docs: update the citation of deepmd-kit v3 #4738
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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>
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Pull Request Overview
This pull request updates the citation details for DeePMD-kit v3 across multiple files. The changes include updating citation keys, journal names, volume/issue/page numbers, DOIs, and corresponding reference links in source code, documentation, and BibTeX entries.
- Updated citation references in C++ source files (pair_deepspin.cpp and pair_deepmd.cpp)
- Adjusted citation details in documentation files (credits.rst, README.md, and deepmd/utils/summary.py)
- Revised BibTeX entry in CITATIONS.bib to reflect the published journal information
Reviewed Changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| source/lmp/pair_deepspin.cpp | Updated citation key and details in the source file |
| source/lmp/pair_deepmd.cpp | Updated citation key and details in the source file |
| doc/credits.rst | Revised citation key in the documentation |
| deepmd/utils/summary.py | Updated citation text for the summary documentation |
| README.md | Corrected citation text and updated DOI thumbnail links |
| CITATIONS.bib | Revised BibTeX entry with journal information |
Comments suppressed due to low confidence (6)
source/lmp/pair_deepspin.cpp:86
- Ensure that the updated citation key and corresponding metadata (journal, volume, pages, DOI) correctly match the published details for DeePMD-kit v3.
@Article{Zeng_JChemTheoryComput_2025_v21_p4375,
source/lmp/pair_deepmd.cpp:86
- Verify that the revised citation details in this file match those in pair_deepspin.cpp and reflect the correct published information.
@Article{Zeng_JChemTheoryComput_2025_v21_p4375,
doc/credits.rst:16
- Double-check that the updated citation key is consistent throughout the documentation and accurately represents the new citation details.
Zeng_JChemTheoryComput_2025_v21_p4375
deepmd/utils/summary.py:45
- Confirm that the citation text here correctly reflects the updated journal reference and is consistent with other citation updates.
Zeng et al, J. Chem. Theory Comput., 21, 4375-4385 (2025)
README.md:39
- Ensure that the updated citation text and DOI badge/link additions accurately reflect the new publication details and are consistent with the other citation updates throughout the project.
Jinzhe Zeng, Duo Zhang, Anyang Peng, Xiangyu Zhang, Sensen He, Yan Wang, Xinzijian Liu, Hangrui Bi, Yifan Li, Chun Cai, Chengqian Zhang, Yiming Du, Jia-Xin Zhu, Pinghui Mo, Zhengtao Huang, Qiyu Zeng, Shaochen Shi, Xuejian Qin, Zhaoxi Yu, Chenxing Luo, Ye Ding, Yun-Pei Liu, Ruosong Shi, Zhenyu Wang, Sigbjørn Løland Bore, Junhan Chang, Zhe Deng, Zhaohan Ding, Siyuan Han, Wanrun Jiang, Guolin Ke, Zhaoqing Liu, Denghui Lu, Koki Muraoka, Hananeh Oliaei, Anurag Kumar Singh, Haohui Que, Weihong Xu, Zhangmancang Xu, Yong-Bin Zhuang, Jiayu Dai, Timothy J. Giese, Weile Jia, Ben Xu, Darrin M. York, Linfeng Zhang, Han Wang. "DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials." J. Chem. Theory Comput. 21 (2025): 4375-4385.
CITATIONS.bib:43
- Verify that the BibTeX entry now includes the correct journal, volume, number, pages, and DOI fields to ensure consistency with the revised citation format.
@article{Zeng_JChemTheoryComput_2025_v21_p4375,
📝 Walkthrough""" WalkthroughThe changes update all references and citations for the DeePMD-kit v3 paper from its previous arXiv preprint to the formal journal publication in the Journal of Chemical Theory and Computation. This includes updating citation metadata, BibTeX entries, citation strings, DOIs, and documentation references across code, documentation, and metadata files. Changes
Sequence Diagram(s)Not applicable: The changes are limited to citation and documentation updates, with no new features or control flow modifications. Possibly related PRs
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Actionable comments posted: 2
🧹 Nitpick comments (2)
CITATIONS.bib (2)
62-67: Verify DOI & standardize issue/number field
- Double-check that the DOI
10.1021/acs.jctc.5c00340corresponds to volume 21(9), pages 4375–4385 of J. Chem. Theory Comput.- The entry uses
number = 9, but other JCTC entries in this file useissue(e.g., lines 27, 272). Consider unifying on one field name for consistency.
68-86: Assess necessity of the abstract field
The multilineabstractfield is comprehensive, but many BibTeX workflows ignore abstracts. If your tooling doesn’t utilize it, consider removing or relocating the abstract to reduce file size and improve maintainability. Otherwise, ensure your parser supports this multiline format.
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CITATIONS.bib(2 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)
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🔇 Additional comments (5)
doc/credits.rst (1)
16-16: Updated citation key for v3 is correct
The entryZeng_JChemTheoryComput_2025_v21_p4375matches the new journal publication details and aligns with the rest of the bibliography.deepmd/utils/summary.py (1)
45-45: SummaryPrinter citation updated correctly
The citation string now references “Zeng et al, J. Chem. Theory Comput., 21, 4375-4385 (2025)”, which matches the formal publication.README.md (1)
39-41: README citation block for v3 paper is correct
The new list item, DOI badge, and link correctly reference the J. Chem. Theory Comput. publication for DeePMD-kit v3.CITATIONS.bib (2)
43-57: Entry key & author list needs verification
Please confirm that the new entry keyZeng_JChemTheoryComput_2025_v21_p4375follows the repository’s naming pattern and that the full author list exactly matches the published article (order, spelling, and diacritics). A mismatch here could cause citation errors or omissions downstream.
58-61: Title formatting looks good
The title is properly wrapped in double braces to preserve capitalization and includes “v3” to distinguish this version. No changes needed here.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## devel #4738 +/- ##
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Coverage 84.69% 84.69%
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Files 697 697
Lines 67473 67474 +1
Branches 3541 3541
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+ Hits 57145 57146 +1
- Misses 9196 9197 +1
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