Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Refactor:Remove the dependency of the Psi in the FFT module #5564

Merged
merged 14 commits into from
Nov 26, 2024
Merged

Refactor:Remove the dependency of the Psi in the FFT module #5564

merged 14 commits into from
Nov 26, 2024

Conversation

A-006
Copy link
Collaborator

@A-006 A-006 commented Nov 21, 2024

Unit Tests and/or Case Tests for my changes

  • In the module_pw/test,there is a Makefile which test the module_fft.Modify the file to test the memory safety and correctness of the fft.

What's changed?

  • Remove the dependency of the psi.h,move the check func of the cufft into the module_fft.

@A-006 A-006 changed the title Refactor:Remove the dependency of the psi in fft. Refactor:Remove the dependency of the psi in fft Nov 21, 2024
@caic99 caic99 removed their request for review November 21, 2024 12:53
@mohanchen mohanchen added the Refactor Refactor ABACUS codes label Nov 22, 2024
@mohanchen mohanchen changed the title Refactor:Remove the dependency of the psi in fft Refactor:Remove the dependency of the Psi in the FFT module Nov 23, 2024
@A-006 A-006 marked this pull request as draft November 23, 2024 08:55
@A-006 A-006 marked this pull request as ready for review November 23, 2024 10:12
@mohanchen mohanchen merged commit 664f996 into deepmodeling:develop Nov 26, 2024
14 checks passed
kluophysics added a commit to kluophysics/abacus-develop that referenced this pull request Nov 29, 2024
@kluophysics
Squashed commit of the following:
5a7c646 
commit 6df9240
Author: Mohan Chen <[email protected]>
Date:   Thu Nov 28 16:06:55 2024 +0800

    Update esolver_ks_lcao.cpp (deepmodeling#5632)

commit 32f1547
Author: Mohan Chen <[email protected]>
Date:   Thu Nov 28 16:06:20 2024 +0800

    Update rdmft_tools.cpp (deepmodeling#5629)

commit 3c54bab
Author: Mohan Chen <[email protected]>
Date:   Thu Nov 28 16:05:20 2024 +0800

    Update rdmft.h (deepmodeling#5628)

commit d236215
Author: Peng Xingliang <[email protected]>
Date:   Thu Nov 28 16:00:58 2024 +0800

    Test: check if abacus end normally in CI test (deepmodeling#5634)

    * Test: check if abacus end normally in CI test

    * comment out 312_NO_GO_wfc_get_wf

    ---------

    Co-authored-by: root <pxlxingliang>

commit 6445ace
Author: Yu Liu <[email protected]>
Date:   Thu Nov 28 15:58:08 2024 +0800

    docs: update SR docs (deepmodeling#5621)

    * docs: update SR docs

    * Refactor: remove useless var in get_s

    * docs: update docs

    * Docs: polish docs

commit 2ae2288
Author: Qianrui Liu <[email protected]>
Date:   Thu Nov 28 15:57:33 2024 +0800

    Refactor : Remove GlobalC::ppcell (deepmodeling#5622)

    * Refactor: remove GlobaC::ppcell

    * [pre-commit.ci lite] apply automatic fixes

    * fix compile

    * fix compile

    * fix bug

    * fix compile after merge

    ---------

    Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>

commit cabc566
Author: liiutao <[email protected]>
Date:   Thu Nov 28 15:50:57 2024 +0800

    Refactor:Remove GlobalC::ucell in module_cell (deepmodeling#5626)

    * modify the cell_index.h

    * update the ucell in set func

    * update the ucell test

    * update the build in print_info

    * update the postion of UnitCell

    * update file in the print_info

commit c141e60
Author: Yu Liu <[email protected]>
Date:   Thu Nov 28 15:49:01 2024 +0800

    Refactor: remove GlocalC::ucell in elecstate_energy_terms.cpp (deepmodeling#5630)

    * Refactor: remove GlocalC::ucell in elecstate_energy_terms.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>

commit 772ca9e
Author: Chen Nuo <[email protected]>
Date:   Thu Nov 28 15:47:52 2024 +0800

    Test: Fix tests to work without MPI (deepmodeling#5631)

commit e500584
Author: Qianrui Liu <[email protected]>
Date:   Thu Nov 28 15:43:38 2024 +0800

    Fix low efficiency of stress_kin in DCU (deepmodeling#5636)

    * fix stuck in out_chg

    * fix DCU low efficiency

commit 7198ec1
Author: JGHan7 <[email protected]>
Date:   Wed Nov 27 20:26:27 2024 +0800

    add RDMFT(Reduced Density Matrix Functional Theory) code (deepmodeling#5325)

    * in last commit, 2 processor has 'malloc(): memory corruption:' because I do three for() to realize gemm and it doesn't support many processors...

    * first push with rdmft writed in abacus-v3.4.4

    * update README.md

    * update README.md again

    * find all parameters used in Veff_rdmft (for hartree and local, XC still has two parameters don't pass), and pass in rdmft_cal() successfully

    * use class Veff_rdmft get correct Ehartree and Eexx, but Etotal is wrong

    * all energy terms correct, ETV_RDMFT = E_one_elec, Ehartree_RDMFT = E_Hartree, EXC_RDMFT = E_exx, but my Etotal doesn't include ion energy terms, etc.

    * z/dgemm_() is used correctly, next step to use pz/dgemm_()

    * just one processor is correct, 2 processors have some problem and maybe the error is occurred in processor 2

    * 2 processors is wrong but 6 processors is correct...

    * check 2 processors error

    * update, realize print Dmn in different processors

    * get successful result in different numbers of processors, and the printout has not been deleted yet

    * get the sum of different processors, that is, get the true total energy of each term

    * delete some printout and next step is replace the pz/dgemm_() used in psiDotPsi()

    * add some comments

    * do some little modifications to make the code more concise

    * just save

    * just save

    * last save before realizing gamma_only calculation

    * gamma_only calculation with errors

    * save with errors in gamma_only

    * gamma_only realization with errors in E_T+nonlocal

    * gamma_only successful with one processors, but multi-processor errors

    * support g(wg)*H_wfc and g(wg)*wfcHwfc with different g(wg) which is provided by HF_XCfunc or power_XCfunc

    * get the special DM used in constructing V_XC, and can be used for split_m2D_ktoR()

    * get the special DM used in constructing V_XC and run successfully (not in numerica meaning)

    * modify the namespace of rdmft_test files from hamilt to rdmft

    * error with using spilt_m2D_ktoR()

    * successfully get Ds_XC, next step is update abacus to have the new interface

    * successfully run rdmft with power functional in multi-k calculation, have tested alpha=1.0, 0.95, 0.5

    * do some little modifications to make the code more concise

    * fix interface provided by class OperatorEXX but having errors when do V_XC.contributeHk(ik)

    * print data of tensor from Ds_XC

    * just save

    * check the length and data of LM->Hexxc and Vxc_fromRI_c.Hexxs

    * have modified op_exx_lcao.h/.cpp, RI_2D_Comm.h/.cpp files, delete the modifying in the future

    * save

    * successfullu add power XC_functional and run correctly with Si soilds in 6 nodes and 6 processors

    * successfully realize power functional with testing Si solids, and some printout need to be deleted

    * Print: last push before delete many printout

    * delete modifying in source code

    * Refactor: first add class RDMFT

    * save

    * get DM used for updating charge/rho

    * try to initial DMR of class DensityMatrix

    * save before modifying gint.cpp

    * update charge using wg&wfc which provided by me successfully

    * delete some comment

    * last save before transfer wg -> natural occupation numbers (occupation_num)

    * successfully transfer wg -> occ_number and get correct result in Muller_XC

    * modifying some variable names, function names and comments (for wg -> occNum)

    * add module_rdmft and copy code here working successfully

    * delete rdmft_test.h/.cpp files in module_hamilt_lcao/... and modify corresponding CMakeLists.txt

    * add rdmft.h, rdmft.cpp, rdmft_tools.cpp files to create class RDMFT

    * just save. In the process of factor function rdmft_cal() -> class RDMFT

    * modify rdmft_solver in esolver_ks_lcao.h/.cpp

    * push with compile error in cal_dm.h( psiMulPsiMpi() function with the same name is wrong )

    * add class rdmft and do rdmft_solver.init() successfully, next step is init V_TV, V_XC...

    * successfully move functions of class RDMFT to rdmft.cpp

    * just save

    * just save

    * factor function rdmft_cal() -> class RDMFT and with running error

    * just save

    * Factor: transfer function rdmft_cal() -> class RDMFT and run in afterscf() successfully

    * just save

    * now get V_local in eiter, next step move it to istep, i.e. together with T_nonlocal

    * move the obtaining of V_local from elec-step to ion-step

    * successfully find where to do update_ion()

    * class RDMFT get correct E_TV and E_hartree, but E_XC=0.0

    * Factor: complete func rdmft_cal() -> class RDMFT and find where to use the RDMFT class object rdmft_solver appropriately

    * save

    * save for debug

    * Fix: fix bug in HkPsi(), transfer 'T'->'C'

    * save

    * Fix: fix nk_total in class RDMFT depend on the Symmetry::symm_flag

    * save

    * test different branch

    * add Dell_abaInstall.sh for Dell_server

    * modify module_rdmft to latest version

    * just save for updating branch rdmft

    * update module_xc for rdmft(WP22,CWP22 and so on)

    * Fix memory bug in XC_Functional_Libxc::cal_gdr()

    * Refactor XC_Functional_Libxc::convert_vtxc_v()

    * merge to abacus-v3.8.0 but don't debug(many, because many functions and interfaces have changed). The scaling_factor_xc issue is not handled

    * merge to abacus-v3.8.0 and add scaling_factor in libxc_cpp files

    * merge to abacus-v3.8.0 and debug is not finished

    * just save

    * just save

    * after merging into abacus-v3.8.0, the first compilation passed, but the program has not been run yet

    * after merging to abacus-v3.8.0, the program ran successfully for the first time, but the call of V_exx was not correct.

    * just save

    * just save

    * just save

    * the Vexx may have error when symmetry==1, skip it and continue do my own code

    * add parameters used in rdmft in input_parameters.h and so on

    * merge all rdmft-code to abacus-v3.8.0, next step is debug and test

    * debug now ,some energy is little different from abacus

    * merge to the latest aABACUS

    * Fix the bug caused by merging the latest ABAUCS, need to test other bugs such as wp22, cwp22 and the difference of energy

    * just save

    * add XC-functional BLYP_LIBXC and BLYP_LR to test

    * stop tracking abaInstall_HZWpara.sh

    * just save

    * just save

    * save

    * just save

    * modify cmake/FindELPA.cmake

    * save

    * add RDMFT(Reduced Density Matrix Functional Theory) code

    * [pre-commit.ci lite] apply automatic fixes

    * delete lib64/ and include/

    * delete some production code and modify some variable/function names

    * save

    * merge to the latest abacus

    * just save

    * add tests for rdmft

    * recover accidentally deleted files

    * move rdmft related functions and their calls from esolver_ks to esolver_ks_lcao, and so on

    * save

    * save

    * [pre-commit.ci lite] apply automatic fixes

    * add '#ifdef __MPI', delete run_rdmft() and so on

    * just save

    * save

    * debug

    * add if(ENABLE_LCAO) in rdmft/CMakeLists.txt

    * save

    * save

    * fix compile problem

    * save

    * modify the error in module_io/test/read_input_ptest.cpp

    * prepare for PR

    * save

    * add symmetry calculation of exx in rdmft

    * add test in esolver_ks_lcao.cpp, function after_scf(): update exx to test the exx_energy get by rdmft is exactly equal to exx_energy by abacus

    * delete rdmft_test.h/.cpp

    * delete the test for exx in esolver_ks_lcao.cpp, after_scf(

    * update test with symmetry, tests/integrate/1001_NO_Si2_dzp_rdmft

    * save

    * [pre-commit.ci lite] apply automatic fixes

    * save

    * delete the new ord_file in tests/

    * last save befor move cal_V_ TV/hartree/XC from rdmft.cpp to cal_V_rdmft.cpp

    * last save before move the functions about update_state from rdmft.cpp to update_state_rdmft.cpp

    * save

    * save

    * [pre-commit.ci lite] apply automatic fixes

    * save

    * modify ab_initio_type to bool rdmft

    * save

    * Fix: let nk_total *= nspin, in rdmft

    * modified according to Mr. Chen's suggestion

    * save

    * save

    * merge the latest abacus

    * [pre-commit.ci lite] apply automatic fixes

    * save

    * add some tests for rdmft

    * save

    * save

    * [pre-commit.ci lite] apply automatic fixes

    * reduce calculation time of tests: rdmft

    * modify some comments

    * modify tests

    * save

    * modify class RDMFT

    * save

    * modify Comments

    * save

    * save

    * save

    * save

    * save

    * modify

    * save

    * [pre-commit.ci lite] apply automatic fixes

    * add a comment in rdmft_cal_hamilt/V.cpp

    * rename rdmft_cal_hamilt.cpp to rdmft_pot_mat.cpp

    * Refactore psiDotPsi()

    * save

    * save

    * save

    * save

    ---------

    Co-authored-by: linpz <[email protected]>
    Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
    Co-authored-by: Mohan Chen <[email protected]>
    Co-authored-by: maki49 <[email protected]>
    Co-authored-by: wqzhou <[email protected]>

commit f084d42
Author: dyzheng <[email protected]>
Date:   Wed Nov 27 17:49:33 2024 +0800

    Feature: output mat of <phi|r|phi> with get_S (deepmodeling#5611)

commit f7b62a7
Author: dyzheng <[email protected]>
Date:   Wed Nov 27 15:00:34 2024 +0800

    Fix: symmetry prec mismatch between real and reciprocal space lattice (deepmodeling#5623)

commit 6cd8fb9
Author: Peng Xingliang <[email protected]>
Date:   Wed Nov 27 09:02:04 2024 +0800

    refactor: modify the default return value of warning quit to 1 (deepmodeling#5556)

    * refactor: modify the default return value of warning quit to 1

    * fix ut

    * fix ut

    * [pre-commit.ci lite] apply automatic fixes

    * comment out UT of hcontainer output

    ---------

    Co-authored-by: root <pxlxingliang>
    Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
    Co-authored-by: Mohan Chen <[email protected]>

commit 1527c37
Author: Haozhi Han <[email protected]>
Date:   Wed Nov 27 09:01:47 2024 +0800

    Refactor: remove #include hsolver.h (deepmodeling#5609)

    * remove #include hsolver.h

    * remove hsolver dependency

commit 664f996
Author: liiutao <[email protected]>
Date:   Tue Nov 26 22:16:00 2024 +0800

    Refactor:Remove the dependency of the Psi in the FFT module (deepmodeling#5564)

    * delete fft.cpp

    * update the psi.h

    * update the header file

    * add clear func

    * change the fft makefile

    * delete fft.h

    * update the Makefile.Obj

    * [pre-commit.ci lite] apply automatic fixes

    * revert check_func

    * update the header file

    * change fft_cpu.h

    ---------

    Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>

commit 5d8dce5
Author: Haozhi Han <[email protected]>
Date:   Tue Nov 26 22:13:51 2024 +0800

    Refactor: move wf_atomic and wavefunc files (deepmodeling#5613)

    * move wf_atomic and wavefunc files

    * [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>

commit 0f569ff
Author: Qianrui Liu <[email protected]>
Date:   Tue Nov 26 22:11:36 2024 +0800

    fix wrong nscf energy of sDFT (deepmodeling#5618)

    add nscf energy tests

commit 3d64446
Author: Yu Liu <[email protected]>
Date:   Tue Nov 26 22:10:02 2024 +0800

    Feature: enable get_s for nspin=4 (deepmodeling#5614)

commit 93ac7e3
Author: Liang Sun <[email protected]>
Date:   Tue Nov 26 18:14:54 2024 +0800

    Refactor: Remove cal_ux from ucell. (deepmodeling#5608)

commit 9bc8960
Author: Haozhi Han <[email protected]>
Date:   Tue Nov 26 13:51:48 2024 +0800

    Refactor: move psiinit file to hsolver folder (deepmodeling#5601)

    * move psiinit to esolver

    * update file name

commit 6df5c6d
Author: jinzx10 <[email protected]>
Date:   Tue Nov 26 10:03:48 2024 +0800

    Grid batching by adapted cut-plane (deepmodeling#5599)

    * initial commit

    * continue...

    * crude test...

    * continue...

    * complete!

    * more test

    * small fix

commit cab5894
Author: Qianrui Liu <[email protected]>
Date:   Tue Nov 26 10:03:21 2024 +0800

    Refactor: split sum_stoband to sum_stoband and cal_storho (deepmodeling#5600)

commit 6a98a1a
Author: Qianrui Liu <[email protected]>
Date:   Tue Nov 26 10:02:09 2024 +0800

    fix stuck in out_chg (deepmodeling#5603)

commit 0fd832e
Author: liiutao <[email protected]>
Date:   Tue Nov 26 10:00:42 2024 +0800

    update the DCU compile (deepmodeling#5563)

    * update the duc compile

    * update the FFT_CUDA in the fft_bundle.cpp

    * update the rcom to rocm

    ---------

    Co-authored-by: Qianrui Liu <[email protected]>

commit 5e94cb2
Author: Yu Liu <[email protected]>
Date:   Mon Nov 25 21:19:59 2024 +0800

    Feature: set relax_nmax=0 to enable dry run (deepmodeling#5595)

    * Feature: set relax_nmax=0 to enable dry run

    * update docs

commit df94f88
Author: Yu Liu <[email protected]>
Date:   Mon Nov 25 19:31:57 2024 +0800

    Refactor: remove template for get_S (deepmodeling#5593)

commit 7e9d081
Author: Yu Liu <[email protected]>
Date:   Mon Nov 25 12:31:04 2024 +0800

    Refactor: move tmp charge density output to esolver_ks (deepmodeling#5592)

commit 0f37fe5
Author: Mohan Chen <[email protected]>
Date:   Mon Nov 25 10:18:35 2024 +0800

    Update operator_lcao.h (deepmodeling#5584)

commit 1fb3347
Author: Mohan Chen <[email protected]>
Date:   Mon Nov 25 10:17:29 2024 +0800

    Update overlap_new.cpp (deepmodeling#5581)

commit 9a5c974
Author: Mohan Chen <[email protected]>
Date:   Mon Nov 25 10:16:25 2024 +0800

    Update LCAO_hamilt.hpp (deepmodeling#5580)

commit 8b048f4
Author: Xinyuan Liang <[email protected]>
Date:   Sun Nov 24 20:51:28 2024 +0800

    modify docs. fix deepmodeling#5575 (deepmodeling#5588)

commit 2ba4117
Author: LUNASEA <[email protected]>
Date:   Sun Nov 24 13:03:43 2024 +0800

    restart from HexxR.csr produced by  out_chg (deepmodeling#5586)

commit 4ac1e8a
Author: Yu Liu <[email protected]>
Date:   Sun Nov 24 12:45:47 2024 +0800

    Refactor: remove GlobalC::ucell in esolver (deepmodeling#5569)

    * Refactor: remove GlobalC::ucell in esolver

    * [pre-commit.ci lite] apply automatic fixes

    * update next_direct

    * Refactor: put ucell as the first parameter

    * rename cell to ucell

    * update unitests

    * update opt_TN.hpp

    ---------

    Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>

commit c9f7973
Author: Mohan Chen <[email protected]>
Date:   Sat Nov 23 16:01:35 2024 +0800

    Update elecstate.cpp (deepmodeling#5579)

commit 9cc044e
Author: dzzz2001 <[email protected]>
Date:   Sat Nov 23 11:31:58 2024 +0800

    Refactor: remove some unused variables in module_gint (deepmodeling#5568)

    * remove some unused variables

    * small change

    * remove some redundant lines

    * modify the class interface of grid_meshk

    * remove grid_index.h

    * modify some comment

    * [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>

commit 2c2ed13
Author: Liang Sun <[email protected]>
Date:   Sat Nov 23 09:47:24 2024 +0800

    Fix: Fix the warning triggered in error of SCAN_END. (deepmodeling#5576)

commit ed2fecf
Author: Haozhi Han <[email protected]>
Date:   Fri Nov 22 21:24:16 2024 +0800

    Refactor: remove `wf` from `esolver` (deepmodeling#5567)

    * repalce wf.npwx

    * change the file name `wfinit`

    * remove wf from esolver

    * fix build bug

commit e0202e0
Author: Haozhi Han <[email protected]>
Date:   Fri Nov 22 11:57:40 2024 +0800

    Refactor: remove `init_wfc`&`mem_saver`&`out_wfc_pw`&`out_wfc_r` of wavefunc in abacus (deepmodeling#5557)

    * remove wavefunc. init_wfc mem_saver out_wfc_pw out_wfc_r in abacus

    * replace WFInit by PSIInit

commit 54b044b
Author: Mohan Chen <[email protected]>
Date:   Fri Nov 22 10:28:19 2024 +0800

    Update mult_psi_dmr.cpp (deepmodeling#5552)

commit 7f7a308
Author: Mohan Chen <[email protected]>
Date:   Fri Nov 22 10:26:13 2024 +0800

    Update gint_gamma.h (deepmodeling#5550)

commit 8af2923
Author: Mohan Chen <[email protected]>
Date:   Fri Nov 22 10:25:22 2024 +0800

    Update init_orb.cpp (deepmodeling#5551)

commit e987240
Author: kirk0830 <[email protected]>
Date:   Fri Nov 22 10:17:23 2024 +0800

    remove the redundant macro in source file (deepmodeling#5562)

commit 20efb88
Author: kirk0830 <[email protected]>
Date:   Fri Nov 22 10:16:09 2024 +0800

    swap the sizeof() be the first multiplier to avoid overflow of int (deepmodeling#5561)

commit 8c3def4
Author: Yu Liu <[email protected]>
Date:   Fri Nov 22 08:44:50 2024 +0800

    Refactor: remove dpks_cal_e_delta_band.cpp (deepmodeling#5560)

    * Refactor: remove dpks_cal_e_delta_band.cpp

    * update esolver_ks_lcao.h

    * update dpks_cal_e_delta_band

commit c13f16f
Author: Yu Liu <[email protected]>
Date:   Fri Nov 22 08:44:09 2024 +0800

    Refactor: remove pw_init_globalc.cpp (deepmodeling#5559)

    Co-authored-by: Qianrui Liu <[email protected]>

commit 203c66d
Author: Yu Liu <[email protected]>
Date:   Thu Nov 21 19:13:56 2024 +0800

    Refactor: remove set_matrix_grid (deepmodeling#5558)

commit a6d0ba1
Author: Yu Liu <[email protected]>
Date:   Thu Nov 21 11:22:35 2024 +0800

    Refactor: remove init_after_vc (deepmodeling#5547)

commit c650aa8
Author: Peng Xingliang <[email protected]>
Date:   Thu Nov 21 09:35:39 2024 +0800

    Test: correct the INPUT of examples/scf/lcao_Cu and the reference of examples/bsse/water (deepmodeling#5536)

    Co-authored-by: root <pxlxingliang>
    Co-authored-by: kirk0830 <[email protected]>

commit fdb405a
Author: Goodchong <[email protected]>
Date:   Thu Nov 21 09:34:50 2024 +0800

    Refactor atom_input and unify the fake atom data structure of grid and atom_input (deepmodeling#5546)

    * Refactor atom_input and unify the fake atom data structure of grid and atom_input.

    * add constructors for atom_input

    * [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>

commit 68220cf
Author: wqzhou <[email protected]>
Date:   Thu Nov 21 09:31:57 2024 +0800

    Test: delete `threshold` files in the examples with warnings and update the `result.ref` files (deepmodeling#5402)

    * delete threshold and update the ref

    * recover some unnecessary changes

    * recover some unnecessary changes

    * recover some unnecessary changes

    * recompile and update the ref

    * add threshold for two unstable tests

    * add threshold for two unstable TDDFT tests

    * update threshold for two unstable TDDFT tests

commit 368495d
Author: LUNASEA <[email protected]>
Date:   Thu Nov 21 09:29:14 2024 +0800

    Feature: LR-TDDFT support reading fxc from file or calculating fxc by a specified charge file (deepmodeling#5393)

    * read fxc or charge for fxc from file

    * move xc-dependent functions to a new file

    * minor fix

    * rename files

    * rename init_fxc as init_xc_kernel

    * update grad and lapl

    * delete useless matrix transformer

    * update comments

    * rename: lr_init_xc_kernel

    * add const before std::set

    * rename variables in PotHxcLR

    * rename gdr as gradrho

    * rename spinsize as n_component

    * use something else to replace the for-loop

    * [pre-commit.ci lite] apply automatic fixes

    * flatten the map

    * use std::any_of

    * rename new/delete_p2 as new/delete_pointer_dim2

    * a usage of std::inner_product

    * rename 2order_nested_ptr

    * add annotation and minor changes

    Co-authored-by: kirk0830 <[email protected]>

    * redesign KernelXC: constructor sets all the members

    fix compile

    fix a initialize bug

    * rename and update doc

    ---------

    Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
    Co-authored-by: kirk0830 <[email protected]>

commit 7dcc282
Author: linpeize <[email protected]>
Date:   Thu Nov 21 09:26:56 2024 +0800

    fix bug: change Mixing_Data::length from int to size_t (deepmodeling#5545)

    * fix bug: change Mixing_Data::length from int to size_t

    * fix bug: change Mixing_Data::length from int to size_t

    * [pre-commit.ci lite] apply automatic fixes

    ---------

    Co-authored-by: linpz <[email protected]>
    Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>

commit c7e46be
Author: dyzheng <[email protected]>
Date:   Wed Nov 20 23:16:16 2024 +0800

    Refactor: replace raw pointers to vector in atom_spec.h (deepmodeling#5521)

    * Refactor: new real space projection DeltaSpin method

    * Refactor: replace raw pointers to vector in atom_spec.h

    * Fix: add namespace

    * Fix: save mass

    * [pre-commit.ci lite] apply automatic fixes

    * Fix: error in CI test

    * Fix: error in CI

    * [pre-commit.ci lite] apply automatic fixes

    ---------

    Co-authored-by: dyzheng <[email protected]>
    Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>

commit 20b2214
Author: kirk0830 <[email protected]>
Date:   Wed Nov 20 23:10:41 2024 +0800

    Fix: recover the use of -1 value of out_chg (deepmodeling#5540)

commit 0ecfbc4
Author: James Misaka <[email protected]>
Date:   Wed Nov 20 13:41:48 2024 +0800

    Fix: support lmax of orbital 8,9 (deepmodeling#5528)

    * Fix: support lmax of orbital 8,9

    * Enhance: throw with information when there are unexpected spetrum symbol

    ---------

    Co-authored-by: kirk0830 <[email protected]>

commit 2649152
Author: Haozhi Han <[email protected]>
Date:   Wed Nov 20 08:53:18 2024 +0800

    Refactor: refactor psi init & wfinit class (deepmodeling#5533)

    * refactor psi init

    * remove useless code
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@Qianruipku Qianruipku Qianruipku approved these changes

@mohanchen mohanchen mohanchen approved these changes

Assignees
No one assigned
Labels
Refactor Refactor ABACUS codes
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@A-006 @mohanchen @Qianruipku