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Fix: support lmax of orbital 8,9 #5528

Merged
merged 3 commits into from
Nov 20, 2024
Merged

Fix: support lmax of orbital 8,9 #5528

merged 3 commits into from
Nov 20, 2024

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QuantumMisaka
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Reminder

  • Have you linked an issue with this pull request?
  • Have you added adequate unit tests and/or case tests for your pull request?
  • Have you noticed possible changes of behavior below or in the linked issue?
  • Have you explained the changes of codes in core modules of ESolver, HSolver, ElecState, Hamilt, Operator or Psi? (ignore if not applicable)

Linked Issue

Supplement for #5507

Unit Tests and/or Case Tests for my changes

  • A unit test is added for each new feature or bug fix.

What's changed?

  • Example: My changes might affect the performance of the application under certain conditions, and I have tested the impact on various scenarios...

Any changes of core modules? (ignore if not applicable)

  • Example: I have added a new virtual function in the esolver base class in order to ...

@kirk0830
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there is a PR by me needed to merge to @QuantumMisaka's lmax9 branch, please wait till my PR is merged

@QuantumMisaka
Merge pull request #1 from kirk0830/lmax9-safe
3c986a1 
Enhance: throw with information when there are unexpected spetrum symbol
@kirk0830
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this PR is mainly completed by @QuantumMisaka, I add minor throw information suggested by @hebrewsnabla.
Thanks for all your contribution!

@mohanchen mohanchen merged commit 0ecfbc4 into deepmodeling:develop Nov 20, 2024
14 checks passed
@mohanchen mohanchen added the Refactor Refactor ABACUS codes label Nov 20, 2024
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
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@kirk0830 kirk0830 kirk0830 approved these changes

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