License and citations

License

MLatom is an open-source software under the MIT license (modified to request proper citations).

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. When this Software or its derivatives are used in scientific publications, it shall be cited as:

Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Peikun Zheng, Yuxinxin Chen, Mario Barbatti, Olexandr Isayev, Cheng Wang, Bao-Xin Xue, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Lina Zhang, Shuang Zhang, Arif Ullah, Quanhao Zhang, Yanchi Ou. MLatom 3: A Platform for Machine Learning-enhanced Computational Chemistry Simulations and Workflows, J. Chem. Theory Comput. 2024, 20, 1193–1213. DOI: 10.1021/acs.jctc.3c01203.
if you use MLatom for the NAMD simulations, please also cite:
- FSSH: Jakub Martinka, Mikołaj Martyka, Biman Medhi, Jiří Pittner, and Pavlo O. Dral. Flexible Framework for Surface Hopping: From Hybrid Schemes for Machine Learning to Benchmarkable Nonadiabatic Dynamics. J. Chem. Theory Comput. 2026, 22, 2467–2479. DOI: 10.1021/acs.jctc.5c02137. Preprint on arXiv: https://arxiv.org/abs/2505.23344.
- LZBL: Lina Zhang, Sebastian Pios, Mikołaj Martyka, Fuchun Ge, Yi-Fan Hou, Yuxinxin Chen, Joanna Jankowska, Lipeng Chen, Mario Barbatti, Pavlo O. Dral. MLatom software ecosystem for surface hopping dynamics in Python with quantum mechanical and machine learning methods. J. Chem. Theory Comput. 2024, 20, 5043–5057. DOI: 10.1021/acs.jctc.4c00468. Preprint on arXiv: https://arxiv.org/abs/2404.06189.
Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou, Yuxinxin Chen, Mikołaj Martyka, Jakub Martinka, Peikun Zheng, Lina Zhang, Xin-Yu Tong, Bao-Xin Xue, Quanhao Zhang, Arif Ullah, Sebastian V. Pios, Vignesh B. Kumar, Yanchi Ou, Max Pinheiro Jr, Yuming Su, Yiheng Dai, Yangtao Chen, Shuang Zhang, Jinming Hu, Matheus O. Bispo, MLatom: A Package for Atomistic Simulations with Machine Learning, version [add version number], Xiamen University, Xiamen, China, 2013-2026. MLatom.com.

The citations for MLatom’s interfaces and features shall be eventually included too. See program output, header.py, ref.json, and MLatom.com.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Citations

Citations mentioned above should be included. For convenience, below we provide some of the citations in the Bibtex format and you can also download EndNote files.

 @article{MLatom 3,
 author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Zheng, Peikun and Chen, Yuxinxin and Barbatti, Mario and Isayev, Olexandr and Wang, Cheng and Xue, Bao-Xin and Pinheiro Jr, Max and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Zhang, Lina and Ullah, Arif and Zhang, Quanhao and Ou, Yanchi},
 title = {MLatom 3: A Platform for Machine Learning-Enhanced Computational Chemistry Simulations and Workflows},
 journal = {J. Chem. Theory Comput.},
 volume = {20},
 number = {3},
 pages = {1193--1213},
 DOI = {10.1021/acs.jctc.3c01203},
 year = {2024},
 type = {Journal Article}
 }

@misc{MLatomProg,
 author = {Dral, Pavlo O. and Ge, Fuchun and Hou, Yi-Fan and Chen, Yuxinxin and Martyka, Mikołaj and Martinka, Jakub and Zheng, Peikun and Zhang, Lina and Tong, Xin-Yu and Xue, Bao-Xin and Zhang, Quanhao and Ullah, Arif and Pios, Sebastian V. and Kumar, Vignesh B. and Ou, Yanchi and Pinheiro Jr, Max and Su, Yuming and Dai, Yiheng and Chen, Yangtao and Zhang, Shuang and Hu, Jinming and Bispo, Matheus O.},
 title = {MLatom: A Package for Atomistic Simulations with Machine Learning},
 year = {2013--2026},
 type = {Computer Program}
 }

 @article{FSSH,
   author = {Martinka, Jakub and Martyka, Mikołaj and Medhi, Biman and Pittner, Jiří and Dral, Pavlo O.},
   title = {Flexible Framework for Surface Hopping: From Hybrid Schemes for Machine Learning to Benchmarkable Nonadiabatic Dynamics},
   journal = {J. Chem. Theory Comput.},
   volume = {22},
   number = {5},
   pages = {2467--2479},
   DOI = {10.1021/acs.jctc.5c02137},
   year = {2026},
   type = {Journal Article}
 }

 @article{LSBL,
   author = {Zhang, L. and Pios, S. V. and Martyka, M. and Ge, F. and Hou, Y. F. and Chen, Y. and Chen, L. and Jankowska, J. and Barbatti, M. and Dral, P. O.},
   title = {MLatom Software Ecosystem for Surface Hopping Dynamics in Python with Quantum Mechanical and Machine Learning Methods},
   journal = {J. Chem. Theory Comput.},
   volume = {20},
   number = {12},
   pages = {5043--5057},
   DOI = {10.1021/acs.jctc.4c00468},
   year = {2024},
   type = {Journal Article}
 }

 @article{MLatom2,
 author = {Dral, Pavlo O. and Ge, Fuchun and Xue, Bao-Xin and Hou, Yi-Fan and Pinheiro Jr, Max and Huang, Jianxing and Barbatti, Mario},
 title = {MLatom 2: An Integrative Platform for Atomistic Machine Learning},
 journal = {Top. Curr. Chem.},
 volume = {379},
 number = {4},
 pages = {27},
 DOI = {10.1007/s41061-021-00339-5},
 year = {2021},
 type = {Journal Article}
 }

 @article{MLatom1,
 author = {Dral, Pavlo O.},
 title = {MLatom: A Program Package for Quantum Chemical Research Assisted by Machine Learning},
 journal = {J. Comput. Chem.},
 volume = {40},
 number = {26},
 pages = {2339--2347},
 DOI = {10.1002/jcc.26004},
 year = {2019},
 type = {Journal Article}
 }