 902_OF_KE_MPN * <Feature> Output more detailed information of Energy in KSDFT * <Test> Update the integrate test 902_OF_KE_MPN * <Feature> In order to check the validity of MPN KEDF, calculate and output TF KEDF when running MPN KEDF. * Check the input rho in the localTest of MPN KEDF * <Feature> Add a new descriptor: r_min = min|r-R| / r0, r0 = (Omega / natom) ** (1/3). * <Fix> Fix the scaling formula of kernel. * Correct the defination of img. * Update parameters * Feature: Add a compile option ENABLE_MLKEDF to control the ML KEDF module. * Feature: Simplify the code. * Support Makefile * Refactor: Remove GlobalC::ucell. Optimize the format of input parameters of ML KEDF. * Refactor: 1. Update annotation. 2. Remove useless parameters and codes. * Doc: Update documents. * Test: Add two integrate tests: 902_OF_KE_MPN and 902_OF_KE_CPN5 * Doc: Update annotations. * Refactor: Update the CMakeLists.txt of nnof * Test: Configure compilation test. * [pre-commit.ci lite] apply automatic fixes * Replace pow with std::pow * 1. Rename potential.h (class Potential) as pauli_potential.h (class PauliPotential). 2. Replace si.gga.psp used by 902_OF_KE_CPN5 with si.lda.lps. * Feature: Provide default parameters for MPN and CPN5 KEDF. * Doc: Update the document of `of_kinetic`. * Update the file names of nnof * Make: Update Makefile, and compile documents. * Remove useless input parameters: `of_ml_nnode` and `of_ml_nlayer` * Update the integrate tests of MPN and CPN5 KEDFs * Add function `get_local_pp_energy` into ElecState to calculatet the energy contributed by local pseudopotential. * Correct the name of eion_elec to elocal_pp, since the nonlocal part is not considered. Delet the output of Ekinetic, since it only works for local pp. * Test: Fix module_elecstate/test/elecstate_energy_test.cpp * [pre-commit.ci lite] apply automatic fixes * Remove useless head file parallel_reduce.h from esolver_ks.cpp * Format ml_tools/data.cpp and ml_tools/grid.cpp * [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>
* Tests: add checks for opening data files by hsolver tests * [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>
* Use template to reconstruct parse_expression * Feature: output R matrix at each MD step * Modify'matrix_HS' to 'matrix' for R matrix output * Merge branches 'develop' and 'develop' of https://github.com/1041176461/abacus-develop into develop * Fix: modify index in parse_expression * Fix: add regfree for parse_expression * Doc: update phonopy doc * Doc: update phonopy doc * fix tdos plot for nspin=2 * optimize dosplot for nspin=2 * fix legend for dosplot * Add files via upload * Update cal_edm_tddft.cpp * Refactor: modify exx loop for relax/md * Update result.ref * Fix wrong parameters in integrate test * Update result.ref * Update result.ref * Update result.ref * Update result.ref * Update result.ref * Update result.ref * Update result.ref * Update result.ref * add exx when istep>0 * Update dos.py * Update esolver_sdft_pw.cpp * Update lcao_before_scf.cpp * Update Exx_LRI_interface.h * Update Exx_LRI_interface.hpp * Fix: compile error * Fix: compile error * Fix: change HSE relax/md result.ref for new framework * Fix: compile error * compatible with exx_iter_finish * Add files via upload * Update esolver_ks_lcao_tddft.h * Update esolver_ks_lcao_tddft.cpp * Fix: support negative value in parse_expression * [pre-commit.ci lite] apply automatic fixes --------- Co-authored-by: jiyuang <[email protected]> Co-authored-by: Qianrui <[email protected]> Co-authored-by: HTZhao <[email protected]> Co-authored-by: maki49 <[email protected]> Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
* Fix: Enhance the computational stability of tau_vw. * Test: Update 919_OF_out_elf * I don't know why 204_NO_KP_NC failed, so modify the annotation to restart the test.
* Fix: update weight in ldos * Test: update LDOS.cube.ref
…ariable and default results of 204_NO_KP_NC example, reconstruct esolver by adding a new file pw_setup.cpp in esolver (#6145) * fix two typos in manual * update output information * fix auto tests * fix typos and unittests * delete dos_nao, use write_dos_lcao directly * update dos codes * add warning_quit in pw basis for PDOS calculations, add doscs for ploting Fermi surface in LCAO basis, add Fermi surface plot function in PW basis when out_dos=3 * add fermi surface plot in pw dos * fix unittest of write_dos_pw * change magnetiation (a name that is too long) to mag * update header files * update md tests * update cmake, remove -Wno-tautological-constant-compare, which seems useless * update mag, it influences a lot of codes... * update mag * update mpi.h * update 204_NO_KP_NC, change scf_thr to 1.0e-7 * output format refactor * update output format * update esolver_ks_pw * fix magnetization esolver * update some formats * found a pw_setup file in esolver * add rho_mix, this belongs to esolver_ks * fix magnetization in DeePKS * update rho_restart.cpp * update rho_restart.cpp * fix json * fix define MPI in ri benchmark * update MPI in ri_benchmark_test.cpp
…ime to test these tests) to accelerate CICD efficiency (#6152)
* Feature: add out_mat_ds to print <phi|dphi> matrix * Fix: decrease the memory of reference files --------- Co-authored-by: dyzheng <[email protected]>
* delete some useless integrate tests (in my opinions, we are wasting time to test these tests) to accelerate CICD efficiency * update get_wf for gamma_only, rename the output files name * change get_wf integreat tests to spin=2 case for multi-k algorithm in LCA * update get_wf_lcao outputs * update CASES_CPU.txt * update 212 and 312 integreate tests about get_wf, refactor the output formats of get_wf * update catch_properties * delete useless sum_xxx codes in integrate/tools * update clean.sh * update integrate tests * change back general_info * update get_pchg and get_wf * fix get_wf_lcao
* update integrate tests of rt-TDDFT * delete a useless gauss test in rt-TDDFT, which has been coverged by current test * update Autotest.sh, delete useless screen output information * refactor some output information * update Autotest.sh
* first use of the fft * fix the cuda test * add gtest * change the test * change recip_to_real func * set C2C * set C2C and C2R * set C2C and C2R * add pw_basis_k C2C * add CmakeLists.txt * remove compile * add the define * add delete * modify the include file * add change for the POOL_WORLD * format document * add the mpi_flag_ * fix bug in the mpi set * modify the mpi_flag_ as flase * set pw_test * Revert "set pw_test" This reverts commit 85785a1. * revert setup * add comment * update offset * reset the for * change the mpi_flag * change the compile error * sperate two lines * add change * use template instead of change * remove tem file --------- Co-authored-by: Qianrui Liu <[email protected]> Co-authored-by: Mohan Chen <[email protected]>
* update integrate tests of rt-TDDFT * delete a useless gauss test in rt-TDDFT, which has been coverged by current test * update Autotest.sh, delete useless screen output information * refactor some output information * update Autotest.sh * delete some charge mixing tests in LCAO * delete smearing tests in NO * change some names * update tests * delete useless RDMFT tests * delete Bravis lattice tests in NO
* Add Finalize function in WARNING QUIT * Fix compilation error * Nooo I haven't been writing codes for a long timeeeeee * Remove dependency test * Confirm removal * Remove useless Dependency
* Update namespace ModuleGint * Update class BlasConnector * Update namespace ModuleGint --------- Co-authored-by: linpz <[email protected]>
* update integrate tests of rt-TDDFT * delete a useless gauss test in rt-TDDFT, which has been coverged by current test * update Autotest.sh, delete useless screen output information * refactor some output information * update Autotest.sh * delete some charge mixing tests in LCAO * delete smearing tests in NO * change some names * update tests * delete useless RDMFT tests * delete Bravis lattice tests in NO * fix a typo in rt-TDDFT * use 6au orbital in 204_NO_NC tests * update 204_NO_NC test * update NC (noncollinear) tests, reduce the computational time * udpate Autotest.sh, put CASES_CPU.txt back * fix some bugs
* Feature: ldos mode for pw * Feature: add a para to control ldos search line * Docs: update docs about ldos_line * Test: update unittest --------- Co-authored-by: Mohan Chen <[email protected]>
…n of ld.init_DMR to before_scf (#6170) Co-authored-by: Mohan Chen <[email protected]>
* Fix: Enhance the computational stability of ELF. Update corresponding integrate tests. * Test: Update 119_PW_out_elf * Test: Update 119_PW_out_elf and 219_PW_out_elf. --------- Co-authored-by: Mohan Chen <[email protected]>
* Fix: Enhance the computational stability of ELF. Update corresponding integrate tests. * Test: Update 119_PW_out_elf * Test: Update 119_PW_out_elf and 219_PW_out_elf. --------- Co-authored-by: Mohan Chen <[email protected]>
…6140) * Add integrate test for v_delta(k) label in DeePKS multi-k calculations. * Add orbital related unit test for DeePKS. * Add vdpre related unit test for DeePKS. * Add check for complex numbers. * Change DeePKS multik UT to minimize file size. * Update gedm_ref.dat. * Rearrange and modify tests in DeePKS. * Fix nscf bug caused by different filename. * Update DeePKS multi-k UT. * Rename jd as README. * Update result.ref. * Update result.ref. * Adjust integrate tests in DeePKS for acceleration. * Remove useless files in DeePKS integrate tests. * Add nscf and relax integrate tests for DeePKS. * Add input check. * Add missing files for DeePKS test. * Temporarily close the check for gedm in DeePKS UT.
* INITIAL COMMIT * MODIFY UNIT TESTS * REMOVE BLAS_CONNECTOR.CPP * FIX MAKEFILE
… style and files (#6179) * reduce the time costs in SDFT examples * modify SDFT codes, put Onsager.txt, je-je.txt, and Chebcoef to OUT directory * reduce the LCAO radius for NO_KP_AFM example * update 204_NO_KP_FM example * update example 260_NO_DJ_PK_PU_S1 * change to 644 for files in PP_ORB * add Fe_gga_6au_100Ry_2s1p1d.orb orbitals to reduce the testing time * reduce testing time for 260_NO_DJ_PK_PU_AFM_URAMPING * 260_NO_DJ_PK_PU_S1 * delete useless outputs * update surface chemistry example * modify the code for comparing Onsager.txt * update mulliken in 204_NO_KP_AFM example * update result.ref in 186_PW_SKG_ALL * update two test results
* Add WARNING_QUIT when Hexx files not exist in hse restart calculations. * Add support of multi-k case for out_dm=1. * Update test and docs. * Update test.
… HSE and LR calculations, reformat the output atomic positions, change 'jd' files in integreate tests to 'README' files (#6182) * reduce the time costs in SDFT examples * modify SDFT codes, put Onsager.txt, je-je.txt, and Chebcoef to OUT directory * reduce the LCAO radius for NO_KP_AFM example * update 204_NO_KP_FM example * update example 260_NO_DJ_PK_PU_S1 * change to 644 for files in PP_ORB * add Fe_gga_6au_100Ry_2s1p1d.orb orbitals to reduce the testing time * reduce testing time for 260_NO_DJ_PK_PU_AFM_URAMPING * 260_NO_DJ_PK_PU_S1 * delete useless outputs * update surface chemistry example * modify the code for comparing Onsager.txt * update mulliken in 204_NO_KP_AFM example * update result.ref in 186_PW_SKG_ALL * update two test results * update output UNIFORM GRID information and 381 and 382 HSE examples * change 383_NO_GO to 383_NO_KP * update EXX examples * add 383 example * update HSE examples * update 385 and 386 cases, change 386 to kP * update some output format, including the atomic positions, the atomic velocties are printed out separately * update HSE directories * update HSE examples * delete 507 * add force and stress in 503 * keep updating HSE examples * delete ntype parameter, which is useless * update HSE testing information * add sz orbital in PP_ORB * update CASES_CPU.txt * update CASES_CPU.txt, move 284 to 511 * delete 291 * update autotests in unitcell_test * update some tests in ions_move * change jd to README * update some README * update some outputs
* MOVE INTERGRATED TEST TO THE LAST * ANOTHER WAY TO WORKOUT * FIX CMAKELISTS
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update to the newest version 2025-04-29