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Fantasia A, Rovaris F, Abou El Kheir O, Marzegalli A, Lanzoni D, Pessina L, Xiao P, Zhou C, Li L, Henkelman G, Scalise E, Montalenti F. Development of a machine learning interatomic potential for exploring pressure-dependent kinetics of phase transitions in germanium. J Chem Phys 2024; 161:014110. [PMID: 38953439 DOI: 10.1063/5.0214588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024] Open
Abstract
We introduce a data-driven potential aimed at the investigation of pressure-dependent phase transitions in bulk germanium, including the estimate of kinetic barriers. This is achieved by suitably building a database including several configurations along minimum energy paths, as computed using the solid-state nudged elastic band method. After training the model based on density functional theory (DFT)-computed energies, forces, and stresses, we provide validation and rigorously test the potential on unexplored paths. The resulting agreement with the DFT calculations is remarkable in a wide range of pressures. The potential is exploited in large-scale isothermal-isobaric simulations, displaying local nucleation in the R8 to β-Sn pressure-induced phase transformation, taken here as an illustrative example.
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Affiliation(s)
- A Fantasia
- Department of Materials Science, University of Milano-Bicocca, 20125 Milano, Italy
| | - F Rovaris
- Department of Materials Science, University of Milano-Bicocca, 20125 Milano, Italy
| | - O Abou El Kheir
- Department of Materials Science, University of Milano-Bicocca, 20125 Milano, Italy
| | - A Marzegalli
- Department of Materials Science, University of Milano-Bicocca, 20125 Milano, Italy
| | - D Lanzoni
- Department of Materials Science, University of Milano-Bicocca, 20125 Milano, Italy
| | - L Pessina
- Department of Materials Science, University of Milano-Bicocca, 20125 Milano, Italy
| | - P Xiao
- Department of Physics and Atmospheric Science, Dalhousie University, 1453 Lord Dalhousie Drive, Halifax, Nova Scotia B3H 4R2, Canada
| | - C Zhou
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Avenue, 518055 Shenzhen, China
| | - L Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Avenue, 518055 Shenzhen, China
| | - G Henkelman
- Department of Chemistry, The University of Texas at Austin, 105 East 24th Street STOP A5300 Austin, Texas 78712, USA
| | - E Scalise
- Department of Materials Science, University of Milano-Bicocca, 20125 Milano, Italy
| | - F Montalenti
- Department of Materials Science, University of Milano-Bicocca, 20125 Milano, Italy
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Gunde M, Jay A, Poberžnik M, Salles N, Richard N, Landa G, Mousseau N, Martin-Samos L, Hemeryck A. Exploring potential energy surfaces to reach saddle points above convex regions. J Chem Phys 2024; 160:232501. [PMID: 38884410 DOI: 10.1063/5.0210097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
Saddle points on high-dimensional potential energy surfaces (PES) play a determining role in the activated dynamics of molecules and materials. Building on approaches dating back more than 50 years, many open-ended transition-state search methods have been developed to follow the direction of negative curvature from a local minimum to an adjacent first-order saddle point. Despite the mathematical justification, these methods can display a high failure rate: using small deformation steps, up to 80% of the explorations can end up in a convex region of the PES, where all directions of negative curvature vanish, while if the deformation is aggressive, a similar fraction of attempts lead to saddle points that are not directly connected to the initial minimum. In high-dimension PES, these reproducible failures were thought to only increase the overall computational cost, without having any effect on the methods' capacity to find all saddle points surrounding a minimum. Using activation-relaxation technique nouveau (ARTn), we characterize the nature of the PES around minima, considerably expanding on previous knowledge. We show that convex regions can lie on activation pathways and that not exploring beyond them can introduce significant bias in the saddle-point search. We introduce an efficient approach for traversing the convex regions, almost eliminating exploration failures, while multiplying by almost 10 the number of identified unique and connected saddle points as compared to the standard ARTn, thus underlining the importance of correctly handling convex regions for completeness of saddle point explorations.
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Affiliation(s)
- M Gunde
- Institute Ruđer Bošković, Bijenička 54, 10000 Zagreb, Croatia
| | - A Jay
- LAAS-CNRS, Université de Toulouse, CNRS, 7 Avenue Du Colonel Roche, 31000 Toulouse, France
| | - M Poberžnik
- Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - N Salles
- CNR-IOM/Democritos National Simulation Center, Istituto Officina dei Materiali, c/o SISSA, Via Bonomea 265, IT-34136 Trieste, Italy
| | - N Richard
- CEA, DAM, DIF, F-91297 Arpajon, France
| | - G Landa
- LAAS-CNRS, Université de Toulouse, CNRS, 7 Avenue Du Colonel Roche, 31000 Toulouse, France
| | - N Mousseau
- Département de Physique, Institut Courtois and Regroupement Québécois sur les Matériaux de Pointe, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7, Canada
| | - L Martin-Samos
- CNR-IOM/Democritos National Simulation Center, Istituto Officina dei Materiali, c/o SISSA, Via Bonomea 265, IT-34136 Trieste, Italy
| | - A Hemeryck
- LAAS-CNRS, Université de Toulouse, CNRS, 7 Avenue Du Colonel Roche, 31000 Toulouse, France
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Liu Y, Qi H, Lei M. Elastic Image Pair Method for Finding Transition States on Potential Energy Surfaces Using Only First Derivatives. J Chem Theory Comput 2022; 18:5108-5115. [PMID: 35771528 DOI: 10.1021/acs.jctc.2c00137] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, an elastic image pair (EIP) method is proposed to search transition states between two potential-energy minima using only first derivatives. In this method, two images are generated, and the spring forces are added to the images to control the distance between the two images. Transition states are reached when the force and the distance of the image pair are both converged. A set of test molecules is optimized using the EIP method, which shows its efficiency in transition state searching compared to other methods. This new method is more stable and reliable in finding transition states with much less computations.
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Affiliation(s)
- Yangqiu Liu
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hexiang Qi
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, China
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F L, HEMERYCK A, Landa G, Brut M. Enhancing DFT-based energy landscape exploration by coupling Quantum Mechanics and Static Modes. Phys Chem Chem Phys 2022; 24:12011-12026. [DOI: 10.1039/d1cp03562b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unravelling the atomic scale diffusion that can occur at the surface, at the interface or into the bulk is challenging: multi-scale modelling approach usually requires intensive prospective calculations and moreover...
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Mandelli D, Parrinello M. A modified nudged elastic band algorithm with adaptive spring lengths. J Chem Phys 2021; 155:074103. [PMID: 34418926 DOI: 10.1063/5.0059593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a modified version of the nudged elastic band (NEB) algorithm to find minimum energy paths connecting two known configurations. We show that replacing the harmonic band-energy term with a discretized version of the Onsager-Machlup action leads to a NEB algorithm with adaptive spring lengths that automatically increase the resolution of the minimum energy path around the saddle point of the potential energy surface. The method has the same computational cost per optimization step of the standard NEB algorithm and does not introduce additional parameters. We present applications to the isomerization of alanine dipeptide, the elimination of hydrogen from ethane, and the healing of a 5-77-5 defect in graphene.
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Affiliation(s)
- D Mandelli
- Atomistic Simulations, Italian Institute of Technology, Via Morego, 30 16163 Genova, Italy
| | - M Parrinello
- Atomistic Simulations, Italian Institute of Technology, Via Morego, 30 16163 Genova, Italy
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Klein J, Fleurat-Lessard P, Pilmé J. New insights in chemical reactivity from quantum chemical topology. J Comput Chem 2021; 42:840-854. [PMID: 33660292 DOI: 10.1002/jcc.26504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 01/13/2023]
Abstract
Based on the quantum chemical topology of the modified electron localization function ELFx , an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange-correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first-order variation in the coulomb intermolecular energy defined in terms of the response to changes in the number of electrons. Illustrative examples with the formation of the dative bond B-N involved in the BH3 NH3 molecule and the typical formation of the hydrogen bond in the canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking of Edual onto the DFT intermolecular interaction energy surface calculated between the both reactants. An automated reaction-path algorithm aimed to determine the most favorable relative orientations when the two molecules approach each other is also outlined.
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Affiliation(s)
- Johanna Klein
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, Paris Cedex, France
| | - Paul Fleurat-Lessard
- Université de Bourgogne, UMR CNRS 6302, Université, Bourgogne Franche-Comté (UBFC), Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), 9 avenue Alain Savary, Dijon Cedex, 21078, France
| | - Julien Pilmé
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, Paris Cedex, France
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