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Paths to which the nudged elastic band converges

Daniel Sheppard, Graeme Henkelman
2011 Journal of Computational Chemistry  
A recent letter to the editor (Quapp and Bofill, J Comput Chem 2010, 31, 2526) claims that the nudged elastic band (NEB) method can converge toward gradient extremal paths and not to steepest descent paths  ...  to the path.  ...  Wolfgang Quapp and Antoni Aguilar-Mogas for supplying their NEB codes and also the anonymous reviewers for their helpful comments.  ... 
doi:10.1002/jcc.21748 pmid:21328409 fatcat:yxiom4lds5drhdaksmjh7oswga

Low-Scaling Algorithm for Nudged Elastic Band Calculations Using a Surrogate Machine Learning Model

José A. Garrido Torres, Paul C. Jennings, Martin H. Hansen, Jacob R. Boes, Thomas Bligaard
2019 Physical Review Letters  
In our surrogate model approach, the cost of converging the elastic band no longer scales with the number of moving images on the path.  ...  We present the incorporation of a surrogate Gaussian Process Regression (GPR) atomistic model to greatly accelerate the rate of convergence of classical Nudged Elastic Band (NEB) calculations.  ...  The Nudged Elastic Band (NEB) algorithm is the most popular method for calculating transition states in chemical systems [1] [2] [3] .  ... 
doi:10.1103/physrevlett.122.156001 fatcat:uj4leuyu7rbbbnjga3zvnpyrm4

A doubly nudged elastic band method for finding transition states

Semen A. Trygubenko, David J. Wales
2004 Journal of Chemical Physics  
A modification of the nudged elastic band (NEB) method is presented that enables stable optimisations to be run using both the limited-memory quasi-Newton (L-BFGS) and slow-response quenched velocity Verlet  ...  We find that the fastest DNEB approach (DNEB/L-BFGS) can be quicker by up to two orders of magnitude.  ...  1 . 1 Graphical representation of the nudged elastic band approach.  ... 
doi:10.1063/1.1636455 pmid:15268346 fatcat:wp6njlkbw5gvvdidihrb26yrea

A growing string method for determining transition states: Comparison to the nudged elastic band and string methods

Baron Peters, Andreas Heyden, Alexis T. Bell, Arup Chakraborty
2004 Journal of Chemical Physics  
than the string method or the nudged elastic band method.  ...  This paper compares the growing string method to the string method and to the nudged elastic band method using the alanine dipeptide rearrangement as an example.  ...  The authors would like to thank Professor Martin Head-Gordon and Q-Chem ͑Ref. 36͒ for supplying the electronic structure code used in this work.  ... 
doi:10.1063/1.1691018 pmid:15267702 fatcat:bchqlrf4bzfeziwsfllkhyrgpi

Nudged elastic band calculations accelerated with Gaussian process regression

Olli-Pekka Koistinen, Freyja B. Dagbjartsdóttir, Vilhjálmur Ásgeirsson, Aki Vehtari, Hannes Jónsson
2017 Journal of Chemical Physics  
Such paths are frequently calculated using the nudged elastic band method, where an initial path is iteratively shifted to the nearest minimum energy path.  ...  as input in the minimum energy path calculation, thereby improving stability and reducing the number of iterations needed for convergence.  ...  We acknowledge the computational resources provided by the Aalto Science-IT project and the Computer Services of the University of Iceland.  ... 
doi:10.1063/1.4986787 pmid:29055305 fatcat:ybmowbk57fdvzaoyzceaf5o3eq

A climbing image nudged elastic band method for finding saddle points and minimum energy paths

Graeme Henkelman, Blas P. Uberuaga, Hannes Jónsson
2000 Journal of Chemical Physics  
A modification of the nudged elastic band method for finding minimum energy paths is presented.  ...  One of the images is made to climb up along the elastic band to converge rigorously on the highest saddle point.  ...  An essential feature of the NEB method, which distinguishes it from other elastic band methods, 23-25 is a force projection which ensures that the spring forces do not interfere with the convergence of  ... 
doi:10.1063/1.1329672 fatcat:ooniihnpvfdlvachyhak4gdez4

Nudged-elastic band method with two climbing images: Finding transition states in complex energy landscapes

Nikolai A. Zarkevich, Duane D. Johnson
2015 Journal of Chemical Physics  
The nudged-elastic band (NEB) method is modified with concomitant two climbing images (C2-NEB) to find a transition state (TS) in complex energy landscapes, such as those with serpentine minimal energy  ...  path (MEP).  ...  INTRODUCTION The Nudged-Elastic band (NEB) method has become a workhorse in determining the transition states (TS) and minimum-energy paths (MEPs) for both fixed-cell 2 and generalized solid-state transformations  ... 
doi:10.1063/1.4905209 pmid:25591337 fatcat:bmspirdd3vb27bxuapemloatra

PASTA: Python Algorithms for Searching Transition stAtes

Sudipta Kundu, Satadeep Bhattacharjee, Seung-Cheol Lee, Manish Jain
2018 Computer Physics Communications  
The module is written in python and can perform nudged elastic band, climbing image nudged elastic band and automated nudged elastic band calculations.  ...  Chemical reactions are often associated with an energy barrier along the reaction pathway which hinders the spontaneity of the reaction.  ...  We thank the Supercomputer Education and Research Centre (SERC) at Indian Institute of Science (IISc) and Korea Institute of Science and Technology (KIST) for providing the computational facilities.  ... 
doi:10.1016/j.cpc.2018.06.026 fatcat:uy7q3x44ivfmtassakvhppetzy

Adaptive nudged elastic band approach for transition state calculation

P. Maragakis, Stefan A. Andreev, Yisroel Brumer, David R. Reichman, Efthimios Kaxiras
2002 Journal of Chemical Physics  
Our algorithm is a variation of the well-established nudged elastic band method and leads to significant improvements in efficiency and accuracy.  ...  We incorporated the climbing image extension of the nudged elastic band method and compared it against the original approach on two-dimensional model potential energy surfaces.  ...  The climbing image nudged elastic band ͑CI-NEB͒ method 7 is an improvement of the original algorithm in which one of the images climbs up to the exact saddle point.  ... 
doi:10.1063/1.1495401 fatcat:mrtwnuwd65dfjiq7qyxk6223x4

A space–time-ensemble parallel nudged elastic band algorithm for molecular kinetics simulation

Aiichiro Nakano
2008 Computer Physics Communications  
A directionally heated nudged elastic band method is introduced to search for thermally activated events without the knowledge of final states, which is then applied to an ensemble of bands in a path ensemble  ...  A scalable parallel algorithm has been designed to study long-time dynamics of many-atom systems based on the nudged elastic band method, which performs mutually constrained molecular dynamics simulations  ...  Numerical tests were performed at the University of Southern California using  ... 
doi:10.1016/j.cpc.2007.09.011 fatcat:5img3cgvtvayvdgsacax7dcdga

Optimization methods for finding minimum energy paths

Daniel Sheppard, Rye Terrell, Graeme Henkelman
2008 Journal of Chemical Physics  
We compare the nudged elastic band ͑NEB͒, doubly nudged elastic band, string, and simplified string methods, each with a set of commonly used optimizers.  ...  path.  ...  ACKNOWLEDGMENTS We would like to thank David Wales and Andri Arnaldsson for helpful comments and suggestions. This work was supported by the National Science Foundation from a NSF-CAREER award ͑No.  ... 
doi:10.1063/1.2841941 pmid:18397052 fatcat:6kqjmww6qrg3jjug2zodcmilde

On the Possible Coordination on a 3MC State Itself? Mechanistic Investigation Using DFT-Based Methods

Adrien Soupart, Fabienne Alary, Jean-Louis Heully, Isabelle M. Dixon
2020 Inorganics  
As estimated from Nudged Elastic Band calculations, the energy barrier along the minimum energy path is 20 kcal/mol.  ...  The approach of the NCMe lone pair contributes to destabilizing the dσ* orbital by electrostatic repulsion.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/inorganics8020015 fatcat:la3u3as6avgwblepupndg3rzdm

Optimal Paths Between Parameter Estimates in Non-linear ODE Systems Using the Nudged Elastic Band Method

Christian Tönsing, Jens Timmer, Clemens Kreutz
2019 Frontiers in Physics  
For optimal path finding, we adapt the nudged elastic band (NEB) method and apply our approach to a benchmark model with a suboptimal optimization result, which yields a preferable grouping of fits afterwards  ...  as typically presumed, or if they are only a result of incompletely converged optimization runs and could be merged by a connecting path to a single optimum by e.g., fine-tuning of the numeric algorithms  ...  Nudged Elastic Band Method Spring methods for path finding, are characterized by an elastic band or a chain-of-states which is applied to a high-dimensional landscape and converges to an optimal path between  ... 
doi:10.3389/fphy.2019.00149 fatcat:n5mlued6n5ejrly3l67nf5f5wu

Finding transition states for crystalline solid-solid phase transformations

K. J. Caspersen, E. A. Carter
2005 Proceedings of the National Academy of Sciences of the United States of America  
Abbreviations: CINEB, climbing image-nudged elastic band; EB, elastic band; MEP, minimum energy path; NEB, nudged elastic band; OF DFT, orbital-free density functional theory; SSNEB, solid-state nudged  ...  II) to the PNAS office.  ...  Validation To validate this new method, which we term the solid-state-nudged elastic band (SSNEB) technique, we investigate solid-solid phase transformations in lithium.  ... 
doi:10.1073/pnas.0408127102 pmid:15863621 pmcid:PMC1100746 fatcat:garv5fx7krfpzcarqutmmw2gii

Twin nucleation in Ti: A study using nudged elastic band (NEB) method [article]

Deepesh Giri, Haitham El Kadiri, Christopher Barrett
2022 arXiv   pre-print
We performed atomistic calculations based on the nudged elastic band method to identify the minimum energy path and activation energy associated with 10-12 twin nucleation in titanium.  ...  The challenge resides mainly in the biased regional lattice transformation associated with twin formation in defiance of its obedience to a threshold stress law which could be fulfilled in regions where  ...  NEB overcomes these shortcomings by using force projection scheme to converge the elastic band to the MEP [31] . There are other available schemes which converge the elastic band to the MEP.  ... 
arXiv:2201.12444v1 fatcat:fqnlz3va55dfpozj6cvaln6hpa
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