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70 changes: 70 additions & 0 deletions CITATIONS.bib
Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,22 @@ @article{Zeng_JChemTheoryComput_2025_v21_p4375
},
}

@article{Han_CommunComputPhys_2018_v23_p629,
annote = {Deep Potential},
title = {
{Deep Potential: A General Representation of a Many-Body Potential Energy
Surface}
},
author = {Jiequn Han and Linfeng Zhang and Roberto Car and Weinan E},
journal = {Commun. Comput. Phys.},
year = 2018,
volume = 23,
number = 3,
pages = {629--639},
doi = {10.4208/cicp.OA-2017-0213},
url = {https://arxiv.org/abs/1707.01478},
}

@article{Lu_CompPhysCommun_2021_v259_p107624,
annote = {GPU support},
title = {
Expand Down Expand Up @@ -120,6 +136,18 @@ @article{Zhang_PhysRevLett_2018_v120_p143001
doi = {10.1103/PhysRevLett.120.143001},
}

@article{Zhang_JChemPhys_2018_v149_p34101,
annote = {coarse-grained model (DeePCG)},
title = {{DeePCG: Constructing Coarse-Grained Models via Deep Neural Networks}},
author = {Linfeng Zhang and Jiequn Han and Han Wang and Roberto Car and Weinan E},
journal = {J. Chem. Phys.},
year = 2018,
volume = 149,
number = 3,
pages = 034101,
doi = {10.1063/1.5027645},
}

@incollection{Zhang_BookChap_NIPS_2018_v31_p4436,
annote = {DeepPot-SE (se\_e2\_a, se\_e2\_r, se\_e3, se\_atten)},
title = {
Expand Down Expand Up @@ -196,6 +224,36 @@ @article{Zhang_npjComputMater_2024_v10_p293
doi = {10.1038/s41524-024-01493-2},
}

@misc{Zhang_2025_DPA3,
annote = {DPA-3 descriptor (dpa3)},
author = {
Duo Zhang and Anyang Peng and Chun Cai and Wentao Li and Yuanchang Zhou and
Jinzhe Zeng and Mingyu Guo and Chengqian Zhang and Bowen Li and Hong Jiang
and Tong Zhu and Weile Jia and Linfeng Zhang and Han Wang
},
title = {{A Graph Neural Network for the Era of Large Atomistic Models}},

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Please keep the canonical BibTeX title identical to the paper metadata. arXiv:2506.01686 is titled “Graph neural network model for the era of large atomistic models”; the current entry adds “A” and omits “model”. The authors, identifier, and year are otherwise correct.

publisher = {arXiv},
year = 2025,
doi = {10.48550/arXiv.2506.01686},
url = {https://arxiv.org/abs/2506.01686},
}

@misc{Li_2026_DPA4,
annote = {DPA-4 descriptor (dpa4, sezm)},
author = {
Tiancheng Li and Wentao Li and Anyang Peng and Jianming Xue and Linfeng
Zhang and Duo Zhang and Han Wang
},
title = {
{{DPA4}: Pushing the Accuracy-Cost Frontier of Interatomic Potentials with
{EMFA} {SO(2)} Convolution}
},
publisher = {arXiv},
year = 2026,
doi = {10.48550/arXiv.2606.02419},
url = {https://arxiv.org/abs/2606.02419},
}

@article{Zhang_PhysPlasmas_2020_v27_p122704,
annote = {frame-specific parameters (e.g. electronic temperature)},
author = {
Expand Down Expand Up @@ -262,6 +320,18 @@ @article{Sommers_PhysChemChemPhys_2020_v22_p10592
doi = {10.1039/D0CP01893G},
}

@misc{Ahart_2026_DeepPolaron,
annote = {atomic charge population (DeepPopulation)},
author = {Christian S. Ahart and Denan Li and Jochen Blumberger and Shi Liu},
title = {
{Polaron Transport in {TiO}$_{2}$ from Machine Learning Molecular Dynamics}
},
publisher = {arXiv},
year = 2026,
doi = {10.48550/arXiv.2606.01763},
url = {https://arxiv.org/abs/2606.01763},
}

@article{Zeng_JChemTheoryComput_2023_v19_p1261,
annote = {fit relative energies},
author = {Jinzhe Zeng and Yujun Tao and Timothy J Giese and Darrin M York},
Expand Down
320 changes: 237 additions & 83 deletions README.md

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45 changes: 45 additions & 0 deletions doc/credits.rst
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,24 @@ Cite DeePMD-kit and methods
Zeng_JChemPhys_2023_v159_p054801
Zeng_JChemTheoryComput_2025_v21_p4375

.. _cite-deep-potential:

- If the original Deep Potential model is used,

.. bibliography::
:filter: False

Han_CommunComputPhys_2018_v23_p629

.. _cite-deepcg:

- If the DeePCG coarse-grained model is used,

.. bibliography::
:filter: False

Zhang_JChemPhys_2018_v149_p34101

- If GPU version is used,

.. bibliography::
Expand Down Expand Up @@ -57,6 +75,24 @@ Cite DeePMD-kit and methods

Zhang_npjComputMater_2024_v10_p293

.. _cite-dpa3:

- If DPA-3 descriptor (`dpa3`) is used,

.. bibliography::
:filter: False

Zhang_2025_DPA3

.. _cite-dpa4:

- If DPA-4 descriptor (`dpa4`, `sezm`) is used,

.. bibliography::
:filter: False

Li_2026_DPA4

- If frame-specific parameters (`fparam`, e.g. electronic temperature) is used,

.. bibliography::
Expand Down Expand Up @@ -85,6 +121,15 @@ Cite DeePMD-kit and methods

Sommers_PhysChemChemPhys_2020_v22_p10592

.. _cite-deeppopulation:

- If fitting atomic charge populations with DeepPopulation,

.. bibliography::
:filter: False

Ahart_2026_DeepPolaron

- If fitting density of states,

.. bibliography::
Expand Down
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