Feature: Add PEXSI Support for Gamma Only LCAO Calculation by Flying-dragon-boxing · Pull Request #3561 · deepmodeling/abacus-develop

Flying-dragon-boxing · 2024-01-28T06:32:54Z

Reminder

Have you explained the changes of codes in core modules of ESolver, HSolver, ElecState, Hamilt, Operator or Psi? (ignore if not applicable)

What's changed?

new diago method (ks_solver) pexsi added to hsolver (diago_pexsi.cpp/.h and folder module_pexsi in module_hsolver)
when ks_solver set to pexsi, pexsi uses DM from its calculation to calculate charge density rho (PEXSI calculates DM instead of psi)
new FindPEXSI.cmake module added to folder cmake
inputs and outputs related to pexsi
Makefile and CMakeLists.txt

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

class DiagoPexsi inherited from hsolver::DiagH
new function dmToRho in class ElecStateLCAO to calculate rho from density matrix given by pexsi solver

* run INPUT.Default() in every process in InputParaTest (deepmodeling#3490) Co-authored-by: kirk0830 <67682086+kirk0830@users.noreply.github.com> * add blas support for FindLAPACK.cmake (deepmodeling#3497) * more unittest of QO: towards orbital selection (deepmodeling#3499) * Fix: fix bug in mulliken charge calculation (deepmodeling#3503) * fix phase * fix case test * Refactor: namespace Conv_Coulomb_Pot_K (deepmodeling#3446) * Refactor: namespace Conv_Coulomb_Pot_K * Refactor: namespace Conv_Coulomb_Pot_K --------- Co-authored-by: wqzhou <33364058+WHUweiqingzhou@users.noreply.github.com> * enable the computation of all zeros in one function call (deepmodeling#3449) Co-authored-by: wqzhou <33364058+WHUweiqingzhou@users.noreply.github.com> * replace ios.eof() by ios.good() to avoid meeting badbit and failbit in reading STRU (deepmodeling#3506) * Build: add ccache to accelerate the testing process (deepmodeling#3509) * Build: add ccache to accelerate the testing process * Update test.yml * Update test.yml * Update test.yml * Docs: to avoid the misunderstanding in docs (deepmodeling#3518) * to avoid the misunderstanding in docs * Update docs/quick_start/hands_on.md Co-authored-by: Chun Cai <amoycaic@gmail.com> --------- Co-authored-by: Chun Cai <amoycaic@gmail.com> * Docs: fix a missing depencency in conda build env (deepmodeling#3508) * Feature: Add ENABLE_RAPIDJSON option to control the output of abacus.json (deepmodeling#3519) Add ENABLE_RAPIDJSON option to control the output of abacus.json * Feature: add python wrapper for math sphbes (deepmodeling#3475) * recommit for review * add python wrapper * remove timer since performace tests add * Feature: support segment split in kline mode in KPT file and `out_band` band output precision control, `8` as default (deepmodeling#3493) * add precision control * correct serial version of nscf_band function * fix issue 3482 * update unit and integrated test * update document * correct unittest and make compatible with false and true * fix: bug in Autotest.sh when result.ref has no totaltimeref (deepmodeling#3523) * Fix : unit test of module_xc (deepmodeling#3524) * Fix: omit small magnetic moments to avoid numerical instability (deepmodeling#3530) * update deltalambda * avoid numerical error in orbMulP * add constrain on Mi * change case reference value * Fix: fix multiple compiler warnings (deepmodeling#3515) * Fix: add noreturn attribute to warning_quit * Add type conversion * fix string literal * fix small number trunctuation * Fix system call returned value not checked * fix missing braket * Refactor parameter_pool.cpp and parameter_pool.h * remove duplicated return statements * Change WARNING_QUIT occurances in tests * Add warning message to help debug UT * output the default precision flag (deepmodeling#3496) Co-authored-by: kirk0830 <67682086+kirk0830@users.noreply.github.com> * Build: Improving CMake performance for finding LibXC and ELPA (deepmodeling#3478) * Fix for finding LibXC and ELPA * For compatibility to previous routines * syntax fix for FindELPA.cmake * Update cmake/FindELPA.cmake Co-authored-by: Chun Cai <amoycaic@gmail.com> * Using CMake interface as default for finding LibXC * update docs * fix for FindLibxc: changing imcompatible if statement * fix for FindLibxc: changing imcompatible if statement * fix for FindLibxc: changing imcompatible if statement * update docs for installing pkg-config * Update FindLibxc.cmake * Update FindLibxc.cmake * remove previous LibXC routine in CMakeLists.txt Co-authored-by: Chun Cai <amoycaic@gmail.com> * Update easy_install.md with Makefile-built LibXC supported * Update easy_install.md to include different behavior in different version on finding ELPA --------- Co-authored-by: Chun Cai <amoycaic@gmail.com> * Docs: correct some docs about mp2 smearing method (deepmodeling#3533) * correct some docs about mp2 smearing method * add docs about mv method * Feature : printing band density (deepmodeling#3501) Co-authored-by: wenfei-li <liwenfei@gmail.com> Co-authored-by: wqzhou <33364058+WHUweiqingzhou@users.noreply.github.com> * add some docs for PR#3501 (deepmodeling#3537) * Feature: enable restart charge density mixing during SCF (deepmodeling#3542) * add a new parameter mixing_restart * do not update rho if iter==mixing_restart * do not update rho if iter==mixing_restart-1 * reset mix and rho_mdata if iter==mixing_restart * fix SCF exit directly since drho=0 if iter=GlobalV::MIXING_RESTART * re-set_mixing in eachiterinit for PW and LCAO * enable SCF restarts in esolver_ks::RUN * add some UnitTests * add some Docs * new inputs added * Update input-main.md (deepmodeling#3551) Solve the format problem mentioned in issue 3543 * Build: fix compatibility issue against toolchain install (deepmodeling#3540) * Fix for finding LibXC and ELPA * For compatibility to previous routines * syntax fix for FindELPA.cmake * Update cmake/FindELPA.cmake Co-authored-by: Chun Cai <amoycaic@gmail.com> * Using CMake interface as default for finding LibXC * update docs * fix for FindLibxc: changing imcompatible if statement * fix for FindLibxc: changing imcompatible if statement * fix for FindLibxc: changing imcompatible if statement * update docs for installing pkg-config * Update FindLibxc.cmake * Update FindLibxc.cmake * remove previous LibXC routine in CMakeLists.txt Co-authored-by: Chun Cai <amoycaic@gmail.com> * Update easy_install.md with Makefile-built LibXC supported * Update easy_install.md to include different behavior in different version on finding ELPA * fix compatibility issue against toolchain * Change default ELPA install routine to old one --------- Co-authored-by: Chun Cai <amoycaic@gmail.com> * Test: Configure performance tests for math libraries (deepmodeling#3511) * add performace test of sphbes functions. * fix benchmark cmake errors * add dependencies for docker * update docs * add performance tests for sphbes * add google benchmark * rewrite benchmark tests in fixtures * disable internal testing in benchmark * merge benchmark into integration test --------- Co-authored-by: StarGrys <771582678@qq.com> * Configure Makefile Compiling, fix typos * Fix Makefile Intel toolchains compile errors * Fix even more PEXSI related Makefile compiling issues * Update hsolver_pw.cpp (deepmodeling#3556) when use_uspp==false, overlap matrix should be E. * Fix: cuda build target (deepmodeling#3276) * Fix: cuda buid target * Update CMakeLists.txt --------- Co-authored-by: Denghui Lu <denghuilu@pku.edu.cn> --------- Co-authored-by: wqzhou <33364058+WHUweiqingzhou@users.noreply.github.com> Co-authored-by: kirk0830 <67682086+kirk0830@users.noreply.github.com> Co-authored-by: Haozhi Han <haozhi.han@outlook.com> Co-authored-by: Zhao Tianqi <hongriTianqi@users.noreply.github.com> Co-authored-by: PeizeLin <78645006+PeizeLin@users.noreply.github.com> Co-authored-by: jinzx10 <jzx016@hotmail.com> Co-authored-by: Chun Cai <amoycaic@gmail.com> Co-authored-by: Peng Xingliang <91927439+pxlxingliang@users.noreply.github.com> Co-authored-by: Jie Li <76780849+jieli-matrix@users.noreply.github.com> Co-authored-by: Wenfei Li <38569667+wenfei-li@users.noreply.github.com> Co-authored-by: Denghui Lu <denghuilu@pku.edu.cn> Co-authored-by: YI Zeping <18586016708@163.com> Co-authored-by: wenfei-li <liwenfei@gmail.com> Co-authored-by: jingan-181 <78459531+jingan-181@users.noreply.github.com> Co-authored-by: StarGrys <771582678@qq.com> Co-authored-by: Haozhi Han <haozhi.han@stu.pku.edu.cn>

Revert "Modify inputs and update to latest version"

Modify Inputs and Update to Latest

This reverts commit d7b402d.

source/module_hsolver/module_pexsi/dist_matrix_transformer.cpp

source/module_hsolver/module_pexsi/dist_ccs_matrix.cpp

WHUweiqingzhou · 2024-04-12T04:48:10Z

please add a test report from the developers' side.
please add an example in abacus-develop/example to show how to use PEXSI.

Flying-dragon-boxing · 2024-04-13T09:44:28Z

pexsi_dm and pexsi_edm are dmk/edmk, which should be indicated
deconstruct methods and memory management may be dealt with better

… s matrices no longer needed

Flying-dragon-boxing · 2024-04-13T14:50:10Z

Test report (based on previous tests): https://xmywuqhxb0.feishu.cn/file/HH0wbFEUuozhYIxPmbGcJZYQnIJ?from=from_copylink

Please let me know if you need further information

mohanchen · 2024-05-04T07:48:04Z

We will soon accept this PR, and continue updating PEXSI-related codes.

WHUweiqingzhou

LGTM.

scott-5 · 2024-10-07T13:12:15Z

Test report (based on previous tests): https://xmywuqhxb0.feishu.cn/file/HH0wbFEUuozhYIxPmbGcJZYQnIJ?from=from_copylink

Please let me know if you need further information

@Flying-dragon-boxing hi, in the test report, PEXSI and GENELPA were compared. What I want to ask is whether PEXSI is also one of the ks_solvers? How do we call PEXSI ? Is the main purpose of PEXSI features performance or something else?

kirk0830 · 2024-10-08T02:08:01Z

@scott-5 hi, you can find all related parameters here: https://abacus.deepmodeling.com/en/latest/advanced/input_files/input-main.html#pexsi, and yes, pexsi is a kind of ks_solver, examples in examples/pexsi folder may help.

scott-5 · 2024-10-08T04:00:05Z

@kirk0830 Thanks. After reading the doc, would it be better to add the pexsi option here: https://abacus.deepmodeling.com/en/latest/advanced/input_files/input-main.html#ks-solver and statements about gamma only lcao calculation.

zhangzh-pku and others added 25 commits May 1, 2023 01:27

feat pexsi

69ad6a7

fix : diag not completed

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Merge branch 'deepmodeling:develop' into develop

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feat

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feat: pexsi hsolver

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Merge branch 'deepmodeling:develop' into develop

51e4df2

CMake building implemented

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Merge remote-tracking branch 'upstream/develop' into develop

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Works

2529afe

adapt to the new container

09da6b1

Turn off USE_PEXSI

f52bd99

Update LibRI to 553c91c

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Merge remote-tracking branch into develop

a5ea7e1

modify include files

90f600e

namespace-ize

3d8c366

new inputs added

8075b14

Configure Makefile Compiling, fix typos

1e428d2

Fix Makefile Intel toolchains compile errors

1264b64

Fix even more PEXSI related Makefile compiling issues

a694146

Merge remote-tracking branch 'upstream/develop' into modify_inputs

4c4bd76

Revert "Modify inputs and update to latest version"

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Merge pull request #3 from Flying-dragon-boxing/revert-2-modify_inputs

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Revert "Modify inputs and update to latest version"

Merge pull request #4 from Flying-dragon-boxing/modify_inputs

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Modify Inputs and Update to Latest

Update FindPEXSI.cmake to fix Comments

c4c5272

mohanchen requested review from dyzheng, haozhihan and pplab January 28, 2024 07:05

Flying-dragon-boxing added 2 commits January 29, 2024 12:52

Fix CI errors

f3e18a4

Fix CI Errors and Merge with Upstream

4d16f56

Flying-dragon-boxing added 3 commits April 9, 2024 14:28

correct nspin related behaviors

5a891f7

add efermi passthrough

d7b402d

Revert "add efermi passthrough"

76774f6

This reverts commit d7b402d.

kirk0830 reviewed Apr 12, 2024

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source/module_hsolver/module_pexsi/dist_matrix_transformer.cpp Show resolved Hide resolved

kirk0830 reviewed Apr 12, 2024

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source/module_hsolver/module_pexsi/dist_ccs_matrix.cpp Outdated Show resolved Hide resolved

Flying-dragon-boxing and others added 5 commits April 13, 2024 18:40

Merge branch 'develop' into resolve_conflict

9f8532a

commits to resolve conversations related to codes

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DM and EDM pointers in pexsi now handled by diagopexsi, and copying h…

569269b

… s matrices no longer needed

add pexsi examples

f8352cb

fix pexsi unit test (original version shouldn't run)

b0ef9ad

Flying-dragon-boxing and others added 5 commits April 17, 2024 11:10

add building docs for pexsi

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Merge branch 'develop' into resolve_conflict

3e5fea8

Merge branch 'develop' into resolve_conflict

69b774a

set cxx standard to c++14, which is required in make_unique

110e5b0

Merge branch 'develop' into resolve_conflict

1ced552

mohanchen approved these changes May 11, 2024

View reviewed changes

Merge branch 'develop' into resolve_conflict

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mohanchen added the Features Needed The features are indeed needed, and developers should have sophisticated knowledge label May 11, 2024

Merge branch 'develop' into resolve_conflict

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WHUweiqingzhou approved these changes May 14, 2024

View reviewed changes

WHUweiqingzhou and others added 2 commits May 14, 2024 10:33

Merge branch 'develop' into resolve_conflict

04db1c1

Merge branch 'develop' into resolve_conflict

29f1efc

mohanchen merged commit 6138a50 into deepmodeling:develop May 15, 2024

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Feature: Add PEXSI Support for Gamma Only LCAO Calculation#3561

Feature: Add PEXSI Support for Gamma Only LCAO Calculation#3561
mohanchen merged 73 commits intodeepmodeling:developfrom
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Flying-dragon-boxing commented Jan 28, 2024

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What's changed?

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

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