From 7c8847cc37f1706488e637382ff21927b1f30844 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Tue, 1 Aug 2023 17:05:20 -0400 Subject: [PATCH 1/4] update citation information --- CITATIONS.bib | 38 ++++++++++++++++---------------- README.md | 8 ++++--- deepmd/train/run_options.py | 2 +- doc/credits.rst | 2 +- doc/index.rst | 2 +- source/lmp/pair_deepmd.cpp | 43 ++++++++++++++++--------------------- 6 files changed, 47 insertions(+), 48 deletions(-) diff --git a/CITATIONS.bib b/CITATIONS.bib index c972503251..afc51cb393 100644 --- 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 index 72d67ca64b..0d212455fd 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,6 @@ DeePMD-kit Manual ======== [![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 index ab06c10423..d5e8858fea 100644 --- 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 index f3d3d50942..5ca03bf68a 100644 --- 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 index 7637b22405..0924328b26 100644 --- 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 `_. + - 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 ` to cite the methods you used. diff --git a/source/lmp/pair_deepmd.cpp b/source/lmp/pair_deepmd.cpp index 3676c4a3fc..b57865deed 100644 --- a/source/lmp/pair_deepmd.cpp +++ b/source/lmp/pair_deepmd.cpp @@ -49,30 +49,25 @@ 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) { From b9317dd3f9b8bbd739503b263e2763b5fbe74493 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 1 Aug 2023 21:06:17 +0000 Subject: [PATCH 2/4] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- CITATIONS.bib | 10 +++++----- source/lmp/pair_deepmd.cpp | 36 ++++++++++++++++++++++++------------ 2 files changed, 29 insertions(+), 17 deletions(-) diff --git a/CITATIONS.bib b/CITATIONS.bib index afc51cb393..09f0f14acb 100644 --- a/CITATIONS.bib +++ b/CITATIONS.bib @@ -19,19 +19,19 @@ @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 Mari{\'a}n Rynik and Li'ang Huang and Ziyao Li and + 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 + 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 + 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, + issue = 5, year = 2023, pages = 054801, doi = {10.1063/5.0155600}, diff --git a/source/lmp/pair_deepmd.cpp b/source/lmp/pair_deepmd.cpp index b57865deed..0be70e9c3e 100644 --- a/source/lmp/pair_deepmd.cpp +++ b/source/lmp/pair_deepmd.cpp @@ -50,18 +50,30 @@ static const char cite_user_deepmd_package[] = " pages = {178--184}\n" "}\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" + " 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" From c12a17426b918059bd03e96fba472d6f438c5e82 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Tue, 1 Aug 2023 17:12:12 -0400 Subject: [PATCH 3/4] fix escape symbols Signed-off-by: Jinzhe Zeng --- source/lmp/pair_deepmd.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/source/lmp/pair_deepmd.cpp b/source/lmp/pair_deepmd.cpp index 0be70e9c3e..dddcea1c32 100644 --- a/source/lmp/pair_deepmd.cpp +++ b/source/lmp/pair_deepmd.cpp @@ -54,7 +54,7 @@ static const char cite_user_deepmd_package[] = "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 " + " 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" @@ -62,7 +62,7 @@ static const char cite_user_deepmd_package[] = "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 " + " 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" From 58b245d4be3ec79135edb3f8645bcb1bf21206fa Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 1 Aug 2023 21:12:39 +0000 Subject: [PATCH 4/4] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- source/lmp/pair_deepmd.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/source/lmp/pair_deepmd.cpp b/source/lmp/pair_deepmd.cpp index dddcea1c32..e60655decc 100644 --- a/source/lmp/pair_deepmd.cpp +++ b/source/lmp/pair_deepmd.cpp @@ -62,7 +62,8 @@ static const char cite_user_deepmd_package[] = "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 " + " 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"