Journal ArticleDOI
A climbing image nudged elastic band method for finding saddle points and minimum energy paths
TLDR
In this article, a modification of the nudged elastic band method for finding minimum energy paths is presented, where one of the images is made to climb up along the elastic band to converge rigorously on the highest saddle point.Abstract:
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. Also, variable spring constants are used to increase the density of images near the top of the energy barrier to get an improved estimate of the reaction coordinate near the saddle point. Applications to CH4 dissociative adsorption on Ir~111! and H2 on Si~100! using plane wave based density functional theory are presented. © 2000 American Institute of Physics. @S0021-9606~00!71246-3#read more
Citations
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CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
Design of electrocatalysts for oxygen- and hydrogen-involving energy conversion reactions
TL;DR: The emphasis of this review is on the origin of the electrocatalytic activity of nanostructured catalysts toward a series of key clean energy conversion reactions by correlating the apparent electrode performance with their intrinsic electrochemical properties.
Journal ArticleDOI
The Atomic Simulation Environment - A Python library for working with atoms
Ask Hjorth Larsen,Ask Hjorth Larsen,Jens Jørgen Mortensen,Jakob Blomqvist,Ivano E. Castelli,Rune Christensen,Marcin Dulak,Jesper Friis,Michael N. Groves,Bjørk Hammer,Cory Hargus,Eric D. Hermes,Paul C. Jennings,Peter Bjerre Jensen,James R. Kermode,John R. Kitchin,Esben L. Kolsbjerg,Joseph Kubal,Kristen Kaasbjerg,Steen Lysgaard,Jon Bergmann Maronsson,Tristan Maxson,Thomas Olsen,Lars Pastewka,Andrew A. Peterson,Carsten Rostgaard,Jakob Schiøtz,Ole Schütt,Mikkel Strange,Kristian Sommer Thygesen,Tejs Vegge,Lasse B. Vilhelmsen,Michael Walter,Zhenhua Zeng,Karsten Wedel Jacobsen +34 more
TL;DR: The atomic simulation environment (ASE) provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.
Journal ArticleDOI
Ab Initio Molecular Simulations with Numeric Atom-Centered Orbitals
Volker Blum,Ralf Gehrke,Felix Hanke,Paula Havu,Ville Havu,Xinguo Ren,Karsten Reuter,Matthias Scheffler +7 more
TL;DR: The construction of transferable, hierarchical basis sets are demonstrated, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set, since all basis functions are strictly localized.
Journal ArticleDOI
LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
Yusry O. El-Dib,Aidan P. Thompson,H. Metin Aktulga,Richard A. Berger,Dan S. Bolintineanu,W. Michael Brown,Paul Stewart Crozier,Pieter J. in 't Veld,Axel Kohlmeyer,Stan Gerald Moore,Trung Dac Nguyen,Ray Shan,Mark J. Stevens,Julien Tranchida,Christian Robert Trott,Steven J. Plimpton +15 more
TL;DR: Several of the fundamental algorithms used in LAMMPS are described along with the design strategies which have made it flexible for both users and developers, and some capabilities recently added to the code which were enabled by this flexibility are highlighted.
References
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Journal ArticleDOI
Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set
Georg Kresse,Jürgen Furthmüller +1 more
TL;DR: A detailed description and comparison of algorithms for performing ab-initio quantum-mechanical calculations using pseudopotentials and a plane-wave basis set is presented in this article. But this is not a comparison of our algorithm with the one presented in this paper.
Journal ArticleDOI
Self-Consistent Equations Including Exchange and Correlation Effects
Walter Kohn,L. J. Sham +1 more
TL;DR: In this paper, the Hartree and Hartree-Fock equations are applied to a uniform electron gas, where the exchange and correlation portions of the chemical potential of the gas are used as additional effective potentials.
Journal ArticleDOI
Soft self-consistent pseudopotentials in a generalized eigenvalue formalism.
TL;DR: Novel features are that the pseudopotential itself becomes charge-state dependent, the usual norm-conservation constraint does not apply, and a generalized eigenproblem is introduced.
Journal ArticleDOI
Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
Graeme Henkelman,Hannes Jónsson +1 more
TL;DR: An improved way of estimating the local tangent in the nudged elastic band method for finding minimum energy paths is presented, and examples given where a complementary method, the dimer method, is used to efficiently converge to the saddle point.
Journal ArticleDOI
The Activated Complex in Chemical Reactions
TL;DR: In this paper, the probability of the activated state is calculated using ordinary statistical mechanics, and the probability multiplied by the rate of decomposition gives the specific rate of reaction, and necessary conditions for general statistical treatment to reduce to the usual kinetic treatment are given.
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