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
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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.Abstract:
An improved way of estimating the local tangent in the nudged elastic band method for finding minimum energy paths is presented. In systems where the force along the minimum energy path is large compared to the restoring force perpendicular to the path and when many images of the system are included in the elastic band, kinks can develop and prevent the band from converging to the minimum energy path. We show how the kinks arise and present an improved way of estimating the local tangent which solves the problem. The task of finding an accurate energy and configuration for the saddle point is also discussed and examples given where a complementary method, the dimer method, is used to efficiently converge to the saddle point. Both methods only require the first derivative of the energy and can, therefore, easily be applied in plane wave based density-functional theory calculations. Examples are given from studies of the exchange diffusion mechanism in a Si crystal, Al addimer formation on the Al(100) surfa...read more
Citations
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Journal ArticleDOI
A climbing image nudged elastic band method for finding saddle points and minimum energy paths
TL;DR: 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.
Journal ArticleDOI
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
Advances in methods and algorithms in a modern quantum chemistry program package
Yihan Shao,Laszlo Fusti Molnar,Yousung Jung,Jörg Kussmann,Christian Ochsenfeld,Shawn T. Brown,Andrew T. B. Gilbert,Lyudmila V. Slipchenko,Sergey V. Levchenko,Darragh P. O’Neill,Robert A. DiStasio,Rohini C. Lochan,Tao Wang,Gregory J. O. Beran,Nicholas A. Besley,John M. Herbert,Ching Yeh Lin,Troy Van Voorhis,Siu Hung Chien,Alexander J. Sodt,Ryan P. Steele,Vitaly A. Rassolov,Paul E. Maslen,Prakashan P. Korambath,Ross D. Adamson,Brian Austin,Jon Baker,Edward F. C. Byrd,Holger Dachsel,Robert J. Doerksen,Andreas Dreuw,Barry D. Dunietz,Anthony D. Dutoi,Thomas R. Furlani,Steven R. Gwaltney,Andreas Heyden,So Hirata,Chao-Ping Hsu,Gary S. Kedziora,Rustam Z. Khalliulin,Phil Klunzinger,Aaron M. Lee,Michael S. Lee,WanZhen Liang,Itay Lotan,Nikhil Nair,Baron Peters,Emil Proynov,Piotr A. Pieniazek,Young Min Rhee,Jim Ritchie,Edina Rosta,C. David Sherrill,Andrew C. Simmonett,Joseph E. Subotnik,H. Lee Woodcock,Weimin Zhang,Alexis T. Bell,Arup K. Chakraborty,Daniel M. Chipman,Frerich J. Keil,Arieh Warshel,Warren J. Hehre,Henry F. Schaefer,Jing Kong,Anna I. Krylov,Peter Gill,Martin Head-Gordon,Martin Head-Gordon +68 more
TL;DR: Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.
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.
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
Modeling solid-state chemistry: Interatomic potentials for multicomponent systems
TL;DR: In this article, a general form for an empirical interatomic potential for multicomponent systems is proposed, which interpolates between potentials for the respective elements to treat heteronuclear bonds.
Journal ArticleDOI
Density Functional Theory of Electronic Structure
TL;DR: In this article, the current status and trends of approximation methods (local density and generalized gradient approximations, hybrid methods) and the new light which density functional theory has been shedding on important concepts like electronegativity, hardness, and chemical reactivity index are discussed.
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