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Refactor: replaced the original atomlink data structure with the Standard Template Library #5642

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Merged
merged 18 commits into from
Dec 2, 2024
Merged

Refactor: replaced the original atomlink data structure with the Standard Template Library #5642

merged 18 commits into from
Dec 2, 2024

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@goodchong goodchong commented Nov 28, 2024 •
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What's changed?

  • The original hash + linked list data structure was replaced by the standard template library.
  • The neighbor list of each atom records a pointer to the FAtom in CellSet memory. It is stored as std::list<FAtom *> adjacent. the data structure of adjacentset been removed.
  • In the previous code, several situations were distinguished according to the pbc flag and expand flag, and the ambiguity caused by variable reuse has been improved.

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

  • module_neighbor

@goodchong goodchong marked this pull request as draft November 28, 2024 10:03
@goodchong goodchong self-assigned this Dec 2, 2024
@goodchong goodchong marked this pull request as ready for review December 2, 2024 06:19
@mohanchen mohanchen added the Refactor Refactor ABACUS codes label Dec 2, 2024
@mohanchen mohanchen merged commit a43cbfb into deepmodeling:develop Dec 2, 2024
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@goodchong goodchong deleted the neighbor2 branch December 4, 2024 05:35
Fisherd99 pushed a commit to Fisherd99/abacus-BSE that referenced this pull request Mar 31, 2025
@goodchong @pre-commit-ci-lite @Fisherd99
Refactor: replaced the original atomlink data structure with the Stan…
b4f4872 
…dard Template Library (deepmodeling#5642)

* A highly aggressive change: replaced the original atomlink data structure with the Standard Template Library.

* fix unittest errors

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

* fix a adj set clear bug and add self to adj list

* use vector to refactor Cellset varible

* remove adjacent set, replaced by std list

* remove set fatom

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

* use 2 layers vector replace undered_map to improve perfermance

* remove a lot useless variable

* remove some useless variables

* refresh unit test to code logic

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

* fix a bug to force quit when test

* fresh unit test according to latest code logic

---------

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

@dyzheng dyzheng Awaiting requested review from dyzheng

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@goodchong goodchong

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@goodchong @mohanchen