deepmodeling · wanghan-iapcm · Aug 7, 2023 · Aug 1, 2023 · Aug 1, 2023 · Aug 1, 2023
diff --git a/CITATIONS.bib b/CITATIONS.bib
@@ -15,27 +15,29 @@ @article{Wang_ComputPhysCommun_2018_v228_p178
     pages = {178--184},
 }
 
-@misc{Zeng_arXiv_2023,
+@Article{Zeng_JChemPhys_2023_v159_p054801,
     annote = {general purpose},
-    title = {{DeePMD-kit v2: A software package for Deep Potential models}},
-    author = {Jinzhe Zeng and Duo Zhang and Denghui Lu and Pinghui Mo and
-            Zeyu Li and Yixiao Chen and Marián Rynik and Li'ang Huang and
-            Ziyao Li and Shaochen Shi and Yingze Wang and Haotian Ye and
-            Ping Tuo and Jiabin Yang and Ye Ding and Yifan Li and Davide
-            Tisi and Qiyu Zeng and Han Bao and Yu Xia and Jiameng Huang
-            and Koki Muraoka and Yibo Wang and Junhan Chang and Fengbo
-            Yuan and Sigbjørn Løland Bore and Chun Cai and Yinnian Lin
-            and Bo Wang and Jiayan Xu and Jia-Xin Zhu and Chenxing Luo and
-            Yuzhi Zhang and Rhys E. A. Goodall and Wenshuo Liang and Anurag
-            Kumar Singh and Sikai Yao and Jingchao Zhang and Renata
-            Wentzcovitch and Jiequn Han and Jie Liu and Weile Jia and
-            Darrin M. York and Weinan E and Roberto Car and Linfeng Zhang
-            and Han Wang},
-    year = {2023},
-    archivePrefix = {arXiv},
-    doi = {10.48550/arXiv.2304.09409}
+    title  = {{DeePMD-kit v2: A software package for deep potential models}},
+    author =   {Jinzhe Zeng and Duo Zhang and Denghui Lu and Pinghui Mo and Zeyu Li
+             and Yixiao Chen and Mari{\'a}n Rynik and Li'ang Huang and Ziyao Li and
+             Shaochen Shi and Yingze Wang and Haotian Ye and Ping Tuo and Jiabin
+             Yang and Ye Ding and Yifan Li and Davide Tisi and Qiyu Zeng and Han
+             Bao and Yu Xia and Jiameng Huang and Koki Muraoka and Yibo Wang and
+             Junhan Chang and Fengbo Yuan and Sigbj{\o}rn L{\o}land Bore and Chun
+             Cai and Yinnian Lin and Bo Wang and Jiayan Xu and Jia-Xin Zhu and
+             Chenxing Luo and Yuzhi Zhang and Rhys E A Goodall and Wenshuo Liang
+             and Anurag Kumar Singh and Sikai Yao and Jingchao Zhang and Renata
+             Wentzcovitch and Jiequn Han and Jie Liu and Weile Jia and Darrin M
+             York and Weinan E and Roberto Car and Linfeng Zhang and Han Wang},
+    journal =  {J. Chem. Phys.},
+    volume =   159,
+    issue =    5,
+    year =    2023,
+    pages  =   054801,
+    doi =      {10.1063/5.0155600},
 }
 
+
 @article{Lu_CompPhysCommun_2021_v259_p107624,
     annote = {GPU support},
     title={{86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million

diff --git a/README.md b/README.md
@@ -5,8 +5,6 @@
 <span style="font-size:larger;">DeePMD-kit Manual</span>
 ========
 [![GitHub release](https://img.shields.io/github/release/deepmodeling/deepmd-kit.svg?maxAge=86400)](https://github.com/deepmodeling/deepmd-kit/releases)
-[![doi:10.1016/j.cpc.2018.03.016](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2018.03.016-blue)](https://doi.org/10.1016/j.cpc.2018.03.016)
-[![Citations](https://citations.njzjz.win/10.1016/j.cpc.2018.03.016)](https://badge.dimensions.ai/details/doi/10.1016/j.cpc.2018.03.016)
 [![offline packages](https://img.shields.io/github/downloads/deepmodeling/deepmd-kit/total?label=offline%20packages)](https://github.com/deepmodeling/deepmd-kit/releases)
 [![conda-forge](https://img.shields.io/conda/dn/conda-forge/deepmd-kit?color=red&label=conda-forge&logo=conda-forge)](https://anaconda.org/conda-forge/deepmd-kit)
 [![pip install](https://img.shields.io/pypi/dm/deepmd-kit?label=pip%20install)](https://pypi.org/project/deepmd-kit)
@@ -49,7 +47,11 @@ For more information, check the [documentation](https://deepmd.readthedocs.io/).
 The project DeePMD-kit is licensed under [GNU LGPLv3.0](./LICENSE).
 If you use this code in any future publications, please cite the following publications for general purpose:
 - Han Wang, Linfeng Zhang, Jiequn Han, and Weinan E. "DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics." Computer Physics Communications 228 (2018): 178-184.
-- 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." [arXiv:2304.09409](https://doi.org/10.48550/arXiv.2304.09409).
+[![doi:10.1016/j.cpc.2018.03.016](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2018.03.016-blue)](https://doi.org/10.1016/j.cpc.2018.03.016)
+[![Citations](https://citations.njzjz.win/10.1016/j.cpc.2018.03.016)](https://badge.dimensions.ai/details/doi/10.1016/j.cpc.2018.03.016)
+- 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)
 
 In addition, please follow [the bib file](CITATIONS.bib) to cite the methods you used.
 

diff --git a/deepmd/train/run_options.py b/deepmd/train/run_options.py
@@ -52,7 +52,7 @@
 CITATION = (
     "Please read and cite:",
     "Wang, Zhang, Han and E, Comput.Phys.Comm. 228, 178-184 (2018)",
-    "Zeng et al, arXiv:2304.09409",
+    "Zeng et al, J. Chem. Phys., 159, 054801 (2023)",
     "See https://deepmd.rtfd.io/credits/ for details.",
 )
 

diff --git a/doc/credits.rst b/doc/credits.rst
@@ -12,7 +12,7 @@ Cite DeePMD-kit and methods
    :filter: False
 
    Wang_ComputPhysCommun_2018_v228_p178
-   Zeng_arXiv_2023
+   Zeng_JChemPhys_2023_v159_p054801
 
 - If GPU version is used,
 

diff --git a/doc/index.rst b/doc/index.rst
@@ -15,7 +15,7 @@ DeePMD-kit is a package written in Python/C++, designed to minimize the effort r
    If you use this code in any future publications, please cite the following publications for general purpose:
 
       - Han Wang, Linfeng Zhang, Jiequn Han, and Weinan E. "DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics." Computer Physics Communications 228 (2018): 178-184.
-      - 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." `arXiv:2304.09409 <https://doi.org/10.48550/arXiv.2304.09409>`_.
+      - 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, 054801 (2023).
 
    In addition, please follow :ref:`this page <cite>` to cite the methods you used.
 

diff --git a/source/lmp/pair_deepmd.cpp b/source/lmp/pair_deepmd.cpp
@@ -49,30 +49,38 @@ static const char cite_user_deepmd_package[] =
     "energy representation and molecular dynamics}},\n"
     "  pages = {178--184}\n"
     "}\n"
-    "@misc{Zeng_arXiv_2023,\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\n"
-    "            Zeyu Li and Yixiao Chen and Marián Rynik and Li'ang Huang "
-    "and\n"
-    "            Ziyao Li and Shaochen Shi and Yingze Wang and Haotian Ye and\n"
-    "            Ping Tuo and Jiabin Yang and Ye Ding and Yifan Li and Davide\n"
-    "            Tisi and Qiyu Zeng and Han Bao and Yu Xia and Jiameng Huang\n"
-    "            and Koki Muraoka and Yibo Wang and Junhan Chang and Fengbo\n"
-    "            Yuan and Sigbjørn Løland Bore and Chun Cai and Yinnian Lin\n"
-    "            and Bo Wang and Jiayan Xu and Jia-Xin Zhu and Chenxing Luo "
-    "and\n"
-    "            Yuzhi Zhang and Rhys E. A. Goodall and Wenshuo Liang and "
-    "Anurag\n"
-    "            Kumar Singh and Sikai Yao and Jingchao Zhang and Renata\n"
-    "            Wentzcovitch and Jiequn Han and Jie Liu and Weile Jia and\n"
-    "            Darrin M. York and Weinan E and Roberto Car and Linfeng "
-    "Zhang\n"
-    "            and Han Wang},\n"
-    "    year = {2023},\n"
-    "    archivePrefix = {arXiv},\n"
-    "    doi = {10.48550/arXiv.2304.09409}\n"
+    "@misc{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 "
+    "Zeyu Li\n"
+    "         and Yixiao Chen and Mari{\\'a}n Rynik and Li'ang Huang and Ziyao "
+    "Li and \n"
+    "         Shaochen Shi and Yingze Wang and Haotian Ye and Ping Tuo and "
+    "Jiabin\n"
+    "         Yang and Ye Ding and Yifan Li and Davide Tisi and Qiyu Zeng and "
+    "Han \n"
+    "         Bao and Yu Xia and Jiameng Huang and Koki Muraoka and Yibo Wang "
+    "and \n"
+    "         Junhan Chang and Fengbo Yuan and Sigbj{\\o}rn L{\\o}land Bore "
+    "and "
+    "Chun\n"
+    "         Cai and Yinnian Lin and Bo Wang and Jiayan Xu and Jia-Xin Zhu "
+    "and \n"
+    "         Chenxing Luo and Yuzhi Zhang and Rhys E A Goodall and Wenshuo "
+    "Liang\n"
+    "         and Anurag Kumar Singh and Sikai Yao and Jingchao Zhang and "
+    "Renata\n"
+    "         Wentzcovitch and Jiequn Han and Jie Liu and Weile Jia and Darrin "
+    "M\n"
+    "         York and Weinan E and Roberto Car and Linfeng Zhang and Han "
+    "Wang},\n"
+    "  journal =  {J. Chem. Phys.},\n"
+    "  volume =   159,\n"
+    "  issue =    5,  \n"
+    "  year =    2023,\n"
+    "  pages  =   054801,\n"
+    "  doi =      {10.1063/5.0155600},\n"
     "}\n\n";
 
 static int stringCmp(const void *a, const void *b) {