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Change namespace A::B{} to namespace A{namespace B{}} #309

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wants to merge 43 commits into from
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Change namespace A::B{} to namespace A{namespace B{}} #309

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PeizeLin
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Change namespace A::B{} to namespace A{namespace B{}}, since namespace A::B{} is a C++17 feature.

mohanchen and others added 30 commits March 28, 2024 09:02
@mohanchen
Update description for ESolver (#3828)
14b9827 
* update timer, add std

* update the format of esolver_fp.cpp

* add description in esolver_fp.h

* update a few esolver files

* update esolver description for LCAO

* update some formats of esolver codes

* update esolver_ks_pw.cpp formats

* update formats of esolver_ks_pw.cpp and esolver_ks_pw.h

* update esolver_ks_lcao_tddft.cpp formats

* update format of esolver_sdft_pw.cpp

* update the format of esolver_sdft_pw_tool.cpp

* keep formating esolver_ks_pw.cpp

* formating esolver_of_interface.cpp

* change GlobalC::ucell to ucell in esolver_ks.cpp

* remove some GlobalC::ucell in esolver_sdft_pw.cpp
@hongriTianqi
Fix: change the unit of decay gradient (#3826)
21a0a5d
@Cstandardlib
Refactor: Removed direct references to GlobalV related to function re…
a7c1865 
…ad_cube. (#3824)

Removed references to GlobalV variables
(defined in module_base/global_variable.h)
in function  and (which depends on ).
@jieli-matrix
Test: save precision results to file when building unit tests (#3829)
0dd5623
@dyzheng
Perf: use converged occupation matrix for initial DFTU calculation in…
1fa4f86 
… MD calculation (#3837)

Co-authored-by: dyzheng <zhengdy@bjaisi.com>
@jieli-matrix
Test: Save simpson test results to file (#3842)
8bc01b1
@ESROAMER
Fix mistakes in TDDFT docs (#3841)
026bfd8 
* Delete examples/tddft/Absoption_spectrum/H2_length directory

* Delete examples/tddft/Absoption_spectrum/H2_vel directory

* Add files via upload

* Update input-main.md
@jieli-matrix
modify the criteria (#3849)
7f05684
@mohanchen
Keep updating esolver and related source files (#3853)
96b72b2 
* update timer, add std

* update the format of esolver_fp.cpp

* add description in esolver_fp.h

* update a few esolver files

* update esolver description for LCAO

* update some formats of esolver codes

* update esolver_ks_pw.cpp formats

* update formats of esolver_ks_pw.cpp and esolver_ks_pw.h

* update esolver_ks_lcao_tddft.cpp formats

* update format of esolver_sdft_pw.cpp

* update the format of esolver_sdft_pw_tool.cpp

* keep formating esolver_ks_pw.cpp

* formating esolver_of_interface.cpp

* change GlobalC::ucell to ucell in esolver_ks.cpp

* remove some GlobalC::ucell in esolver_sdft_pw.cpp

* refactor the code before getting rid of RA in esolver_lcao

* refactor before getting rid of LOWF

* refactor before getting rid of LCAO_hamilt.h and LCAO_matrix.h

* refactor wavefunc_in_pw

* refactor density matrix

* refactor the format cal_dm_psi.cpp

* format forces.cpp

* refactor esolver_of_tool.cpp

* change member function beforescf in Esolver to before_scf

* change afterscf to after_scf

* change updatepot to update_pot

* change eachiterinit to iter_init, change eachiterfinish to iter_finish

* refactor esolvers, change member function names of most esolvers

* reformat esolver.h

* update tests for esolvers
@AmengFromCDH
Add files via upload (#3858)
b39847e 
some variables initialized
@OldDriver233
Fix: potentially uninitialized variables in calculation (#3834)
fe07b2e
@mohanchen
Refactoring LCAO codes. (#3860)
034316e 
* update timer, add std

* update the format of esolver_fp.cpp

* add description in esolver_fp.h

* update a few esolver files

* update esolver description for LCAO

* update some formats of esolver codes

* update esolver_ks_pw.cpp formats

* update formats of esolver_ks_pw.cpp and esolver_ks_pw.h

* update esolver_ks_lcao_tddft.cpp formats

* update format of esolver_sdft_pw.cpp

* update the format of esolver_sdft_pw_tool.cpp

* keep formating esolver_ks_pw.cpp

* formating esolver_of_interface.cpp

* change GlobalC::ucell to ucell in esolver_ks.cpp

* remove some GlobalC::ucell in esolver_sdft_pw.cpp

* refactor the code before getting rid of RA in esolver_lcao

* refactor before getting rid of LOWF

* refactor before getting rid of LCAO_hamilt.h and LCAO_matrix.h

* refactor wavefunc_in_pw

* refactor density matrix

* refactor the format cal_dm_psi.cpp

* format forces.cpp

* refactor esolver_of_tool.cpp

* change member function beforescf in Esolver to before_scf

* change afterscf to after_scf

* change updatepot to update_pot

* change eachiterinit to iter_init, change eachiterfinish to iter_finish

* refactor esolvers, change member function names of most esolvers

* reformat esolver.h

* update tests for esolvers

* add TITLE in esolver_ks_lcao

* update esolver_ks_lcao

* update esolver_lcao

* update timer::tick in esolver_lcao

* try to delete LCAO_Matrix in LCAO_Hamilt, and try to delete Parallel_Orbitals in Force_k

* fix the compiling issue with LCAO_hamilt.hpp

* try to divide the FORCE_k.cpp into several small files
@WHUweiqingzhou
delete a extra bracket (#3863)
222f1f2
@Pureorangeade
Update berryphase.cpp (#3876)
6814360 
* Update berryphase.cpp

Initialize ik_1 and ik_2 in berryphase.cpp

* Update berryphase.cpp

Initialize modulus in berryphase.cpp
@mohanchen
Refactor LCAO step 2 (#3874)
81540d0 
* update timer, add std

* update the format of esolver_fp.cpp

* add description in esolver_fp.h

* update a few esolver files

* update esolver description for LCAO

* update some formats of esolver codes

* update esolver_ks_pw.cpp formats

* update formats of esolver_ks_pw.cpp and esolver_ks_pw.h

* update esolver_ks_lcao_tddft.cpp formats

* update format of esolver_sdft_pw.cpp

* update the format of esolver_sdft_pw_tool.cpp

* keep formating esolver_ks_pw.cpp

* formating esolver_of_interface.cpp

* change GlobalC::ucell to ucell in esolver_ks.cpp

* remove some GlobalC::ucell in esolver_sdft_pw.cpp

* refactor the code before getting rid of RA in esolver_lcao

* refactor before getting rid of LOWF

* refactor before getting rid of LCAO_hamilt.h and LCAO_matrix.h

* refactor wavefunc_in_pw

* refactor density matrix

* refactor the format cal_dm_psi.cpp

* format forces.cpp

* refactor esolver_of_tool.cpp

* change member function beforescf in Esolver to before_scf

* change afterscf to after_scf

* change updatepot to update_pot

* change eachiterinit to iter_init, change eachiterfinish to iter_finish

* refactor esolvers, change member function names of most esolvers

* reformat esolver.h

* update tests for esolvers

* add TITLE in esolver_ks_lcao

* update esolver_ks_lcao

* update esolver_lcao

* update timer::tick in esolver_lcao

* try to delete LCAO_Matrix in LCAO_Hamilt, and try to delete Parallel_Orbitals in Force_k

* fix the compiling issue with LCAO_hamilt.hpp

* try to divide the FORCE_k.cpp into several small files

* divide FORCE_k into foverlap_k.cpp ftvnl_dphi_k.cpp fvl_dphi_k.cpp fvnl_dbeta_k.cpp four files

* get rid of UHM in FORCE_k.cpp

* cannot compile, but I have modified some files in order to get rid of Gint_k and Gint_Gamma in UHM

* keep updating, cannot run

* update write_Vxc, cannot run yet

* keep updating gint_gamma and gint_k

* update LCAO_matrix.cpp

* divide force files, and update Makefile.Objects

* update LCAO_hamilt.cpp
@flinky-ai
#3867 (#3871)
8959127
@aFlyingOctopus
Update ORB_atomic.cpp (#3835)
974ebed 
initialize variable
@dyzheng
Test: add unit test of DFTUNew and refactor some code (#3814)
42a086e 
* Fix: not use static member in DFTUNew

* Test: add unit test of DFTUNew

* Test: add nspin=2 test and delete GlobalV::CURRENT_SPIN in DFTUNew

* add annotation for dftu.h

* Refactor: new dftu code with suggestions by developers

---------

Co-authored-by: dyzheng <zhengdy@bjaisi.com>
@WHUweiqingzhou
Fix: fix a bug in get_dmk_vector() and make some refactor of get-fu…
c78456c 
…nction (#3893)

* fix a bug in get_dmk_vector() and make some refactor of get-function

* override to avoid compile error
@maki49
Feature & Refactor: read and write Hexx(R) in CSR format (#3727)
dc7938b 
* refactor sparse output

* read HexxR in CSR

* parallel support

* remove test code

* comments

* recover multiple process

* refactor singleR

* change func names
@DylanWRh
initialize some variables (#3846)
fc9a0de 
* initialize some variables

* fix a semicolon

* Update sincos.cpp

* Update mathzone_add1.cpp

* Update mathzone_add1.cpp

* Update opt_DCsrch.cpp

* Update broyden_mixing.cpp

* Update pulay_mixing.cpp

* Update math_sphbes_test.cpp

* Update ORB_gen_tables.cpp

* Update ORB_table_phi.cpp

* Update math_sphbes_test.cpp
@sunliang98
<Fix> Fix the hexadecimal output in MD with OFDFT (#3896)
cb69fb3
@randomname23333
Update klist.cpp (#3908)
e49fce2
@Haerxile
Initialized some variables in projgen.cpp (#3905)
b62a807
@dyzheng
Fix: compiling warning in veff_lcao.cpp (#3901)
d6f00d0 
Co-authored-by: dyzheng <zhengdy@bjaisi.com>
@Luckken21
llk_initialization of read_atoms.cpp (#3900)
2ae3609 
Co-authored-by: Lukai Lin <14197186+lukai-lin@user.noreply.gitee.com>
@Zjhjunhao @mohanchen
Update read_rhog.cpp (#3887)
d4fab4d 
Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
@charches @mohanchen
initialized winput::imp_pao = 0 in winput.cpp (#3897)
ed8593a 
Co-authored-by: charches <charches@DESKTOP-AB7IADE>
Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
@Esperanzalukas
initialize some variables (#3904)
9fb1e4d
@Fisheory @mohanchen
Update bessel_basis.cpp (#3910)
e88495d 
Initialize variable "no_use_c4"

Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
bot10032 and others added 13 commits April 3, 2024 16:20
@bot10032 @mohanchen
Update bessel_basis.cpp (#3911)
af44d22 
Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
@mohanchen
Refactor LCAO code Step 3 (#3914)
8bee71b 
* update timer, add std

* update the format of esolver_fp.cpp

* add description in esolver_fp.h

* update a few esolver files

* update esolver description for LCAO

* update some formats of esolver codes

* update esolver_ks_pw.cpp formats

* update formats of esolver_ks_pw.cpp and esolver_ks_pw.h

* update esolver_ks_lcao_tddft.cpp formats

* update format of esolver_sdft_pw.cpp

* update the format of esolver_sdft_pw_tool.cpp

* keep formating esolver_ks_pw.cpp

* formating esolver_of_interface.cpp

* change GlobalC::ucell to ucell in esolver_ks.cpp

* remove some GlobalC::ucell in esolver_sdft_pw.cpp

* refactor the code before getting rid of RA in esolver_lcao

* refactor before getting rid of LOWF

* refactor before getting rid of LCAO_hamilt.h and LCAO_matrix.h

* refactor wavefunc_in_pw

* refactor density matrix

* refactor the format cal_dm_psi.cpp

* format forces.cpp

* refactor esolver_of_tool.cpp

* change member function beforescf in Esolver to before_scf

* change afterscf to after_scf

* change updatepot to update_pot

* change eachiterinit to iter_init, change eachiterfinish to iter_finish

* refactor esolvers, change member function names of most esolvers

* reformat esolver.h

* update tests for esolvers

* add TITLE in esolver_ks_lcao

* update esolver_ks_lcao

* update esolver_lcao

* update timer::tick in esolver_lcao

* try to delete LCAO_Matrix in LCAO_Hamilt, and try to delete Parallel_Orbitals in Force_k

* fix the compiling issue with LCAO_hamilt.hpp

* try to divide the FORCE_k.cpp into several small files

* divide FORCE_k into foverlap_k.cpp ftvnl_dphi_k.cpp fvl_dphi_k.cpp fvnl_dbeta_k.cpp four files

* get rid of UHM in FORCE_k.cpp

* cannot compile, but I have modified some files in order to get rid of Gint_k and Gint_Gamma in UHM

* keep updating, cannot run

* update write_Vxc, cannot run yet

* keep updating gint_gamma and gint_k

* update LCAO_matrix.cpp

* divide force files, and update Makefile.Objects

* update LCAO_hamilt.cpp

* delete genH pointer in UHM

* divide LCAO_hamilt.cpp into small codes, grid_init.cpp is the first one

* update grid_init in esolver_ks_lcao

* add a new namespace named sparse_format, most of the functions that originally belong to LCAO_hamilt should be moved to sparse_format

* cannot find the mismatch of DFTU

* fix the DFTU error

* update
@mohanchen
Enable 'calculation=test_memory" function again (#3919)
534d1d8 
* update timer, add std

* update the format of esolver_fp.cpp

* add description in esolver_fp.h

* update a few esolver files

* update esolver description for LCAO

* update some formats of esolver codes

* update esolver_ks_pw.cpp formats

* update formats of esolver_ks_pw.cpp and esolver_ks_pw.h

* update esolver_ks_lcao_tddft.cpp formats

* update format of esolver_sdft_pw.cpp

* update the format of esolver_sdft_pw_tool.cpp

* keep formating esolver_ks_pw.cpp

* formating esolver_of_interface.cpp

* change GlobalC::ucell to ucell in esolver_ks.cpp

* remove some GlobalC::ucell in esolver_sdft_pw.cpp

* refactor the code before getting rid of RA in esolver_lcao

* refactor before getting rid of LOWF

* refactor before getting rid of LCAO_hamilt.h and LCAO_matrix.h

* refactor wavefunc_in_pw

* refactor density matrix

* refactor the format cal_dm_psi.cpp

* format forces.cpp

* refactor esolver_of_tool.cpp

* change member function beforescf in Esolver to before_scf

* change afterscf to after_scf

* change updatepot to update_pot

* change eachiterinit to iter_init, change eachiterfinish to iter_finish

* refactor esolvers, change member function names of most esolvers

* reformat esolver.h

* update tests for esolvers

* add TITLE in esolver_ks_lcao

* update esolver_ks_lcao

* update esolver_lcao

* update timer::tick in esolver_lcao

* try to delete LCAO_Matrix in LCAO_Hamilt, and try to delete Parallel_Orbitals in Force_k

* fix the compiling issue with LCAO_hamilt.hpp

* try to divide the FORCE_k.cpp into several small files

* divide FORCE_k into foverlap_k.cpp ftvnl_dphi_k.cpp fvl_dphi_k.cpp fvnl_dbeta_k.cpp four files

* get rid of UHM in FORCE_k.cpp

* cannot compile, but I have modified some files in order to get rid of Gint_k and Gint_Gamma in UHM

* keep updating, cannot run

* update write_Vxc, cannot run yet

* keep updating gint_gamma and gint_k

* update LCAO_matrix.cpp

* divide force files, and update Makefile.Objects

* update LCAO_hamilt.cpp

* delete genH pointer in UHM

* divide LCAO_hamilt.cpp into small codes, grid_init.cpp is the first one

* update grid_init in esolver_ks_lcao

* add a new namespace named sparse_format, most of the functions that originally belong to LCAO_hamilt should be moved to sparse_format

* cannot find the mismatch of DFTU

* fix the DFTU error

* update

* enable the test_memory function again by setting calcalculation parameter in INPUT file

* update memory record functions
@yang2022i @mohanchen
initialize some variables (#3917)
2065971 
Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
@RobertRainbow @mohanchen
initial the file : source/module_ri/RI_2D_Comm.cpp and ABF_Construct …
3d1ad16 
…(#3898)

* initial the file source/module_ri/RI_2D_Comm.cpp

* the second initialization of module_ri/RI_2D_Comm.cpp

* initialize the file ABFS-Construct-PCA

* initialize the file ABF_Costruct_

* initialize the file ABFs_Construct-PCA.cpp

---------

Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
@mohanchen @maki49
LCAO refactor step 4 (#3921)
4356f9f 
* update timer, add std

* update the format of esolver_fp.cpp

* add description in esolver_fp.h

* update a few esolver files

* update esolver description for LCAO

* update some formats of esolver codes

* update esolver_ks_pw.cpp formats

* update formats of esolver_ks_pw.cpp and esolver_ks_pw.h

* update esolver_ks_lcao_tddft.cpp formats

* update format of esolver_sdft_pw.cpp

* update the format of esolver_sdft_pw_tool.cpp

* keep formating esolver_ks_pw.cpp

* formating esolver_of_interface.cpp

* change GlobalC::ucell to ucell in esolver_ks.cpp

* remove some GlobalC::ucell in esolver_sdft_pw.cpp

* refactor the code before getting rid of RA in esolver_lcao

* refactor before getting rid of LOWF

* refactor before getting rid of LCAO_hamilt.h and LCAO_matrix.h

* refactor wavefunc_in_pw

* refactor density matrix

* refactor the format cal_dm_psi.cpp

* format forces.cpp

* refactor esolver_of_tool.cpp

* change member function beforescf in Esolver to before_scf

* change afterscf to after_scf

* change updatepot to update_pot

* change eachiterinit to iter_init, change eachiterfinish to iter_finish

* refactor esolvers, change member function names of most esolvers

* reformat esolver.h

* update tests for esolvers

* add TITLE in esolver_ks_lcao

* update esolver_ks_lcao

* update esolver_lcao

* update timer::tick in esolver_lcao

* try to delete LCAO_Matrix in LCAO_Hamilt, and try to delete Parallel_Orbitals in Force_k

* fix the compiling issue with LCAO_hamilt.hpp

* try to divide the FORCE_k.cpp into several small files

* divide FORCE_k into foverlap_k.cpp ftvnl_dphi_k.cpp fvl_dphi_k.cpp fvnl_dbeta_k.cpp four files

* get rid of UHM in FORCE_k.cpp

* cannot compile, but I have modified some files in order to get rid of Gint_k and Gint_Gamma in UHM

* keep updating, cannot run

* update write_Vxc, cannot run yet

* keep updating gint_gamma and gint_k

* update LCAO_matrix.cpp

* divide force files, and update Makefile.Objects

* update LCAO_hamilt.cpp

* delete genH pointer in UHM

* divide LCAO_hamilt.cpp into small codes, grid_init.cpp is the first one

* update grid_init in esolver_ks_lcao

* add a new namespace named sparse_format, most of the functions that originally belong to LCAO_hamilt should be moved to sparse_format

* cannot find the mismatch of DFTU

* fix the DFTU error

* update

* enable the test_memory function again by setting calcalculation parameter in INPUT file

* update memory record functions

* add sparse_format_u

* keep refactoring LCAO_hamilt

* rename sparse format files, which are originally defined in LCAO_hamilt.h

* add spar_u.h and spar_u.cpp

* update sparse matrix

* add spar_exx

* update LCAO_hamilt.cpp

* tear down LCAO_hamilt.h and .cpp, DONE.

* keep updating spar

* fix the bugs after deleting LCAO_hamilt

* continue

* fix some errors when compiling

* fix compiling errors in DOS

* fix errors without uhm

* remove directly use of LM in spar_hsr.cpp

* update spa_ files

* keep cleaning the mass left by UHM

* finnaly, all files can be compiled without uhm

* previous commit has problems, now it has been fixed.

* fix makefile bugs

* fix exx compiling errors

* fix exx problems

* update exx

* fix exx

* in some sense, the exx code is a disaster

* let's fix exx again

* fix undefination

* fix a bug in LCAO Refactor Step 4, I accidently forgot to add & for Grid_Driver& _grid in output_mat_sparse.h

---------

Co-authored-by: maki49 <1579492865@qq.com>
@caic99
Docs: update the default recommended requirements for conda (#3924)
ee0dc6f 
* Docs: update the default recommended requirements for conda

* update variant grammar
@1041176461 @Qianruipku
Fix: dos plot for nspin=2 (#3928)
270b307 
* 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

---------

Co-authored-by: jiyuang <jiyuyang@mail.ustc.com>
Co-authored-by: Qianrui <76200646+Qianruipku@users.noreply.github.com>
@WHUweiqingzhou @mohanchen
Feature: add so-called U-Ramping method to improve DFTU convergence (…
125581b 
…#3890)

* add a new input parameter uramping, default is -1.0

* add a new member uramping in dftu.h and value it in Input_conv::Convert()

* add a new member U0 in dftu.h and value it in Input_conv::Convert()

* set U zero if uramping > 0.1 in Input_conv::Convert()

* add a new member function DFTU::uramping_update() to change U during SCF

* add a new member function DFTU::U_converged() to check if U=U0

* add uramping in esolver_lcao::iter_init() and change conv_elec

* make some minor changes

* fix bug which only restart once

* add a new member mixing_restart_count in Charge_Mixing

* add U output at iter 1

* fix build error without LCAO

* add some output of U value during U-Raming

* add some docs about uramping

* modify under some comments

* add a space in output

* add docs abouht DFTU in converge.md

* add recommendations of mixing_restart in input-main.md

* add some comment to explain why mixing_restart_count is int instead of bool

* add ref & in mix_dmr()

* add a new CI case 260_NO_DJ_PK_PU_AFM_URAMPING

* rename chgmix->mixing_restart as mixing_restart_step to avoid misunderstanding between GlobalV::MIXING_RESTART

* keep verbosity of judge in esolver to remind others mixing_dmr is only called in this case.

---------

Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
@haozhihan @mohanchen
Feature: Add a new Davidson iteration method called subspace davidson…
21d40ce 
… for pw basis (#3903)

* add new_dav method which is same to davidson method for pw basis

* add new_dav method for pw basis which is more efficient than origin dav method

* fix ilaenv interface bug

* update new_dav method 3.5

* implement new_dav method for pw basis (cpu version, one core)

* fix bug of dav method for pw basis

* debug for new davidson method

* opt some value setting for new_dav files

* format and reorganize the code

* fix CUDA compile bug

* format diago_newdav.cpp

* Implement multi-core parallelism of the new davidson method

* fix build bug for without mpi

* replace new-dav of subspace-dav

* change file name from diago_newdav to diago_subspacedav

* fix build bug for tests

* change the name of subspacedav to dav_subspace

* fix build bug in Integration Test

---------

Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
@hongriTianqi @mohanchen
Feature: add force and stress output for noncollinear calculation wit…
aacf171 
…h soc (#3933)

* release force warning in noncollinear case

* foverlap and ft pulay

* fix ft foverlap add VNL_pulay

* FH and pulay force of VNL with soc

* noncollinear stress calculation

* treat GlobalV::NSPIN and GlobalV::NPOL

* treat globalV

* treat GlobalC::ucell

* treat GlobalC::ORB

* treat GridD

* rewrite some if sentence

* treat GlobalC GlobalV and if sentence

* treat nspin_

---------

Co-authored-by: Mohan Chen <mohan.chen.chen.mohan@gmail.com>
@haozhihan
update cal_elem func (#3953)
49737e5 
avoiding matrix transposition can computational efficiency.
@PeizeLin
change namespace A::B{} to namespace A{namespace B{}}
41640ce
@PeizeLin PeizeLin closed this Apr 11, 2024
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