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Wang J, Gao H, Han Y, Ding C, Pan S, Wang Y, Jia Q, Wang HT, Xing D, Sun J. MAGUS: machine learning and graph theory assisted universal structure searcher. Natl Sci Rev 2023; 10:nwad128. [PMID: 37332628 PMCID: PMC10275355 DOI: 10.1093/nsr/nwad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/30/2023] [Accepted: 04/28/2023] [Indexed: 06/20/2023] Open
Abstract
Crystal structure predictions based on first-principles calculations have gained great success in materials science and solid state physics. However, the remaining challenges still limit their applications in systems with a large number of atoms, especially the complexity of conformational space and the cost of local optimizations for big systems. Here, we introduce a crystal structure prediction method, MAGUS, based on the evolutionary algorithm, which addresses the above challenges with machine learning and graph theory. Techniques used in the program are summarized in detail and benchmark tests are provided. With intensive tests, we demonstrate that on-the-fly machine-learning potentials can be used to significantly reduce the number of expensive first-principles calculations, and the crystal decomposition based on graph theory can efficiently decrease the required configurations in order to find the target structures. We also summarized the representative applications of this method on several research topics, including unexpected compounds in the interior of planets and their exotic states at high pressure and high temperature (superionic, plastic, partially diffusive state, etc.); new functional materials (superhard, high-energy-density, superconducting, photoelectric materials), etc. These successful applications demonstrated that MAGUS code can help to accelerate the discovery of interesting materials and phenomena, as well as the significant value of crystal structure predictions in general.
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Affiliation(s)
| | | | | | - Chi Ding
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Shuning Pan
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yong Wang
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Qiuhan Jia
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hui-Tian Wang
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Dingyu Xing
- National Laboratory of Solid State Microstructures, School of Physics and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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Wang X, Wang Z, Gao P, Zhang C, Lv J, Wang H, Liu H, Wang Y, Ma Y. Data-driven prediction of complex crystal structures of dense lithium. Nat Commun 2023; 14:2924. [PMID: 37217498 DOI: 10.1038/s41467-023-38650-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Lithium (Li) is a prototypical simple metal at ambient conditions, but exhibits remarkable changes in structural and electronic properties under compression. There has been intense debate about the structure of dense Li, and recent experiments offered fresh evidence for yet undetermined crystalline phases near the enigmatic melting minimum region in the pressure-temperature phase diagram of Li. Here, we report on an extensive exploration of the energy landscape of Li using an advanced crystal structure search method combined with a machine-learning approach, which greatly expands the scale of structure search, leading to the prediction of four complex Li crystal structures containing up to 192 atoms in the unit cell that are energetically competitive with known Li structures. These findings provide a viable solution to the observed yet unidentified crystalline phases of Li, and showcase the predictive power of the global structure search method for discovering complex crystal structures in conjunction with accurate machine learning potentials.
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Affiliation(s)
- Xiaoyang Wang
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education and State Key Laboratory of Superhard Materials, College of Physics, Jilin University, 130012, Changchun, People's Republic of China
- Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, 100094, Beijing, People's Republic of China
| | - Zhenyu Wang
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education and State Key Laboratory of Superhard Materials, College of Physics, Jilin University, 130012, Changchun, People's Republic of China
| | - Pengyue Gao
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education and State Key Laboratory of Superhard Materials, College of Physics, Jilin University, 130012, Changchun, People's Republic of China
| | - Chengqian Zhang
- DP Technology, 100080, Beijing, People's Republic of China
- College of Engineering, Peking University, 100871, Beijing, People's Republic of China
| | - Jian Lv
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education and State Key Laboratory of Superhard Materials, College of Physics, Jilin University, 130012, Changchun, People's Republic of China.
| | - Han Wang
- Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, 100094, Beijing, People's Republic of China.
- HEDPS, CAPT, College of Engineering, Peking University, 100871, Beijing, People's Republic of China.
| | - Haifeng Liu
- Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, 100094, Beijing, People's Republic of China
| | - Yanchao Wang
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education and State Key Laboratory of Superhard Materials, College of Physics, Jilin University, 130012, Changchun, People's Republic of China
| | - Yanming Ma
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education and State Key Laboratory of Superhard Materials, College of Physics, Jilin University, 130012, Changchun, People's Republic of China.
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Duwal S, McCoy CA, Dolan Iii DH, Melton CA, Knudson MD, Root S, Hacking R, Farfan B, Johnson C, Alexander CS, Seagle CT. Samarium: from a distorted-fcc phase to melting under dynamic compression using in-situ x-ray diffraction. Sci Rep 2022; 12:16777. [PMID: 36202947 PMCID: PMC9537147 DOI: 10.1038/s41598-022-21332-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Lattice and electronic structure interactions for f-electrons are fundamental challenges for lanthanide equation of state development. Difficulties in first-principles calculations, such as density functional theory (DFT), emphasize the need for well-characterized experimental data. Here, we measure in-situ x-ray diffraction of shocked samarium (Sm) and temperature along the Hugoniot for the first time, providing direct evidence for phase transitions. We report direct evidence of a distorted fcc (dfcc) phase at 23 GPa. Shocked samarium melts from the dfcc phase starting at 33 GPa (1333 K), with complete melt at 40 GPa (1468 K). Previous work indicated shock melt at 27 GPa (1200 K), underscoring the significance of x-ray measurements for detecting phase transitions. Interestingly, our observed melting is in sharp contrast with the melting reported by a diamond anvil cell study. These experimental data can tightly constrain first principles calculations and serve as key touchstones for equation of state modeling.
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Affiliation(s)
- Sakun Duwal
- Sandia National Laboratories, Albuquerque, NM, 87125, USA.
| | - Chad A McCoy
- Sandia National Laboratories, Albuquerque, NM, 87125, USA
| | | | - Cody A Melton
- Sandia National Laboratories, Albuquerque, NM, 87125, USA
| | | | - Seth Root
- Sandia National Laboratories, Albuquerque, NM, 87125, USA
| | - Richard Hacking
- Mission Support and Test Services, Albuquerque Operations, Albuquerque, NM, 87125, USA
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Bommannavar A, Chow P, Ferry R, Hrubiak R, Humble F, Kenney-Benson C, Lv M, Meng Y, Park C, Popov D, Rod E, Somayazulu M, Shen G, Smith D, Smith J, Xiao Y, Velisavljevic N. Overview of HPCAT and capabilities for studying minerals and various other materials at high-pressure conditions. PHYSICS AND CHEMISTRY OF MINERALS 2022; 49:36. [PMID: 35992384 PMCID: PMC9377298 DOI: 10.1007/s00269-022-01209-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
High-Pressure Collaborative Access Team (HPCAT) is a synchrotron-based facility located at the Advanced Photon Source (APS). With four online experimental stations and various offline capabilities, HPCAT is focused on providing synchrotron x-ray capabilities for high pressure and temperature research and supporting a broad user community. Overall, the array of online/offline capabilities is described, including some of the recent developments for remote user support and the concomitant impact of the current pandemic. General overview of work done at HPCAT and with a focus on some of the minerals relevant work and supporting capabilities is also discussed. With the impending APS-Upgrade (APS-U), there is a considerable effort within HPCAT to improve and add capabilities. These are summarized briefly for each of the end-stations.
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Affiliation(s)
- Arunkumar Bommannavar
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Paul Chow
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Rich Ferry
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Rostislav Hrubiak
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Freda Humble
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Curtis Kenney-Benson
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Mingda Lv
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Yue Meng
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Changyong Park
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Dmitry Popov
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Eric Rod
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Maddury Somayazulu
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Guoyin Shen
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Dean Smith
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Jesse Smith
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Yuming Xiao
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
| | - Nenad Velisavljevic
- High Pressure Collaborative Access Team (HPCAT), X-Ray Science Division, Argonne National Laboratory, Lemont, IL 60439 USA
- Physics Division, Lawrence Livermore National Laboratory, Livermore, CA 94550 USA
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The high-pressure lithium-palladium and lithium-palladium-hydrogen systems. Sci Rep 2022; 12:12341. [PMID: 35853930 PMCID: PMC9296626 DOI: 10.1038/s41598-022-16694-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/13/2022] [Indexed: 11/08/2022] Open
Abstract
The lithium-palladium and lithium-palladium-hydrogen systems are investigated at high pressures at and above room temperature. Two novel lithium-palladium compounds are found below [Formula: see text]. An ambient temperature phase is tentatively assigned as [Formula: see text], with [Formula: see text] Å at 8.64 GPa, isostructural with [Formula: see text]. The other phase occurs at high-temperature and is [Formula: see text], [Formula: see text] Å at 3.88 GPa and 200 [Formula: see text], similar to [Formula: see text], which is also known at high pressure. The presence of hydrogen in the system results in an [Formula: see text] structure with [Formula: see text] Å at 9.74 GPa. This persists up to [Formula: see text], the highest pressure studied. Below [Formula: see text] an fcc phase with a large unit cell, [Formula: see text] Å at 0.39 GPa, is also observed in the presence of hydrogen. On heating the hydrogen containing system at 4 GPa the [Formula: see text] phases persists to the melting point of lithium. In both systems melting the lithium results in the loss of crystalline diffraction from palladium containing phases. This is attributed to dissolution of the palladium in the molten lithium, and on cooling the palladium remains dispersed.
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Shu Y, Kono Y, Ohira I, Hrubiak R, Kenney-Benson C, Somayazulu M, Velisavljevic N, Shen G. Structural Changes in Liquid Lithium under High Pressure. J Phys Chem B 2020; 124:7258-7262. [PMID: 32692917 DOI: 10.1021/acs.jpcb.0c05324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have experimentally studied the effect of compression on the structure of liquid lithium (Li) by multiangle energy dispersive X-ray diffraction in a large-volume cupped-Drickamer-Toroidal cell. The structure factors, s(q), of liquid Li have been successfully determined under an isothermal compression at 600 ± 30 K and at pressures up to 11.5 GPa. The first peak position in s(q) is found to increase with increasing pressure and is showing an obvious slope change starting at ∼7.5 GPa. The slope change is interpreted as a structural change from bcc-like to fcc-like local ordering in liquid Li. At pressures above 8.7 GPa, the liquid Li becomes predominantly fcc-like up to the highest pressure of 11.5 GPa in this study. The observed structural changes in liquid Li are consistent with the recently determined melting curve of Li.
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Affiliation(s)
- Yu Shu
- High Pressure Collaborative Access Team, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Yoshio Kono
- Geodynamics Research Center, Ehime University, Ehime 790-8577, Japan
| | - Itaru Ohira
- Geodynamics Research Center, Ehime University, Ehime 790-8577, Japan.,Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC 20015, United States
| | - Rostislav Hrubiak
- High Pressure Collaborative Access Team, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Curtis Kenney-Benson
- High Pressure Collaborative Access Team, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Maddury Somayazulu
- High Pressure Collaborative Access Team, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Nenad Velisavljevic
- High Pressure Collaborative Access Team, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Physics Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Guoyin Shen
- High Pressure Collaborative Access Team, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
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Méndez ASJ, Marquardt H, Husband RJ, Schwark I, Mainberger J, Glazyrin K, Kurnosov A, Otzen C, Satta N, Bednarcik J, Liermann HP. A resistively-heated dynamic diamond anvil cell (RHdDAC) for fast compression x-ray diffraction experiments at high temperatures. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:073906. [PMID: 32752811 DOI: 10.1063/5.0007557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
A resistively-heated dynamic diamond anvil cell (RHdDAC) setup is presented. The setup enables the dynamic compression of samples at high temperatures by employing a piezoelectric actuator for pressure control and internal heaters for high temperature. The RHdDAC facilitates the precise control of compression rates and was tested in compression experiments at temperatures up to 1400 K and pressures of ∼130 GPa. The mechanical stability of metallic glass gaskets composed of a FeSiB alloy was examined under simultaneous high-pressure/high-temperature conditions. High-temperature dynamic compression experiments on H2O ice and (Mg, Fe)O ferropericlase were performed in combination with time-resolved x-ray diffraction measurements to characterize crystal structures and compression behaviors. The employment of high brilliance synchrotron radiation combined with two fast GaAs LAMBDA detectors available at the Extreme Conditions Beamline (P02.2) at PETRA III (DESY) facilitates the collection of data with excellent pressure resolution. The pressure-temperature conditions achievable with the RHdDAC combined with its ability to cover a wide range of compression rates and perform tailored compression paths offers perspectives for a variety of future experiments under extreme conditions.
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Affiliation(s)
- A S J Méndez
- Photon Sciences, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - H Marquardt
- Department of Earth Sciences, University of Oxford, OX1 3AN Oxford, United Kingdom
| | - R J Husband
- Photon Sciences, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - I Schwark
- Photon Sciences, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - J Mainberger
- Photon Sciences, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - K Glazyrin
- Photon Sciences, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - A Kurnosov
- Bayerisches Geoinstitut BGI, University of Bayreuth, 95440 Bayreuth, Germany
| | - C Otzen
- Photon Sciences, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - N Satta
- Bayerisches Geoinstitut BGI, University of Bayreuth, 95440 Bayreuth, Germany
| | - J Bednarcik
- Department of Condensed Matter Physics, Institute of Physics, P.J. Šafárik University, 041 54 Košice, Slovakia
| | - H-P Liermann
- Photon Sciences, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
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