CrySPAI: A New Crystal Structure Prediction Software Based on Artificial Intelligence
Abstract
:1. Introduction
2. Materials and Methods
2.1. Implementations of CrySPAI
2.1.1. EOA Module
2.1.2. DFT Module
2.1.3. DNN Module
2.2. Adaptive Volume Adjustment Algorithm
3. Results
3.1. Framework of CrySPAI
3.2. Applications on Crystal Structure Prediction of CrySPAI
3.2.1. Parameters and Files Preparation
3.2.2. Crystal Structure Prediction
4. Discussion
4.1. Volume Prediction Performance
4.2. Swarm Intelligence Algorithm Performance
4.3. Capability Performance of CrySPAI in Crystal Structure Search
5. Conclusions
- Dependence on training data. CrySPAI’s prediction accuracy is heavily dependent on the quality and diversity of the training data used for DNN. To address this, we plan to expand the training dataset to cover a broader range of materials, ensuring better generalization and improved performance.
- Scalability to complex systems. While CrySPAI is currently effective for inorganic materials, its application to highly complex systems, such as amorphous materials, organic materials, or systems with strong electron correlation effects, may require additional computational resources or tailored methods. Future iterations of CrySPAI will involve specific adaptations to handle these complex systems effectively.
- Generalizability to experimental conditions. CrySPAI predictions are now conducted under idealized computational conditions (e.g., 0 K and no pressure). These may differ from experimental conditions, and some phase transitions and defect states will also have been thrown away. In the future versions, we will extend CrySPAI’s capabilities to simulate dynamic processes, offering deeper insights into material behaviors under realistic conditions.
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Bergerhoff, G.; Hundt, R.; Sievers, R.; Brown, I.D. The Inorganic Crystal Structure Data Base. J. Chem. Inf. Comput. Sci. 1983, 23, 66–69. [Google Scholar] [CrossRef]
- Villars, P.; Cenzual, K.; Gladyshevskii, R.; Iwata, S. PAULING FILE—Towards a holistic view. Chem. Met. Alloys 2018, 11, 43–76. [Google Scholar] [CrossRef]
- Curtarolo, S.; Hart, G.L.W.; Nardelli, M.B.; Mingo, N.; Sanvito, S.; Levy, O. The high-throughput highway to computational materials design. Nat. Mater. 2013, 12, 191–201. [Google Scholar] [CrossRef]
- Curtarolo, S.; Morgan, D.; Ceder, G. Accuracy of ab initio methods in predicting the crystal structures of metals: A review of 80 binary alloys. Calphad Comput. Coupling Phase Diagr. Thermochem. 2005, 29, 163–211. [Google Scholar] [CrossRef]
- Hart, G.L.W.; Curtarolo, S.; Massalski, T.B.; Levy, O. Comprehensive search for new phases and compounds in binary alloy systems based on platinum-group metals, using a computational first-principles approach. Phys. Rev. X 2014, 3, 1–33. [Google Scholar] [CrossRef]
- Doll, K.; Schön, J.C.; Jansen, M. Global exploration of the energy landscape of solids on the ab initio level. Phys. Chem. Chem. Phys. 2007, 9, 6128–6133. [Google Scholar] [CrossRef]
- Oganov, A.R.; Glass, C.W. Evolutionary crystal structure prediction as a tool in materials design. J. Phys. Condens. Matter 2008, 20, 064210. [Google Scholar] [CrossRef] [PubMed]
- Lyakhov, A.O.; Oganov, A.R.; Stokes, H.T.; Zhu, Q. New developments in evolutionary structure prediction algorithm USPEX. Comput. Phys. Commun. 2013, 184, 1172–1182. [Google Scholar] [CrossRef]
- Ji, M.; Umemoto, K.; Wang, C.-Z.; Ho, K.-M.; Wentzcovitch, R.M. Ultrahigh-pressure phases of H2O ice predicted using an adaptive genetic algorithm. Phys. Rev. B 2011, 84, 220105. [Google Scholar] [CrossRef]
- Wu, S.; Umemoto, K.; Ji, M.; Wang, C.Z.; Ho, K.M.; Wentzcovitch, R.M. Identification of post-pyrite phase transitions in SiO2 by a genetic algorithm. Phys. Rev. B-Condens. Matter Mater. Phys. 2011, 83, 6–9. [Google Scholar] [CrossRef]
- Wu, S.Q.; Ji, M.; Wang, C.Z.; Nguyen, M.C.; Zhao, X.; Umemoto, K.; Wentzcovitch, R.M.; Ho, K.M. An adaptive genetic algorithm for crystal structure prediction. J. Phys. Condens. Matter 2013, 26, 035402. [Google Scholar] [CrossRef] [PubMed]
- Wang, Y.; Lv, J.; Zhu, L.; Ma, Y. Crystal structure prediction via particle-swarm optimization. Phys. Rev. B-Condens. Matter Mater. Phys. 2010, 82, 094116. [Google Scholar] [CrossRef]
- Wang, Y.; Lv, J.; Zhu, L.; Ma, Y. CALYPSO: A method for crystal structure prediction. Comput. Phys. Commun. 2012, 183, 2063–2070. [Google Scholar] [CrossRef]
- Pickard, C.J.; Needs, R.J. Ab initio random structure searching. J. Phys. Condens. Matter 2011, 23, 053201. [Google Scholar] [CrossRef]
- Lonie, D.C.; Zurek, E. XtalOpt: An open-source evolutionary algorithm for crystal structure prediction. Comput. Phys. Commun. 2011, 182, 372–387. [Google Scholar] [CrossRef]
- Ouyang, R. Exploiting Ionic Radii for Rational Design of Halide Perovskites. Chem. Mater. 2020, 32, 595–604. [Google Scholar] [CrossRef]
- Bartel, C.J.; Sutton, C.; Goldsmith, B.R.; Ouyang, R.; Musgrave, C.B.; Ghiringhelli, L.M.; Scheffler, M. New tolerance factor to predict the stability of perovskite oxides and halides. Sci. Adv. 2019, 5, eaav0693. [Google Scholar] [CrossRef] [PubMed]
- Kusne, A.G.; Yu, H.; Wu, C.; Zhang, H.; Hattrick-Simpers, J.; DeCost, B.; Sarker, S.; Oses, C.; Toher, C.; Curtarolo, S.; et al. On-the-fly closed-loop materials discovery via Bayesian active learning. Nat. Commun. 2020, 11, 5966. [Google Scholar] [CrossRef]
- Schleder, G.R.; Padilha, A.C.; Acosta, C.M.; Costa, M.; Fazzio, A. From DFT to machine learning: Recent approaches to materials science-A review. J. Phys. Mater. 2019, 2, 032001. [Google Scholar] [CrossRef]
- Schmidt, J.; Marques, M.R.G.; Botti, S.; Marques, M.A.L. Recent advances and applications of machine learning in solid-state materials science. NPJ Comput. Mater. 2019, 5, 83. [Google Scholar] [CrossRef]
- Wei, J.; Chu, X.; Sun, X.; Xu, K.; Deng, H.; Chen, J.; Wei, Z.; Lei, M. Machine learning in materials science. InfoMat 2019, 1, 338–358. [Google Scholar] [CrossRef]
- Mortazavi, B.; Podryabinkin, E.V.; Novikov, I.S.; Roche, S.; Rabczuk, T.; Zhuang, X.; Shapeev, A.V. Efficient machine-learning based interatomic potentialsfor exploring thermal conductivity in two-dimensional materials. J. Phys. Mater. 2020, 3, 02LT02. [Google Scholar] [CrossRef]
- Vasudevan, R.; Pilania, G.; Balachandran, P.V. Machine learning for materials design and discovery. J. Appl. Phys. 2021, 129, 070401. [Google Scholar] [CrossRef]
- Xie, T.; Grossman, J.C. Crystal Graph Convolutional Neural Networks for an Accurate and Interpretable Prediction of Material Properties. Phys. Rev. Lett. 2018, 120, 145301. [Google Scholar] [CrossRef]
- Chen, C.; Ye, W.; Zuo, Y.; Zheng, C.; Ong, S.P. Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals. Chem. Mater. 2019, 31, 3564–3572. [Google Scholar] [CrossRef]
- Yuan, Y.; Chen, Z.; Feng, T.; Xiong, F.; Wang, J.; Wang, Y.; Wang, Z. Tripartite interaction representation algorithm for crystal graph neural networks. Scientific Reports 2024, 14, 24881. [Google Scholar] [CrossRef] [PubMed]
- Chen, C.; Ong, S.P. A universal graph deep learning interatomic potential for the periodic table. Nat. Comput. Sci. 2022, 2, 718–728. [Google Scholar] [CrossRef] [PubMed]
- Deng, B.; Zhong, P.; Jun, K.; Riebesell, J.; Han, K.; Bartel, C.J.; Ceder, G. CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling. Nat. Mach. Intell. 2023, 5, 1031–1041. [Google Scholar] [CrossRef]
- Xie, F.; Lu, T.; Meng, S.; Liu, M. GPTFF: A high-accuracy out-of-the-box universal AI force field for arbitrary inorganic materials. Sci. Bull. 2024, 69, 3525–3532. [Google Scholar] [CrossRef]
- Artrith, N.; Urban, A. An implementation of artificial neural-network potentials for atomistic materials simulations: Performance for TiO2. Comput. Mater. Sci. 2016, 114, 135–150. [Google Scholar] [CrossRef]
- Zhang, L.; Lin, D.-Y.; Wang, H.; Car, R.; E, W. Active learning of uniformly accurate interatomic potentials for materials simulation. Phys. Rev. Mater. 2019, 3, 023804. [Google Scholar] [CrossRef]
- Zhang, L.; Han, J.; Wang, H.; Car, R.; E, W. Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics. Phys. Rev. Lett. 2018, 120, 143001. [Google Scholar] [CrossRef] [PubMed]
- Wang, J.; Gao, H.; Han, Y.; Ding, C.; Pan, S.; Wang, Y.; Jia, Q.; Wang, H.-T.; Xing, D.; Sun, J. MAGUS: Machine learning and graph theory assisted universal structure searcher. Natl. Sci. Rev. 2023, 10, nwad128. [Google Scholar] [CrossRef]
- Cheng, G.; Gong, X.G.; Yin, W.J. Crystal structure prediction by combining graph network and optimization algorithm. Nat. Commun. 2022, 13, 1492. [Google Scholar] [CrossRef] [PubMed]
- Merchant, A.; Batzner, S.; Schoenholz, S.S.; Aykol, M.; Cheon, G.; Cubuk, E.D. Scaling deep learning for materials discovery. Nature 2023, 624, 80–85. [Google Scholar] [CrossRef]
- Liu, Z.-W.; Wang, Z.-G.; Guo, J.-L.; Wang, Y.-G. Deep Learning Method for Crystal Structure Prediction. Comput. Syst. Appl. 2021, 30, 40–49. [Google Scholar]
- Zhao, X.; Shu, Q.; Nguyen, M.C.; Wang, Y.; Ji, M.; Xiang, H.; Ho, K.-M.; Gong, X.; Wang, C.-Z. Interface Structure Prediction from First-Principles. J. Phys. Chem. C 2014, 118, 9524–9530. [Google Scholar] [CrossRef]
- Liu, Z.; Guo, J.; Chen, Z.; Wang, Z.; Sun, Z.; Li, X.; Wang, Y. Swarm intelligence for new materials. Comput. Mater. Sci. 2022, 214, 111699. [Google Scholar] [CrossRef]
- Perdew, J.P.; Burke, K.; Ernzerhof, M. Generalized gradient approximation made simple. Phys. Rev. Lett. 1996, 77, 3865–3868. [Google Scholar] [CrossRef]
- Artrith, N.; Urban, A.; Ceder, G. Efficient and accurate machine-learning interpolation of atomic energies in compositions with many species. Phys. Rev. B 2017, 96, 014112. [Google Scholar] [CrossRef]
NAME | Description | Default Value | Type |
---|---|---|---|
entry 1atom | element | no default value | string list |
atomn | number of each atom | no default value | int list |
avolume | atomic volume of structure | calculated by Equation (2) | float list |
aenergy | atomic energy | atomn*0.0 [a] | float list |
crystalsys | crystal system of target structure | all | string |
Structure | atomType | atomNumber | Volume of Cell (Å3) | TargSpg /PredSpg | c/aBias | siteBias |
---|---|---|---|---|---|---|
Si | Si | 8 | 160.1 | 227/227 | 0 | 0.175 |
TiO2 | O, Ti | 8, 4 | 136.28 | 227/227 | −0.259 | 0.258 |
Mg | Mg | 2 | 45.41 | 194/194 | 0.048 | 0.440 |
CaTiO3 | Ca, O, Ti | 1, 3, 1 | 59.17 | 194/194 | 0 | 0.419 |
Structure | TargVol/PredVol (Å3) | TargSpg/PredSpg | Tolerance (Å) |
---|---|---|---|
Cu4 | 50.007/47.238 | 225/225 | 0.2 |
Ni4 | 42.842/43.774 | 225/225 | 0.01 |
Mg2 | 45.405/46.454 | 194/194 | 0.1 |
Zn2 | 30.319/29.792 | 194/194 | 0.2 |
Zr2 | 46.299/46.570 | 194/194 | 0.1 |
Structure | Optimized Method | Loss | Dataset Size | Loop Number |
---|---|---|---|---|
Li | back-propagation algorithm | 0.074 | 668 | Null |
swarm intelligence algorithm | 0.009 | 673 | 1 | |
Ca | back-propagation algorithm | 0.075 | 1279 | Null |
swarm intelligence algorithm | 0.053 | 1216 | 1 | |
Mn | back-propagation algorithm | 0.042 | 1135 | Null |
swarm intelligence algorithm | 0.05 | 1335 | 2 |
Structure | Algorithm | Prototype Structures | Generations | Npop |
---|---|---|---|---|
Si | CALYPSO | Diamond | 8//5 | 16 |
GSGO | Diamond | 15 | 16 | |
CrySPAI | Diamond | 2 | 16 | |
SiC | CALYPSO | Zinc blende | 8//5 | 12 |
GSGO | Zinc blende | 5 | 12 | |
CrySPAI | Zinc blende | 1 | 12 | |
GaAs | CALYPSO | Zinc blende | 16//5 | 12 |
GSGO | Zinc blende | 19 | 12 | |
CrySPAI | Zinc blende | 2 | 12 |
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Wang, Z.; Chen, Z.; Yuan, Y.; Wang, Y. CrySPAI: A New Crystal Structure Prediction Software Based on Artificial Intelligence. Inventions 2025, 10, 26. https://doi.org/10.3390/inventions10020026
Wang Z, Chen Z, Yuan Y, Wang Y. CrySPAI: A New Crystal Structure Prediction Software Based on Artificial Intelligence. Inventions. 2025; 10(2):26. https://doi.org/10.3390/inventions10020026
Chicago/Turabian StyleWang, Zongguo, Ziyi Chen, Yang Yuan, and Yangang Wang. 2025. "CrySPAI: A New Crystal Structure Prediction Software Based on Artificial Intelligence" Inventions 10, no. 2: 26. https://doi.org/10.3390/inventions10020026
APA StyleWang, Z., Chen, Z., Yuan, Y., & Wang, Y. (2025). CrySPAI: A New Crystal Structure Prediction Software Based on Artificial Intelligence. Inventions, 10(2), 26. https://doi.org/10.3390/inventions10020026