Related Publications#
EON is actively used by groups across the world, we limit ourselves to a few here, pull requests are welcome.
Jónsson Group#
Method :: The Gaussian Process Regression accelerated dimer in C++ from Goswami et al. [2.8.0_GMK+25].
Method :: Bayesian Hierarchical measures for benchmarking computational chemistry software by Goswami [2.8.0_Gos25].
Method :: Quaternion-based removal of external degrees of freedom Melander et al. [2.8.0_MLJonsson15].
Application :: Tight-binding charge transfer model Maras et al. [2.8.0_MSTetot+15].
Application :: H diffusion on ice at low temperature Ásgeirsson et al. [2.8.0_AsgeirssonJonssonW17].
Application :: Reassignment of Au cluster magic numbers Garden et al. [2.8.0_GPJonsson18].
Application :: Structure and properties of an edge dislocation in Rutile TiO_2 Maras et al. [2.8.0_MSI+19].
Method :: Energy-weighted springs and eigenvector following for NEB Ásgeirsson et al. [2.8.0_AsgeirssonBB+21].
Application :: Indirect mechanism of Au adatom diffusion on Si(100) Peña-Torres et al. [2.8.0_PenaTorresASJonsson22].
Application :: Reassignment of magic numbers for icosahedral Au clusters Kloppenburg et al. [2.8.0_KPL+22].
Method :: Improved NEB initialization using pair potential surface traversal Schmerwitz et al. [2.8.0_SAsgeirssonJonsson24].
Lab-COSMO#
Demonstration of RO-NEB-CI in Bigi et al. [2.8.0_BAL+25] which covers the metatensor ecosystem.
Henkelman Group#
Method :: Distributed Replica Dynamics Zhang et al. [2.8.0_ZCH15].
Application :: Collective atomic displacements in solid-solid phase transformations Duncan et al. [2.8.0_DHT+16].
Application :: Transformation of close packed beta-W to body centered alpha-W Barmak et al. [2.8.0_BLH+17].
Application :: AKMC for surface segregation in PdAu nanoparticles Li et al. [2.8.0_LLD+19].
Method :: Optimization of fingerprints for neural network potentials Li et al. [2.8.0_LLS+20].
Application :: EAM potential for hydrogen on palladium surfaces Ciufo and Henkelman [2.8.0_CH20].
Method/Review :: Off-Lattice Kinetic Monte Carlo Methods Trochet et al. [2.8.0_TMBelandH20].
Application :: Atomistic mechanisms of binary alloy surface segregation Garza et al. [2.8.0_GLN+22].
Method/Software :: Atom-centered machine-learning force field package Li et al. [2.8.0_LCL+23].
Other Relevant Publications#
Application :: Evaluation of force fields for anthracene crystal growth Grančič et al. [2.8.0_GranvcivcBMC15].
Application :: Diffusion mechanisms in Li-CO2 systems Bunjaku et al. [2.8.0_BPL16].
Method :: Sphere Encapsulated Monte Carlo for large aromatic systems Bowal et al. [2.8.0_BGranvcivcMK19].
Method :: Influence of integration formulations on the FIRE method Shuang et al. [2.8.0_SXS+19].
Application :: Contrasting motif preferences of platinum and gold nanoclusters Lambie et al. [2.8.0_LWB+19].
References#
Katayun Barmak, Jiaxing Liu, Liam Harlan, Penghao Xiao, Juliana Duncan, and Graeme Henkelman. Transformation of topologically close-packed β-W to body-centered cubic α-W: comparison of experiments and computations. Journal of Chemical Physics, 147(15):152709, July 2017. doi:10.1063/1.4995261.
Filippo Bigi, Joseph W. Abbott, Philip Loche, Arslan Mazitov, Davide Tisi, Marcel F. Langer, Alexander Goscinski, Paolo Pegolo, Sanggyu Chong, Rohit Goswami, Sofiia Chorna, Matthias Kellner, Michele Ceriotti, and Guillaume Fraux. Metatensor and metatomic: foundational libraries for interoperable atomistic machine learning. August 2025. arXiv:2508.15704, doi:10.48550/arXiv.2508.15704.
Kimberly Bowal, Peter Grančič, Jacob W. Martin, and Markus Kraft. Sphere encapsulated monte carlo: obtaining minimum energy configurations of large aromatic systems. Journal of Physical Chemistry A, 123(33):7303–7313, August 2019. doi:10.1021/acs.jpca.9b04821.
Teutë Bunjaku, Andreas Pedersen, and Mathieu Luisier. Diffusion mechanisms in Li0.5CoO2—a computational study. Applied Physics Letters, 108(15):153902, April 2016. doi:10.1063/1.4945689.
Ryan A. Ciufo and Graeme Henkelman. Embedded atom method potential for hydrogen on palladium surfaces. Journal of Molecular Modeling, 26(12):1–6, November 2020. doi:10.1007/s00894-020-04588-x.
Juliana Duncan, Ari Harjunmaa, Rye Terrell, Ralf Drautz, Graeme Henkelman, and Jutta Rogal. Collective atomic displacements during complex phase boundary migration in solid-solid phase transformations. Physical Review Letters, 116(3):35701, January 2016. doi:10.1103/PhysRevLett.116.035701.
Anna L. Garden, Andreas Pedersen, and Hannes Jónsson. Reassignment of `magic numbers' for Au clusters of decahedral and FCC structural motifs. Nanoscale, 10(11):5124–5132, 2018. doi:10.1039/C7NR09440J.
Richard B. Garza, Jiyoung Lee, Mai H. Nguyen, Andrew Garmon, Danny Perez, Meng Li, Judith C. Yang, Graeme Henkelman, and Wissam A. Saidi. Atomistic mechanisms of binary alloy surface segregation from nanoseconds to seconds using accelerated dynamics. Journal of Chemical Theory and Computation, 18(7):4447–4455, July 2022. doi:10.1021/acs.jctc.2c00303.
Rohit Goswami. Bayesian hierarchical models for quantitative estimates for performance metrics applied to saddle search algorithms. AIP Advances, 15(8):85210, August 2025. doi:10.1063/5.0283639.
Rohit Goswami, Maxim Masterov, Satish Kamath, Alejandro Pena-Torres, and Hannes Jónsson. Efficient Implementation of Gaussian Process Regression Accelerated Saddle Point Searches with Application to Molecular Reactions. Journal of Chemical Theory and Computation, July 2025. doi:10.1021/acs.jctc.5c00866.
Peter Grančič, Rita Bylsma, Hugo Meekes, and Herma M. Cuppen. Evaluation of all-atom force fields for anthracene crystal growth. Crystal Growth & Design, 15(4):1625–1633, April 2015. doi:10.1021/cg5013507.
Jan Kloppenburg, Andreas Pedersen, Kari Laasonen, Miguel A. Caro, and Hannes Jónsson. Reassignment of magic numbers for icosahedral Au clusters: 310, 564, 928 and 1426. Nanoscale, 14(25):9053–9060, 2022. doi:10.1039/D2NR01763F.
Stephanie G. Lambie, Geoffrey R. Weal, Caroline E. Blackmore, Richard E. Palmer, and Anna L. Garden. Contrasting motif preferences of platinum and gold nanoclusters between 55 and 309 atoms. Nanoscale Advances, 1(6):2416–2425, 2019. doi:10.1039/C9NA00122K.
Lei Li, Ryan A. Ciufo, Jiyoung Lee, Chuan Zhou, Bo Lin, Jaeyoung Cho, Naman Katyal, and Graeme Henkelman. Atom-centered machine-learning force field package. Computer Physics Communications, 292:108883, November 2023. doi:10.1016/j.cpc.2023.108883.
Lei Li, Hao Li, Ieuan D. Seymour, Lucas Koziol, and Graeme Henkelman. Pair-distribution-function guided optimization of fingerprints for atom-centered neural network potentials. The Journal of Chemical Physics, 152(22):224102, June 2020. doi:10.1063/5.0007391.
Lei Li, Xinyu Li, Zhiyao Duan, Randall J. Meyer, Rob Carr, Sumathy Raman, Lucas Koziol, and Graeme Henkelman. Adaptive kinetic monte carlo simulations of surface segregation in PdAu nanoparticles. Nanoscale, 11(21):10524–10535, 2019. doi:10.1039/c9nr01858a.
Emile Maras, Mitsuhiro Saito, Kazutoshi Inoue, Hannes Jónsson, Yuichi Ikuhara, and Keith P. McKenna. Determination of the structure and properties of an edge dislocation in rutile TiO2. Acta Materialia, 163:199–207, January 2019. doi:10.1016/j.actamat.2018.10.015.
Emile Maras, Nicolas Salles, Robert Tétot, Tapio Ala-Nissila, and Hannes Jónsson. Improved tight-binding charge transfer model and calculations of energetics of a step on the rutile TiO\textsubscript 2 (110) surface. Journal of Physical Chemistry C, 119(19):10391–10399, May 2015. doi:10.1021/acs.jpcc.5b01580.
Marko Melander, Kari Laasonen, and Hannes Jónsson. Removing External Degrees of Freedom from Transition-State Search Methods using Quaternions. Journal of Chemical Theory and Computation, 11(3):1055–1062, March 2015. doi:10.1021/ct501155k.
Yorick L. A. Schmerwitz, Vilhjálmur Ásgeirsson, and Hannes Jónsson. Improved Initialization of Optimal Path Calculations Using Sequential Traversal over the Image-Dependent Pair Potential Surface. Journal of Chemical Theory and Computation, 20(1):155–163, January 2024. doi:10.1021/acs.jctc.3c01111.
Fei Shuang, Pan Xiao, Ronghao Shi, Fujiu Ke, and Yilong Bai. Influence of integration formulations on the performance of the fast inertial relaxation engine (FIRE) method. Computational Materials Science, 156:135–141, January 2019. doi:10.1016/j.commatsci.2018.09.049.
Mickaël Trochet, Normand Mousseau, Laurent Karim Béland, and Graeme Henkelman. Off-Lattice Kinetic Monte Carlo Methods. In Wanda Andreoni and Sidney Yip, editors, Handbook of Materials Modeling: Methods: Theory and Modeling, pages 715–743. Springer International Publishing, Cham, 2020. doi:10.1007/978-3-319-44677-6_29.
Liang Zhang, Samuel T. Chill, and Graeme Henkelman. Distributed replica dynamics. Journal of Chemical Physics, 143(17):174112, November 2015. doi:10.1063/1.4934987.
V. Ásgeirsson, H. Jónsson, and K. T. Wikfeldt. Long-Time Scale Simulations of Tunneling-Assisted Diffusion of Hydrogen on Ice Surfaces at Low Temperature. The Journal of Physical Chemistry C, 121(3):1648–1657, January 2017. doi:10.1021/acs.jpcc.6b10636.
Vilhjálmur Ásgeirsson, Benedikt Orri Birgisson, Ragnar Bjornsson, Ute Becker, Frank Neese, Christoph Riplinger, and Hannes Jónsson. Nudged Elastic Band Method for Molecular Reactions Using Energy-Weighted Springs Combined with Eigenvector Following. Journal of Chemical Theory and Computation, 17(8):4929–4945, August 2021. doi:10.1021/acs.jctc.1c00462.
Alejandro Peña-Torres, Abid Ali, Michail Stamatakis, and Hannes Jónsson. Indirect mechanism of Au adatom diffusion on the Si(100) surface. Physical Review B, 105(20):205411, May 2022. doi:10.1103/PhysRevB.105.205411.