diff --git a/pyproject.toml b/pyproject.toml index 970f9a8..1c4ebd7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -128,6 +128,7 @@ ignore = [ "PLR0912", # Too many branches "PLR0913", # Too many arguments "PLR0915", # Too many statements + "PLR0917", # Too many positional arguments "PLR2004", # Magic-value-comparison TODO fix these "PLW2901", # Outer for loop variable overwritten by inner assignment target "PLW0603", # Using the global statement to update `_el_ox_states_wiki` is discouraged TODO fix these diff --git a/src/elementembeddings/utils/config.py b/src/elementembeddings/utils/config.py index 546f023..775b714 100644 --- a/src/elementembeddings/utils/config.py +++ b/src/elementembeddings/utils/config.py @@ -31,282 +31,330 @@ } CITATIONS = { "magpie": [ - "@article{ward2016general," - "title={A general-purpose machine learning framework for " - "predicting properties of inorganic materials}," - "author={Ward, Logan and Agrawal, Ankit and Choudhary, Alok " - "and Wolverton, Christopher}," - "journal={npj Computational Materials}," - "volume={2}," - "number={1}," - "pages={1--7}," - "year={2016}," - "publisher={Nature Publishing Group}}", + ( + "@article{ward2016general," + "title={A general-purpose machine learning framework for " + "predicting properties of inorganic materials}," + "author={Ward, Logan and Agrawal, Ankit and Choudhary, Alok " + "and Wolverton, Christopher}," + "journal={npj Computational Materials}," + "volume={2}," + "number={1}," + "pages={1--7}," + "year={2016}," + "publisher={Nature Publishing Group}}" + ), ], "magpie_sc": [ - "@article{ward2016general," - "title={A general-purpose machine learning framework for " - "predicting properties of inorganic materials}," - "author={Ward, Logan and Agrawal, Ankit and Choudhary, Alok " - "and Wolverton, Christopher}," - "journal={npj Computational Materials}," - "volume={2}," - "number={1}," - "pages={1--7}," - "year={2016}," - "publisher={Nature Publishing Group}}", + ( + "@article{ward2016general," + "title={A general-purpose machine learning framework for " + "predicting properties of inorganic materials}," + "author={Ward, Logan and Agrawal, Ankit and Choudhary, Alok " + "and Wolverton, Christopher}," + "journal={npj Computational Materials}," + "volume={2}," + "number={1}," + "pages={1--7}," + "year={2016}," + "publisher={Nature Publishing Group}}" + ), ], "mat2vec": [ - "@article{tshitoyan2019unsupervised," - "title={Unsupervised word embeddings capture latent knowledge " - "from materials science literature}," - "author={Tshitoyan, Vahe and Dagdelen, John and Weston, Leigh " - "and Dunn, Alexander and Rong, Ziqin and Kononova, Olga " - "and Persson, Kristin A and Ceder, Gerbrand and Jain, Anubhav}," - "journal={Nature}," - "volume={571}," - "number={7763}," - "pages={95--98}," - "year={2019}," - "publisher={Nature Publishing Group} }", + ( + "@article{tshitoyan2019unsupervised," + "title={Unsupervised word embeddings capture latent knowledge " + "from materials science literature}," + "author={Tshitoyan, Vahe and Dagdelen, John and Weston, Leigh " + "and Dunn, Alexander and Rong, Ziqin and Kononova, Olga " + "and Persson, Kristin A and Ceder, Gerbrand and Jain, Anubhav}," + "journal={Nature}," + "volume={571}," + "number={7763}," + "pages={95--98}," + "year={2019}," + "publisher={Nature Publishing Group} }" + ), ], "matscholar": [ - "@article{weston2019named," - "title={Named entity recognition and normalization applied to " - "large-scale information extraction from the materials " - "science literature}," - "author={Weston, Leigh and Tshitoyan, Vahe and Dagdelen, John and " - "Kononova, Olga and Trewartha, Amalie and Persson, Kristin A and " - "Ceder, Gerbrand and Jain, Anubhav}," - "journal={Journal of chemical information and modeling}," - "volume={59}," - "number={9}," - "pages={3692--3702}," - "year={2019}," - "publisher={ACS Publications} }", + ( + "@article{weston2019named," + "title={Named entity recognition and normalization applied to " + "large-scale information extraction from the materials " + "science literature}," + "author={Weston, Leigh and Tshitoyan, Vahe and Dagdelen, John and " + "Kononova, Olga and Trewartha, Amalie and Persson, Kristin A and " + "Ceder, Gerbrand and Jain, Anubhav}," + "journal={Journal of chemical information and modeling}," + "volume={59}," + "number={9}," + "pages={3692--3702}," + "year={2019}," + "publisher={ACS Publications} }" + ), ], "megnet16": [ - "@article{chen2019graph," - "title={Graph networks as a universal machine learning framework " - "for molecules and crystals}," - "author={Chen, Chi and Ye, Weike and Zuo, Yunxing and " - "Zheng, Chen and Ong, Shyue Ping}," - "journal={Chemistry of Materials}," - "volume={31}," - "number={9}," - "pages={3564--3572}," - "year={2019}," - "publisher={ACS Publications} }", + ( + "@article{chen2019graph," + "title={Graph networks as a universal machine learning framework " + "for molecules and crystals}," + "author={Chen, Chi and Ye, Weike and Zuo, Yunxing and " + "Zheng, Chen and Ong, Shyue Ping}," + "journal={Chemistry of Materials}," + "volume={31}," + "number={9}," + "pages={3564--3572}," + "year={2019}," + "publisher={ACS Publications} }" + ), ], "oliynyk": [ - " @article{oliynyk2016high," - "title={High-throughput machine-learning-driven synthesis " - "of full-Heusler compounds}," - "author={Oliynyk, Anton O and Antono, Erin and Sparks, Taylor D and " - "Ghadbeigi, Leila and Gaultois, Michael W and " - "Meredig, Bryce and Mar, Arthur}," - "journal={Chemistry of Materials}," - "volume={28}," - "number={20}," - "pages={7324--7331}," - "year={2016}," - "publisher={ACS Publications} }", + ( + " @article{oliynyk2016high," + "title={High-throughput machine-learning-driven synthesis " + "of full-Heusler compounds}," + "author={Oliynyk, Anton O and Antono, Erin and Sparks, Taylor D and " + "Ghadbeigi, Leila and Gaultois, Michael W and " + "Meredig, Bryce and Mar, Arthur}," + "journal={Chemistry of Materials}," + "volume={28}," + "number={20}," + "pages={7324--7331}," + "year={2016}," + "publisher={ACS Publications} }" + ), ], "oliynyk_sc": [ - " @article{oliynyk2016high," - "title={High-throughput machine-learning-driven synthesis " - "of full-Heusler compounds}," - "author={Oliynyk, Anton O and Antono, Erin and Sparks, Taylor D and " - "Ghadbeigi, Leila and Gaultois, Michael W and " - "Meredig, Bryce and Mar, Arthur}," - "journal={Chemistry of Materials}," - "volume={28}," - "number={20}," - "pages={7324--7331}," - "year={2016}," - "publisher={ACS Publications} }", + ( + " @article{oliynyk2016high," + "title={High-throughput machine-learning-driven synthesis " + "of full-Heusler compounds}," + "author={Oliynyk, Anton O and Antono, Erin and Sparks, Taylor D and " + "Ghadbeigi, Leila and Gaultois, Michael W and " + "Meredig, Bryce and Mar, Arthur}," + "journal={Chemistry of Materials}," + "volume={28}," + "number={20}," + "pages={7324--7331}," + "year={2016}," + "publisher={ACS Publications} }" + ), ], "skipatom": [ - "@article{antunes2022distributed," - "title={Distributed representations of atoms and materials " - "for machine learning}," - "author={Antunes, Luis M and Grau-Crespo, Ricardo and Butler, Keith T}," - "journal={npj Computational Materials}," - "volume={8}," - "number={1}," - "pages={1--9}," - "year={2022}," - "publisher={Nature Publishing Group} }", + ( + "@article{antunes2022distributed," + "title={Distributed representations of atoms and materials " + "for machine learning}," + "author={Antunes, Luis M and Grau-Crespo, Ricardo and Butler, Keith T}," + "journal={npj Computational Materials}," + "volume={8}," + "number={1}," + "pages={1--9}," + "year={2022}," + "publisher={Nature Publishing Group} }" + ), ], "mod_petti": [ - "@article{glawe2016optimal," - "title={The optimal one dimensional periodic table: " - "a modified Pettifor chemical scale from data mining}," - "author={Glawe, Henning and Sanna, Antonio and Gross, " - "EKU and Marques, Miguel AL}," - "journal={New Journal of Physics}," - "volume={18}," - "number={9}," - "pages={093011}," - "year={2016}," - "publisher={IOP Publishing} }", + ( + "@article{glawe2016optimal," + "title={The optimal one dimensional periodic table: " + "a modified Pettifor chemical scale from data mining}," + "author={Glawe, Henning and Sanna, Antonio and Gross, " + "EKU and Marques, Miguel AL}," + "journal={New Journal of Physics}," + "volume={18}," + "number={9}," + "pages={093011}," + "year={2016}," + "publisher={IOP Publishing} }" + ), ], "crystallm": [ - "@article{antunes2023crystal," - "title={Crystal structure generation " - "with autoregressive large language modeling}," - "author={Antunes, Luis M and Butler, Keith T and Grau-Crespo, Ricardo}," - "journal={arXiv preprint arXiv:2307.04340}," - "year={2023}}", + ( + "@article{antunes2023crystal," + "title={Crystal structure generation " + "with autoregressive large language modeling}," + "author={Antunes, Luis M and Butler, Keith T and Grau-Crespo, Ricardo}," + "journal={arXiv preprint arXiv:2307.04340}," + "year={2023}}" + ), ], "xenonpy": [ - "@article{liu2021machine," - "title={Machine learning to predict quasicrystals from chemical compositions}," - "author={Liu, Chang and Fujita, Erina and " - "Katsura, Yukari and Inada, Yuki and Ishikawa, Asuka and " - "Tamura, Ryuji and Kimura, Kaoru and Yoshida, Ryo}," - "journal={Advanced Materials}," - "volume={33}," - "number={36}," - "pages={2102507}," - "year={2021}," - "publisher={Wiley Online Library}" - "}", - "@article{kusaba2022crystal," - "title={Crystal structure prediction with machine " - "learning-based element substitution}," - "author={Kusaba, Minoru and Liu, Chang and Yoshida, Ryo}," - "journal={Computational Materials Science}," - "volume={211}," - "pages={111496}," - "year={2022}," - "publisher={Elsevier}" - "}", - "@article{kusaba2023representation," - "title={Representation of materials by kernel mean embedding}," - "author={Kusaba, Minoru and Hayashi, Yoshihiro and " - "Liu, Chang and Wakiuchi, Araki and Yoshida, Ryo}," - "journal={Physical Review B}," - "volume={108}," - "number={13}," - "pages={134107}," - "year={2023}," - "publisher={APS}" - "}", + ( + "@article{liu2021machine," + "title={Machine learning to predict quasicrystals from chemical compositions}," + "author={Liu, Chang and Fujita, Erina and " + "Katsura, Yukari and Inada, Yuki and Ishikawa, Asuka and " + "Tamura, Ryuji and Kimura, Kaoru and Yoshida, Ryo}," + "journal={Advanced Materials}," + "volume={33}," + "number={36}," + "pages={2102507}," + "year={2021}," + "publisher={Wiley Online Library}" + "}" + ), + ( + "@article{kusaba2022crystal," + "title={Crystal structure prediction with machine " + "learning-based element substitution}," + "author={Kusaba, Minoru and Liu, Chang and Yoshida, Ryo}," + "journal={Computational Materials Science}," + "volume={211}," + "pages={111496}," + "year={2022}," + "publisher={Elsevier}" + "}" + ), + ( + "@article{kusaba2023representation," + "title={Representation of materials by kernel mean embedding}," + "author={Kusaba, Minoru and Hayashi, Yoshihiro and " + "Liu, Chang and Wakiuchi, Araki and Yoshida, Ryo}," + "journal={Physical Review B}," + "volume={108}," + "number={13}," + "pages={134107}," + "year={2023}," + "publisher={APS}" + "}" + ), ], "cgnf": [ - "@article{jang2024synthesizability," - "title={Synthesizability of materials stoichiometry " - "using semi-supervised learning}," - "author={Jang, Jidon and Noh, Juhwan and Zhou, Lan " - "and Gu, Geun Ho and Gregoire, John M and Jung, Yousung}," - "journal={Matter}," - "volume={7}," - "number={6}," - "pages={2294--2312}," - "year={2024}", + ( + "@article{jang2024synthesizability," + "title={Synthesizability of materials stoichiometry " + "using semi-supervised learning}," + "author={Jang, Jidon and Noh, Juhwan and Zhou, Lan " + "and Gu, Geun Ho and Gregoire, John M and Jung, Yousung}," + "journal={Matter}," + "volume={7}," + "number={6}," + "pages={2294--2312}," + "year={2024}" + ), ], "mace_mp0": [ - "@article{batatia2024foundation," - "title={A foundation model for atomistic materials chemistry}," - "author={Batatia, Ilyes and Benner, Philipp and Chiang, Yuan " - "and Elena, Alin M. and Kov{\\'a}cs, D{\\'a}vid P. " - "and Riebesell, Janosh and others}," - "journal={arXiv preprint arXiv:2401.00096}," - "year={2024}}", + ( + "@article{batatia2024foundation," + "title={A foundation model for atomistic materials chemistry}," + "author={Batatia, Ilyes and Benner, Philipp and Chiang, Yuan " + "and Elena, Alin M. and Kov{\\'a}cs, D{\\'a}vid P. " + "and Riebesell, Janosh and others}," + "journal={arXiv preprint arXiv:2401.00096}," + "year={2024}}" + ), ], "sevennet": [ - "@article{park2024scalable," - "title={Scalable parallel algorithm for graph neural network " - "interatomic potentials in molecular dynamics simulations}," - "author={Park, Yutack and Kim, Jaesun and Hwang, Seungwoo " - "and Han, Seungwu}," - "journal={arXiv preprint arXiv:2402.03789}," - "year={2024}}", + ( + "@article{park2024scalable," + "title={Scalable parallel algorithm for graph neural network " + "interatomic potentials in molecular dynamics simulations}," + "author={Park, Yutack and Kim, Jaesun and Hwang, Seungwoo " + "and Han, Seungwu}," + "journal={arXiv preprint arXiv:2402.03789}," + "year={2024}}" + ), ], "orb_v2": [ - "@article{neumann2024orb," - "title={ORB: A Fast, Scalable Neural Network Potential}," - "author={Neumann, Mark and Gin, James and Rhodes, Benjamin " - "and Bennett, Steven and Li, Zhiyi and Choubisa, Hitarth " - "and Hussey, Arthur and Godwin, Jonathan}," - "journal={arXiv preprint arXiv:2410.22570}," - "year={2024}}", + ( + "@article{neumann2024orb," + "title={ORB: A Fast, Scalable Neural Network Potential}," + "author={Neumann, Mark and Gin, James and Rhodes, Benjamin " + "and Bennett, Steven and Li, Zhiyi and Choubisa, Hitarth " + "and Hussey, Arthur and Godwin, Jonathan}," + "journal={arXiv preprint arXiv:2410.22570}," + "year={2024}}" + ), ], "chgnet": [ - "@article{deng2023chgnet," - "title={{CHGNet} as a pretrained universal neural network potential " - "for charge-informed atomistic modelling}," - "author={Deng, Bowen and Zhong, Peichen and Jun, KyuJung and " - "Riebesell, Janosh and Han, Kevin and Bartel, Christopher J " - "and Ceder, Gerbrand}," - "journal={Nature Machine Intelligence}," - "volume={5}," - "number={9}," - "pages={1031--1041}," - "year={2023}," - "publisher={Nature Publishing Group}}", + ( + "@article{deng2023chgnet," + "title={{CHGNet} as a pretrained universal neural network potential " + "for charge-informed atomistic modelling}," + "author={Deng, Bowen and Zhong, Peichen and Jun, KyuJung and " + "Riebesell, Janosh and Han, Kevin and Bartel, Christopher J " + "and Ceder, Gerbrand}," + "journal={Nature Machine Intelligence}," + "volume={5}," + "number={9}," + "pages={1031--1041}," + "year={2023}," + "publisher={Nature Publishing Group}}" + ), ], "matscibert": [ - "@article{gupta2022matscibert," - "title={{MatSciBERT}: A materials domain language model for text " - "mining and information extraction}," - "author={Gupta, Tanishq and Zaki, Mohd and Krishnan, NM Anoop " - "and Mausam}," - "journal={npj Computational Materials}," - "volume={8}," - "number={1}," - "pages={102}," - "year={2022}," - "publisher={Nature Publishing Group}}", + ( + "@article{gupta2022matscibert," + "title={{MatSciBERT}: A materials domain language model for text " + "mining and information extraction}," + "author={Gupta, Tanishq and Zaki, Mohd and Krishnan, NM Anoop " + "and Mausam}," + "journal={npj Computational Materials}," + "volume={8}," + "number={1}," + "pages={102}," + "year={2022}," + "publisher={Nature Publishing Group}}" + ), ], "chemeleon": [ - "@article{park2025chemeleon," - "title={Crystal structure generation and property optimization " - "using a generative graph neural network}," - "author={Park, Hyunsoo and Onwuli, Anthony O. and Walsh, Aron}," - "journal={Nature Communications}," - "volume={16}," - "pages={4869}," - "year={2025}," - "doi={10.1038/s41467-025-59636-y}," - "publisher={Nature Publishing Group}}", + ( + "@article{park2025chemeleon," + "title={Crystal structure generation and property optimization " + "using a generative graph neural network}," + "author={Park, Hyunsoo and Onwuli, Anthony O. and Walsh, Aron}," + "journal={Nature Communications}," + "volume={16}," + "pages={4869}," + "year={2025}," + "doi={10.1038/s41467-025-59636-y}," + "publisher={Nature Publishing Group}}" + ), ], "skipspecies": [ - "@article{Onwuli_Butler_Walsh_2024, " - "title={Ionic species representations for materials informatics}, " - "DOI={10.26434/chemrxiv-2024-8621l}, " - "journal={ChemRxiv}, " - "author={Onwuli, Anthony and Butler, Keith T. and Walsh, Aron}, year={2024}} " - "This content is a preprint and has not been peer-reviewed.", - "@article{antunes2022distributed," - "title={Distributed representations of atoms and materials " - "for machine learning}," - "author={Antunes, Luis M and Grau-Crespo, Ricardo and Butler, Keith T}," - "journal={npj Computational Materials}," - "volume={8}," - "number={1}," - "pages={1--9}," - "year={2022}," - "publisher={Nature Publishing Group} }", + ( + "@article{Onwuli_Butler_Walsh_2024, " + "title={Ionic species representations for materials informatics}, " + "DOI={10.26434/chemrxiv-2024-8621l}, " + "journal={ChemRxiv}, " + "author={Onwuli, Anthony and Butler, Keith T. and Walsh, Aron}, year={2024}} " + "This content is a preprint and has not been peer-reviewed." + ), + ( + "@article{antunes2022distributed," + "title={Distributed representations of atoms and materials " + "for machine learning}," + "author={Antunes, Luis M and Grau-Crespo, Ricardo and Butler, Keith T}," + "journal={npj Computational Materials}," + "volume={8}," + "number={1}," + "pages={1--9}," + "year={2022}," + "publisher={Nature Publishing Group} }" + ), ], "skipspecies_induced": [ - "@article{Onwuli_Butler_Walsh_2024, " - "title={Ionic species representations for materials informatics}, " - "DOI={10.26434/chemrxiv-2024-8621l}, " - "journal={ChemRxiv}, " - "author={Onwuli, Anthony and Butler, Keith T. and Walsh, Aron}, year={2024}} " - "This content is a preprint and has not been peer-reviewed.", - "@article{antunes2022distributed," - "title={Distributed representations of atoms and materials " - "for machine learning}," - "author={Antunes, Luis M and Grau-Crespo, Ricardo and Butler, Keith T}," - "journal={npj Computational Materials}," - "volume={8}," - "number={1}," - "pages={1--9}," - "year={2022}," - "publisher={Nature Publishing Group} }", + ( + "@article{Onwuli_Butler_Walsh_2024, " + "title={Ionic species representations for materials informatics}, " + "DOI={10.26434/chemrxiv-2024-8621l}, " + "journal={ChemRxiv}, " + "author={Onwuli, Anthony and Butler, Keith T. and Walsh, Aron}, year={2024}} " + "This content is a preprint and has not been peer-reviewed." + ), + ( + "@article{antunes2022distributed," + "title={Distributed representations of atoms and materials " + "for machine learning}," + "author={Antunes, Luis M and Grau-Crespo, Ricardo and Butler, Keith T}," + "journal={npj Computational Materials}," + "volume={8}," + "number={1}," + "pages={1--9}," + "year={2022}," + "publisher={Nature Publishing Group} }" + ), ], }