docs: add v3 paper citations (#4619)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## 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.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

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>

Author: njzjz

CITATIONS.bib

@@ -40,6 +40,31 @@ @article{Zeng_JChemPhys_2023_v159_p054801
   doi          = {10.1063/5.0155600},
 }
 
+@article{Zeng_arXiv_2025_p2502.19161,
+  annote       = {general purpose},
+  author       = {
+    Jinzhe Zeng and Duo Zhang and Anyang Peng and Xiangyu Zhang and Sensen He
+    and Yan Wang and Xinzijian Liu and Hangrui Bi and Yifan Li and Chun Cai and
+    Chengqian Zhang and Yiming Du and Jia-Xin Zhu and Pinghui Mo and Zhengtao
+    Huang and Qiyu Zeng and Shaochen Shi and Xuejian Qin and Zhaoxi Yu and
+    Chenxing Luo and Ye Ding and Yun-Pei Liu and Ruosong Shi and Zhenyu Wang
+    and Sigbj{\o}rn L{\o}land Bore and Junhan Chang and Zhe Deng and Zhaohan
+    Ding and Siyuan Han and Wanrun Jiang and Guolin Ke and Zhaoqing Liu and
+    Denghui Lu and Koki Muraoka and Hananeh Oliaei and Anurag Kumar Singh and
+    Haohui Que and Weihong Xu and Zhangmancang Xu and Yong-Bin Zhuang and Jiayu
+    Dai and Timothy J. Giese and Weile Jia and Ben Xu and Darrin M. York and
+    Linfeng Zhang and Han Wang
+  },
+  title        = {
+    {DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning
+    Potentials}
+  },
+  journal      = {arXiv},
+  year         = 2025,
+  pages        = {2502.19161},
+  doi          = {10.48550/arXiv.2502.19161},
+}
+
 @article{Lu_CompPhysCommun_2021_v259_p107624,
   annote       = {GPU support},
   title        = {

README.md

@@ -36,6 +36,7 @@ If you use this code in any future publications, please cite the following publi
 - Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik, Li'ang Huang, Ziyao Li, Shaochen Shi, Yingze Wang, Haotian Ye, Ping Tuo, Jiabin Yang, Ye Ding, Yifan Li, Davide Tisi, Qiyu Zeng, Han Bao, Yu Xia, Jiameng Huang, Koki Muraoka, Yibo Wang, Junhan Chang, Fengbo Yuan, Sigbjørn Løland Bore, Chun Cai, Yinnian Lin, Bo Wang, Jiayan Xu, Jia-Xin Zhu, Chenxing Luo, Yuzhi Zhang, Rhys E. A. Goodall, Wenshuo Liang, Anurag Kumar Singh, Sikai Yao, Jingchao Zhang, Renata Wentzcovitch, Jiequn Han, Jie Liu, Weile Jia, Darrin M. York, Weinan E, Roberto Car, Linfeng Zhang, Han Wang. "DeePMD-kit v2: A software package for deep potential models." J. Chem. Phys. 159 (2023): 054801.
   [![doi:10.1063/5.0155600](https://img.shields.io/badge/DOI-10.1063%2F5.0155600-blue)](https://doi.org/10.1063/5.0155600)
   [![Citations](https://citations.njzjz.win/10.1063/5.0155600)](https://badge.dimensions.ai/details/doi/10.1063/5.0155600)
+- 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." [arXiv:2502.19161](https://arxiv.org/abs/2502.19161).
 
 In addition, please follow [the bib file](CITATIONS.bib) to cite the methods you used.
 
@@ -68,14 +69,16 @@ In addition to building up potential energy models, DeePMD-kit can also be used
 - Non-von-Neumann.
 - C API to interface with the third-party packages.
 
-See [our latest paper](https://doi.org/10.1063/5.0155600) for details of all features until v2.2.3.
+See [our v2 paper](https://doi.org/10.1063/5.0155600) for details of all features until v2.2.3.
 
 #### v3
 
 - Multiple backends supported. Add PyTorch and JAX backends.
 - The DPA-2 model.
 - Plugin mechanisms for external models.
 
+See [our v3 paper](https://doi.org/10.48550/arXiv.2502.19161) for details of all features until v3.0.
+
 ## Install and use DeePMD-kit
 
 Please read the [online documentation](https://deepmd.readthedocs.io/) for how to install and use DeePMD-kit.

deepmd/utils/summary.py

@@ -42,6 +42,7 @@ class SummaryPrinter(ABC):
         "Please read and cite:",
         "Wang, Zhang, Han and E, Comput.Phys.Comm. 228, 178-184 (2018)",
         "Zeng et al, J. Chem. Phys., 159, 054801 (2023)",
+        "Zeng et al, arxiv:2502.19161",
         "See https://deepmd.rtfd.io/credits/ for details.",
     )
 

doc/credits.rst

@@ -13,6 +13,7 @@ Cite DeePMD-kit and methods
 
    Wang_ComputPhysCommun_2018_v228_p178
    Zeng_JChemPhys_2023_v159_p054801
+   Zeng_arXiv_2025_p2502.19161
 
 - If GPU version is used,
 

source/lmp/pair_deepmd.cpp

@@ -50,7 +50,7 @@ static const char cite_user_deepmd_package[] =
     "energy representation and molecular dynamics}},\n"
     "  pages = {178--184}\n"
     "}\n"
-    "@misc{Zeng_JChemPhys_2023_v159_p054801,\n"
+    "@article{Zeng_JChemPhys_2023_v159_p054801,\n"
     "  title  = {{DeePMD-kit v2: A software package for deep potential "
     "models}},\n"
     "  author =   {Jinzhe Zeng and Duo Zhang and Denghui Lu and Pinghui Mo and "
@@ -82,6 +82,38 @@ static const char cite_user_deepmd_package[] =
     "  year =    2023,\n"
     "  pages  =   054801,\n"
     "  doi =      {10.1063/5.0155600},\n"
+    "}\n"
+    "@Article{Zeng_arXiv_2025_p2502.19161,\n"
+    "  annote       = {general purpose},\n"
+    "    author =   {Jinzhe Zeng and Duo Zhang and Anyang Peng and Xiangyu "
+    "Zhang and Sensen\n"
+    "             He and Yan Wang and Xinzijian Liu and Hangrui Bi and Yifan "
+    "Li and Chun\n"
+    "             Cai and Chengqian Zhang and Yiming Du and Jia-Xin Zhu and "
+    "Pinghui Mo\n"
+    "             and Zhengtao Huang and Qiyu Zeng and Shaochen Shi and "
+    "Xuejian Qin and\n"
+    "             Zhaoxi Yu and Chenxing Luo and Ye Ding and Yun-Pei Liu and "
+    "Ruosong Shi\n"
+    "             and Zhenyu Wang and Sigbj{\\o}rn L{\\o}land Bore and Junhan "
+    "Chang and\n"
+    "             Zhe Deng and Zhaohan Ding and Siyuan Han and Wanrun Jiang "
+    "and Guolin\n"
+    "             Ke and Zhaoqing Liu and Denghui Lu and Koki Muraoka and "
+    "Hananeh Oliaei\n"
+    "             and Anurag Kumar Singh and Haohui Que and Weihong Xu and "
+    "Zhangmancang\n"
+    "             Xu and Yong-Bin Zhuang and Jiayu Dai and Timothy J. Giese "
+    "and Weile\n"
+    "             Jia and Ben Xu and Darrin M. York and Linfeng Zhang and Han "
+    "Wang},\n"
+    "    title =    {{DeePMD-kit v3: A Multiple-Backend Framework for Machine "
+    "Learning\n"
+    "             Potentials}},\n"
+    "    journal =  {arXiv},\n"
+    "    year =     2025,\n"
+    "    pages =    {2502.19161},\n"
+    "    doi =      {10.48550/arXiv.2502.19161},\n"
     "}\n\n";
 
 PairDeepMD::PairDeepMD(LAMMPS *lmp)

source/lmp/pair_deepspin.cpp

@@ -50,7 +50,7 @@ static const char cite_user_deepmd_package[] =
     "energy representation and molecular dynamics}},\n"
     "  pages = {178--184}\n"
     "}\n"
-    "@misc{Zeng_JChemPhys_2023_v159_p054801,\n"
+    "@article{Zeng_JChemPhys_2023_v159_p054801,\n"
     "  title  = {{DeePMD-kit v2: A software package for deep potential "
     "models}},\n"
     "  author =   {Jinzhe Zeng and Duo Zhang and Denghui Lu and Pinghui Mo and "
@@ -82,6 +82,38 @@ static const char cite_user_deepmd_package[] =
     "  year =    2023,\n"
     "  pages  =   054801,\n"
     "  doi =      {10.1063/5.0155600},\n"
+    "}\n"
+    "@Article{Zeng_arXiv_2025_p2502.19161,\n"
+    "  annote       = {general purpose},\n"
+    "    author =   {Jinzhe Zeng and Duo Zhang and Anyang Peng and Xiangyu "
+    "Zhang and Sensen\n"
+    "             He and Yan Wang and Xinzijian Liu and Hangrui Bi and Yifan "
+    "Li and Chun\n"
+    "             Cai and Chengqian Zhang and Yiming Du and Jia-Xin Zhu and "
+    "Pinghui Mo\n"
+    "             and Zhengtao Huang and Qiyu Zeng and Shaochen Shi and "
+    "Xuejian Qin and\n"
+    "             Zhaoxi Yu and Chenxing Luo and Ye Ding and Yun-Pei Liu and "
+    "Ruosong Shi\n"
+    "             and Zhenyu Wang and Sigbj{\\o}rn L{\\o}land Bore and Junhan "
+    "Chang and\n"
+    "             Zhe Deng and Zhaohan Ding and Siyuan Han and Wanrun Jiang "
+    "and Guolin\n"
+    "             Ke and Zhaoqing Liu and Denghui Lu and Koki Muraoka and "
+    "Hananeh Oliaei\n"
+    "             and Anurag Kumar Singh and Haohui Que and Weihong Xu and "
+    "Zhangmancang\n"
+    "             Xu and Yong-Bin Zhuang and Jiayu Dai and Timothy J. Giese "
+    "and Weile\n"
+    "             Jia and Ben Xu and Darrin M. York and Linfeng Zhang and Han "
+    "Wang},\n"
+    "    title =    {{DeePMD-kit v3: A Multiple-Backend Framework for Machine "
+    "Learning\n"
+    "             Potentials}},\n"
+    "    journal =  {arXiv},\n"
+    "    year =     2025,\n"
+    "    pages =    {2502.19161},\n"
+    "    doi =      {10.48550/arXiv.2502.19161},\n"
     "}\n\n";
 
 PairDeepSpin::PairDeepSpin(LAMMPS *lmp)