ABACUS-v2.2.1 : Hotfix for v2.2.0

Feature changed:

• deepks : allow reading embedding model by @wenfei-li in deepmodeling#822
• Feature: Add module surchem. by @Asuna981002 in deepmodeling#846

Bug fixed:

• Fix uninited rcutmax by @maki49 in deepmodeling#821
• Fix bug: the opended file 'data-H' is not closed by @pxlxingliang in deepmodeling#820
• Fix a delete in parallel_orbitals by @maki49 in deepmodeling#827
• Fix : attempt to fix search_radius error in 'unit' test by @wenfei-li in deepmodeling#825
• Fix: rewrite MD_dump when step=0 by @YuLiu98 in deepmodeling#824
• Fix: add .gitignore items for generated files in tests/deepks/*. by @caic99 in deepmodeling#829
• Fix: gint : removed obsolete codes by @wenfei-li in deepmodeling#831
• Build: fix sanitizer test logic. by @caic99 in deepmodeling#832
• Fix: deleted useless file, output right occupied band for soc case by @dyzheng in deepmodeling#826
• Build: Add libnpy, googletest in docker env. by @caic99 in deepmodeling#840
• Fix: potential array access overflow in gamma vl by @caic99 in deepmodeling#845
• Build: fix static analysis workflow logic. by @caic99 in deepmodeling#847
• Fix: misuse of '=' in assertion by @caic99 in deepmodeling#850
• Fix: variable not initialized in for-loop by @caic99 in deepmodeling#851
• Doc: Format markdown files. by @caic99 in deepmodeling#855
• docs: move developers.md to CONTRIBUTING.md. by @caic99 in deepmodeling#856
• Fix: update the default value of md_tfreq by @YuLiu98 in deepmodeling#857
• docs: fix path link to docs/ by @caic99 in deepmodeling#858
• Fix: modify documentation, comment, and HSE input by @wenfei-li in deepmodeling#859
• Fix: remove invalid warning in Pseudopot_upf::read_pseudo_upf201. by @sunliang98 in deepmodeling#862
• Fix: 1. only init wfc once for MD and relax; 2. reset PW_DIAG_THR every Ionic step. 3. 17 test cases reference updated by @dyzheng in deepmodeling#864
• Fix: 1, 2D-block allocation error. 2, not print charge density cube file if out_chg is 0 by @dyzheng in deepmodeling#868
• Fix: 1. update Makefile.system and Makefile.vars by @PeizeLin in #122
• Fix: Adjust bands output for DFT+DMFT by @Qx80610702 in #123
• Fix: 1. fix bug for 'dft_functional = hse' in LOOP_elec::solver() by @PeizeLin in #124
• Merge Makefile bugfix by @dyzheng in #133

Test updates:

• Test: update UT branches by @caic99 in deepmodeling#835
• Test: change testing target to merged reference by @caic99 in deepmodeling#838
• Test: add the unit test of parallel diagonalization by ELPA by @pxlxingliang in deepmodeling#839
• Test(pw): cg of HSolver with larger H matrices by @hongriTianqi in deepmodeling#863
• Test: rename CI step by @caic99 in deepmodeling#853
• CI: Enable static code analysis. by @caic99 in deepmodeling#854
• Build: update testing strategy by @caic99 in deepmodeling#852
• Test(pw): add UT of Charge::sum_band() by @hongriTianqi in deepmodeling#860
• Test(LCAO): add the UT of ELPA/SCALAPACK diagonalization by @pxlxingliang in deepmodeling#861

Refactors:

• Update esolver.h by @Qianruipku in deepmodeling#843
• Refactor: move Global.h dependency from header to cpp files, by @dyzheng in deepmodeling#842
• Merge: HSolver to develop, diagonalization for PW and LCAO has finished. by @dyzheng in deepmodeling#848

Full Changelog: v2.2.0...v2.2.1

v2.2.0

New features for users:

• Feature: Optimized the calculation of structure factor with B-spline interpolation method. (Qianruipku #370 #371 #375 )
• Feature: The function of using the same random number seed to produce the initial trial wave function is added to the plane wave code. (Qianruipku #285 #284 #278 dyzheng #308 )
• Feature: SOC modulation function is added, used by set parameter "soc_lambda" (dyzheng #232 #258 #333 #336 #340 )
• Feature: Added parameter "symmetry_prec" to control symmetry precision. (LiuXiaohui123321 #333 )
• Feature: Added independent code for drawing electric band. (jiyuyang #333 )
• Feature: The SCAN exchange-correlation functional was added in the plane wave basis set. (wenfei-li #231 #236 #245 #253 #257 #262 #264 #292 #294 #296 #309 dyzheng #238 caic99 #268 )
• Feature: Added sparse matrix format for Hamiltonian matrix.(jingan #159 jingan-181 #75 )
• Feature: Molecular dynamics calculation in plane wave code is added. (dyzheng #99 )
• Feature: The DeePKS descriptor function was added. (maki49 #6 #15 #21 #24 #44 #67 #197 )
• Feature: Classical force field is added for molecular dynamics, including LJ potential and DP potential. (YuLiu98 #169 #306 #311 #368 #327 )
• Feature: Modified STRU file format, now you can import initial velocities and magnetic moments. (lyb9812 #234 #287 #295 #307 #355 ZhouGD2000 #312 #342 )
• Feature: BLPS pseudopotential file is supported. (sunliang98 #316 #318 #323 )
• Feature: BSSE function is added. (PeizeLin #4 )
• Feature: Stochastic DFT method is added. (Qianruipku #38 )
• Feature: The SCAN exchange-correlation functional was added in the plane wave basis set. (wenfei-li #309 #296 #294 #292 #264 #262 #257 #253 #245 #236 #231 dyzheng #238 caic99 #268 )
• Feature: DeePKS Function with LCAO code is added, multi core test is still in developing. (maki49 #52 #60 #65 #67 #177 #178 #197 #218 #346 )
• Feature: Time dependent DFT(TDDFT) is added, still in test.(HeFuxiang94 #30 #33 #34 #45 #51 #54 #280 #335 #361 #363 )
• Feature: A linear algorithm for Structure Factor by @Qianruipku in deepmodeling#370
• Feature: add stress calculation for LJ potential by @YuLiu98 in deepmodeling#368
• Feature: Newelpa and reconstruction merge to develop branch, compatible for current deepks branch. by @dyzheng in deepmodeling#395
• Feature: Deepks parallelization : gamma point by @wenfei-li in deepmodeling#404
• Feature: update scalapack_gvx from Peizelin and update openmp for gint_k_vl.cpp from Liu Xiaohui by @dyzheng in deepmodeling#434
• Feature: merge openmp update and PDOS+soc by @dyzheng in deepmodeling#410
• Feature: Update distribution method 1. by @sunliang98 in deepmodeling#431
• Feature: Add cudafft by @Qianruipku in deepmodeling#435
• Feature: merge scalapack update to develop branch by @dyzheng in deepmodeling#436
• Feature: Add variables(nsz2ip, ...) to header file, and update distribution_method1. by @sunliang98 in deepmodeling#433
• Feature: multi-k descriptor; fix small bug by @wenfei-li in deepmodeling#413
• Feature: Deepks multi-k : energy by @wenfei-li in deepmodeling#419
• Feature: Deepks : multi-k, force by @wenfei-li in deepmodeling#426
• Deepks : add comment; rearrange code; test case by @wenfei-li in deepmodeling#455
• Deepks : remove lcao_descriptor_new.cpp by @wenfei-li in deepmodeling#459
• Deepks : move libnpy dependence by @wenfei-li in deepmodeling#461
• Deepks : fix compile with cmake; set enable deepks as default; modify autotest by @wenfei-li in deepmodeling#466
• Deepks : multi-k and paralleliation for grad_vx by @wenfei-li in deepmodeling#472
• Feature: Add distributeg_method2 and corresponding unit tests. by @sunliang98 in deepmodeling#510
• Feature: by @Qianruipku in deepmodeling#554
• Print: add absolute k spacing in BANDS_1.dat by @hongriTianqi in deepmodeling#571
• Feature: Langevin method in MD by @YuLiu98 in deepmodeling#572
• Feature: Merge from cuda11 to develop by @Asuna981002 in deepmodeling#622
• Feature: enabling the orbital (band gap) training in DeePKS by @ouqi0711 in deepmodeling#617
• Feature: INPUT parameters refactor by @YuLiu98 in #810 #813
• Feature: Sto dft by @Qianruipku in #4
• Feature: output jle(r) by @maki49 in #8
• Feature: read descriptor basis by @maki49 in #10
• Feature: output 5D overlap table between lcao and descriptor orbitals by @maki49 in #11
• Feature: out lcao-line descriptor by @maki49 in #15
• Feature: add the input parameter for accuracy of symmetry: symmetry_prec by @LiuXiaohui123321 in #47
• Feature: add band structure and DOS plotting tools by @1041176461 in #51
• Feature: Newelpa by @pplab in #60
• Feature: add PDOS with soc by @1041176461 in #70
• Feature: add class Diag_Scalapack_gvx by @PeizeLin in #74
• Feature: add opt_orb_pytorch_dpsi by @PeizeLin in #80
• Feature: Integrate pytorch+dpsi method into original orbital-generation-script by @wszhang in #86
• Feature: Output SR sparse matrix separately by @jingan-181 in #95
• Feature: DFT+DMFT and DFT+U by @Qx80610702 in #98

Performance updates for users:

• Perf: The efficiency of plane-wave code was optimized by updating the CG method in self-consistent calculations. (by Qianruipku before #1 )
• Perf: Improved cache memory for wave function for gamma_only method in LCAO code. (Liuxiaohui123321 dyzheng #367)
• Perf: Improved DFT+U memory cost and efficiency. (Quxin #260 #222 Quxin80610702 #222 ZhouGD2000 #357 #249 )
• Perf: Improved the efficiency of non-local pseudopotential part in Hamiltonian matrix, still in test now. (wenfei-li #352 #354 #365 #372 )
• Perf: LCAO nonlocal force & stress: switch to new method by @wenfei-li in deepmodeling#365
• Perf: LCAO : new method for nonlocalPP, k points by @wenfei-li in deepmodeling#372
• Perf: vnl : make it faster for large system by @wenfei-li in deepmodeling#427
• Perf: deepks : acceleration for multi-k by @wenfei-li in deepmodeling#524
• Perf: by @Qianruipku in deepmodeling#535
• Perf: by @Qianruipku in deepmodeling#540
• Perf: optimize the program by @Qianruipku in deepmodeling#542
• Perf: optimize efficiency by @Qianruipku in deepmodeling#544
• Perf: by @Qianruipku in deepmodeling#548
• Perf: by @Qianruipku in deepmodeling#549
• Perf optimized non-local part for Stress and Forces calculation in PW base by @dyzheng in deepmodeling#559
• Perf: sum_band() in pw base; fix: memory leak by @dyzheng in deepmodeling#586
• Perf: Modified the recommended values for exx-related input parameters in input-main.md by @ouqi0711 in deepmodeling#723
• Perf: optimize hpsi and cgdiag by @Qianruipku in #9
• Perf: improve cinitcgg function by @Qianruipku in #6
• Perf: optimize src_lcao/LCAO_gen_fixedH.cpp by @YuLiu98 in #16
• Perf: 1. optimize Numerical_Basis::cal_overlap_Sq() to gemm by @PeizeLin in #65
• Perf: OpenMP optimization for local potential and charge density under k-points line by @LiuXiaohui123321 in #76
• Perf: 1. optimize Write_Wfc_Realspace::write_charge_realspace_1() by @PeizeLin in #103
• Perf: OpenMP optimization for nonlocal pseudo-potential under gamma-only line by @LiuXiaohui123321 in #108

Documentation updates for users:

• Doc: The online manual was added. (wenfei-li #122 #129 #144 #164 #172 #202 #209 #200 #187 maki49 #165 #166 caic99 #190 #241 #199 #214 #330 #268 lyb9812 #325 sunliang98 #316 mohanchen #41)
• Doc: updated some documentation for INPUT variables by @dyzheng in https:...