docs: add v3 paper citations #4619

njzjz · 2025-02-27T04:24:28Z

Summary by CodeRabbit

Documentation
- Added a new citation for the "DeePMD-kit v3" article in various documentation files.
- Clarified references to distinguish between the "v2" and "v3" publications.
- Enhanced bibliography and credits details for improved clarity.
Chores
- Revised citation formatting across the package to reflect formal publication standards.

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>

Copilot

PR Overview

This PR updates documentation by adding the v3 paper citations for DeePMD-kit. It provides an additional citation entry in the summary module and updates the README with the new v3 citation information.

Added v3 paper citation reference in deepmd/utils/summary.py.
Included the v3 paper citation in README.md along with a labeling update for the v2 paper.
Updated links in README.md to reference the new v3 citation.

Reviewed Changes

File	Description
deepmd/utils/summary.py	Added new v3 paper citation entry to the citation list.
README.md	Added new v3 citation information and reworded the v2 reference.

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

README.md:80

The v3 paper citation contains an incorrect DOI link; update it to the correct arXiv URL (e.g., https://arxiv.org/abs/2502.19161) to accurately reference the v3 paper.

See [our v3 paper](https://doi.org/5.0155600) for details of all features until v3.0.

deepmd/utils/summary.py

coderabbitai · 2025-02-27T04:28:03Z

📝 Walkthrough

Walkthrough

This update integrates a new citation for the DeePMD-kit v3 article by Zeng et al. across multiple documentation and source files. The changes add a new article entry with complete bibliographic details in the bibliography file, update reference texts in the README, and append the new citation to the citation tuple in the summary utility. Additionally, modifications in several source files change the citation type from @misc to @article for a 2023 entry and add a corresponding 2025 entry. A redundant line in the credits document has also been removed.

Changes

File(s)	Change Summary
`CITATIONS.bib`	Added new article entry `@article{Zeng_arXiv_2025_p2502.19161}` with fields: `annote`, `author`, `title`, `journal`, `year`, `pages`, and `doi`.
`README.md`	Added a new citation for the DeePMD-kit v3 paper, updated reference text from "latest paper" to "v2 paper," and introduced a new "v3 paper" reference.
`deepmd/utils/summary.py`	Appended `"Zeng et al, arxiv:2502.19161"` to the `CITATION` tuple in the `SummaryPrinter` class.
`doc/credits.rst`	Added bibliography entry `Zeng_arXiv_2025_p2502.19161` and removed the line beginning with "If GPU version is used,".
`source/lmp/pair_deepmd.cpp`, `source/lmp/pair_deepspin.cpp`	Updated citation entry for the 2023 paper from `@misc` to `@article` and added a new citation entry `@Article{Zeng_arXiv_2025_p2502.19161}`.

Possibly related PRs

docs: document plugin mechanisms and deepmd-gnn #4345: The changes in the main PR, which involve adding a new citation entry for a paper by Jinzhe Zeng, are related to the modifications in the retrieved PR that also include updates to citations in the README.md file, specifically referencing the same paper.
docs: update DPA-2 citation #4483: The changes in the main PR, which involve adding a new citation for a 2025 article by Jinzhe Zeng, are related to the retrieved PR that updates citations in the documentation, as both involve modifications to citation entries for works authored by Zeng.

Suggested reviewers

iProzd
wanghan-iapcm

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README.md

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Actionable comments posted: 1

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Reviewing files that changed from the base of the PR and between 47bbd65 and 80570dc.

📒 Files selected for processing (6)

CITATIONS.bib (1 hunks)
README.md (2 hunks)
deepmd/utils/summary.py (1 hunks)
doc/credits.rst (1 hunks)
source/lmp/pair_deepmd.cpp (2 hunks)
source/lmp/pair_deepspin.cpp (2 hunks)

✅ Files skipped from review due to trivial changes (3)

deepmd/utils/summary.py
source/lmp/pair_deepmd.cpp
source/lmp/pair_deepspin.cpp

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🔇 Additional comments (4)

doc/credits.rst (1)

16-16: Citation correctly added for v3 paper.

The new bibliography entry for the v3 paper has been properly added to the document.

CITATIONS.bib (1)

43-66: Citation entry properly formatted and complete.

The new citation entry for the DeePMD-kit v3 paper is well-structured with all required fields (author, title, journal, year, pages, DOI) and follows the same formatting style as other entries in the file.

README.md (2)

39-39: DeePMD-kit v3 citation correctly added.

The citation for the v3 paper has been properly added with complete author list and arXiv reference.

72-72: Reference text updated appropriately.

Changed "our latest paper" to "our v2 paper" which is more specific and future-proof.

README.md

codecov · 2025-02-27T05:10:11Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.58%. Comparing base (47bbd65) to head (8c97c4d).
Report is 73 commits behind head on devel.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #4619      +/-   ##
==========================================
- Coverage   84.58%   84.58%   -0.01%     
==========================================
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  Lines       64544    64543       -1     
  Branches     3538     3539       +1     
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Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Signed-off-by: Jinzhe Zeng <njzjz@qq.com>

## Summary by CodeRabbit - **Documentation** - Added a new citation for the "DeePMD-kit v3" article in various documentation files. - Clarified references to distinguish between the "v2" and "v3" publications. - Enhanced bibliography and credits details for improved clarity. - **Chores** - Revised citation formatting across the package to reflect formal publication standards.  --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn> Signed-off-by: Jinzhe Zeng <njzjz@qq.com> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> (cherry picked from commit 918d4de)

njzjz added 2 commits February 27, 2025 12:22

docs: add v3 paper citations

23dcd67

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>

no

80570dc

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>

Copilot AI review requested due to automatic review settings February 27, 2025 04:24

Copilot AI reviewed Feb 27, 2025

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github-actions bot added Python LAMMPS Docs labels Feb 27, 2025

njzjz requested a review from wanghan-iapcm February 27, 2025 05:48

Update README.md

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Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Signed-off-by: Jinzhe Zeng <njzjz@qq.com>

wanghan-iapcm approved these changes Feb 27, 2025

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wanghan-iapcm enabled auto-merge February 27, 2025 05:55

njzjz added this to the v3.0.2 milestone Feb 27, 2025

wanghan-iapcm added this pull request to the merge queue Feb 27, 2025

Merged via the queue into deepmodeling:devel with commit 918d4de Feb 27, 2025
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coderabbitai bot mentioned this pull request Mar 1, 2025

[r3.0] release v3.0.2 #4589

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coderabbitai bot mentioned this pull request May 13, 2025

docs: update the citation of deepmd-kit v3 #4738

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coderabbitai bot mentioned this pull request Jun 4, 2025

Doc: update DPA3 reference #4781

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coderabbitai bot mentioned this pull request Aug 8, 2025

docs: add docs about LAMMPS D3 dispersion #4875

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