LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Thompson, Aidan P.; Aktulga, H. Metin; Berger, Richard; Bolintineanu, Dan S.; Brown, W. Michael; Crozier, Paul S.; in 't Veld, Pieter J.; Kohlmeyer, Axel; Moore, Stan G.; Nguyen, Trung Dac; Shan, Ray; Stevens, Mark J.; Tranchida, Julien; Trott, Christian; Plimpton, Steven J.

doi:10.1016/j.cpc.2021.108171

Title: LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Journal Article · Tue Feb 01 00:00:00 EST 2022 · Computer Physics Communications

DOI:https://doi.org/10.1016/j.cpc.2021.108171· OSTI ID:1821775

;

; Bolintineanu, Dan S.; Brown, W. Michael;

;

; Moore, Stan G.; Nguyen, Trung Dac; Shan, Ray; Stevens, Mark J.; Tranchida, Julien; Trott, Christian; Plimpton, Steven J.

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesoscale to continuum. Reasons for its popularity are that it provides a wide variety of particle interaction models for different materials, that it runs on any platform from a single CPU core to the largest supercomputers with accelerators, and that it gives users control over simulation details, either via the input script or by adding code for new interatomic potentials, constraints, diagnostics, or other features needed for their models. As a result, hundreds of people have contributed new capabilities to LAMMPS and it has grown from fifty thousand lines of code in 2004 to a million lines today. In this paper 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. We also highlight some capabilities recently added to the code which were enabled by this flexibility, including dynamic load balancing, on-the-fly visualization, magnetic spin dynamics models, and quantum-accuracy machine learning interatomic potentials.

View Journal Article

Cite

Export

Save

Research Organization:: Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Fusion Energy Sciences (FES)

Grant/Contract Number:: NA0003525; AC02-06CH11357

OSTI ID:: 1821775

Alternate ID(s):: OSTI ID: 1872034

Report Number(s):: SAND2022-6924J; S0010465521002836; 108171; PII: S0010465521002836

Journal Information:: Computer Physics Communications, Journal Name: Computer Physics Communications Vol. 271 Journal Issue: C; ISSN 0010-4655

Publisher:: ElsevierCopyright Statement

Country of Publication:: Netherlands

Language:: English

References (195)

Direct simulation Monte Carlo on petaflop supercomputers and beyond Plimpton, S. J.; Moore, S. G.; Borner, A. Physics of Fluids, Vol. 31, Issue 8 https://doi.org/10.1063/1.5108534	journal	August 2019
Incorporating surface polarization effects into large-scale coarse-grained Molecular Dynamics simulation Nguyen, Trung Dac; Li, Honghao; Bagchi, Debarshee Computer Physics Communications, Vol. 241 https://doi.org/10.1016/j.cpc.2019.03.006	journal	August 2019
Shell model simulations by adiabatic dynamics Mitchell, P. J.; Fincham, D. Journal of Physics: Condensed Matter, Vol. 5, Issue 8 https://doi.org/10.1088/0953-8984/5/8/006	journal	February 1993
Vectorized link cell Fortran code for molecular dynamics simulations for a large number of particles Grest, Gary S.; Dünweg, Burkhard; Kremer, Kurt Computer Physics Communications, Vol. 55, Issue 3 https://doi.org/10.1016/0010-4655(89)90125-2	journal	October 1989
Probing eukaryotic cell mechanics via mesoscopic simulations Lykov, Kirill; Nematbakhsh, Yasaman; Shang, Menglin PLOS Computational Biology, Vol. 13, Issue 9 https://doi.org/10.1371/journal.pcbi.1005726	journal	September 2017
VORO++ : A three-dimensional Voronoi cell library in C++ Rycroft, Chris H. Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 19, Issue 4 https://doi.org/10.1063/1.3215722	journal	December 2009
Electronegativity: The density functional viewpoint Parr, Robert G.; Donnelly, Robert A.; Levy, Mel The Journal of Chemical Physics, Vol. 68, Issue 8 https://doi.org/10.1063/1.436185	journal	April 1978
Diffusion in Lennard‐Jones fluids using dual control volume grand canonical molecular dynamics simulation (DCV‐GCMD) Heffelfinger, Grant S.; Swol, Frank van The Journal of Chemical Physics, Vol. 100, Issue 10 https://doi.org/10.1063/1.466849	journal	May 1994
Sequence-dependent thermodynamics of a coarse-grained DNA model Šulc, Petr; Romano, Flavio; Ouldridge, Thomas E. The Journal of Chemical Physics, Vol. 137, Issue 13 https://doi.org/10.1063/1.4754132	journal	October 2012
Moment Tensor Potentials: A Class of Systematically Improvable Interatomic Potentials Shapeev, Alexander V. Multiscale Modeling & Simulation, Vol. 14, Issue 3 https://doi.org/10.1137/15M1054183	journal	January 2016
CHARMM: The biomolecular simulation program Brooks, B. R.; Brooks, C. L.; Mackerell, A. D. Journal of Computational Chemistry, Vol. 30, Issue 10 https://doi.org/10.1002/jcc.21287	journal	July 2009
A climbing image nudged elastic band method for finding saddle points and minimum energy paths Henkelman, Graeme; Uberuaga, Blas P.; Jónsson, Hannes The Journal of Chemical Physics, Vol. 113, Issue 22, p. 9901-9904 https://doi.org/10.1063/1.1329672	journal	December 2000
New empirical approach for the structure and energy of covalent systems Tersoff, J. Physical Review B, Vol. 37, Issue 12 https://doi.org/10.1103/PhysRevB.37.6991	journal	April 1988
Modified embedded-atom potentials for cubic materials and impurities Baskes, M. I. Physical Review B, Vol. 46, Issue 5 https://doi.org/10.1103/PhysRevB.46.2727	journal	August 1992
Spin-lattice model for cubic crystals Nieves, P.; Tranchida, J.; Arapan, S. Physical Review B, Vol. 103, Issue 9 https://doi.org/10.1103/PhysRevB.103.094437	journal	March 2021
Extending the accuracy of the SNAP interatomic potential form Wood, Mitchell A.; Thompson, Aidan P. The Journal of Chemical Physics, Vol. 148, Issue 24 https://doi.org/10.1063/1.5017641	journal	June 2018
Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm Lamoureux, Guillaume; Roux, Benoı̂t The Journal of Chemical Physics, Vol. 119, Issue 6 https://doi.org/10.1063/1.1589749	journal	August 2003
Dynamics of entangled linear polymer melts: A molecular‐dynamics simulation Kremer, Kurt; Grest, Gary S. The Journal of Chemical Physics, Vol. 92, Issue 8 https://doi.org/10.1063/1.458541	journal	April 1990
Importance of corners in fracture of highly crosslinked polymeric adhesives Stevens, Mark J. The Journal of Chemical Physics, Vol. 149, Issue 17 https://doi.org/10.1063/1.5055243	journal	November 2018
Temperature-accelerated dynamics for simulation of infrequent events So/rensen, Mads R.; Voter, Arthur F. The Journal of Chemical Physics, Vol. 112, Issue 21 https://doi.org/10.1063/1.481576	journal	June 2000
Probing the limits of metal plasticity with molecular dynamics simulations Zepeda-Ruiz, Luis A.; Stukowski, Alexander; Oppelstrup, Tomas Nature, Vol. 550, Issue 7677 https://doi.org/10.1038/nature23472	journal	September 2017
Large-Scale Molecular-Dynamics Simulation of 19 Billion Particles Kadau, Kai; Germann, Timothy C.; Lomdahl, Peter S. International Journal of Modern Physics C, Vol. 15, Issue 01 https://doi.org/10.1142/S0129183104005590	journal	January 2004
Equilibration of long chain polymer melts in computer simulations Auhl, Rolf; Everaers, Ralf; Grest, Gary S. The Journal of Chemical Physics, Vol. 119, Issue 24 https://doi.org/10.1063/1.1628670	journal	December 2003
Large-scale, long-term nonadiabatic electron molecular dynamics for describing material properties and phenomena in extreme environments Jaramillo-Botero, Andres; Su, Julius; Qi, An Journal of Computational Chemistry, Vol. 32, Issue 3 https://doi.org/10.1002/jcc.21637	journal	September 2010
Classical atomistic simulations of surfaces and heterogeneous interfaces with the charge-optimized many body (COMB) potentials Liang, Tao; Shan, Tzu-Ray; Cheng, Yu-Ting Materials Science and Engineering: R: Reports, Vol. 74, Issue 9 https://doi.org/10.1016/j.mser.2013.07.001	journal	September 2013
Smoothed Particle Hydrodynamics and Its Diverse Applications Monaghan, J. J. Annual Review of Fluid Mechanics, Vol. 44, Issue 1 https://doi.org/10.1146/annurev-fluid-120710-101220	journal	January 2012
A two-temperature model of radiation damage in α-quartz Phillips, Carolyn L.; Magyar, Rudolph J.; Crozier, Paul S. The Journal of Chemical Physics, Vol. 133, Issue 14 https://doi.org/10.1063/1.3481356	journal	October 2010
Charge-optimized many-body potential for the hafnium/hafnium oxide system Shan, Tzu-Ray; Devine, Bryce D.; Kemper, Travis W. Physical Review B, Vol. 81, Issue 12 https://doi.org/10.1103/PhysRevB.81.125328	journal	March 2010
Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid Mackay, F. E.; Ollila, S. T. T.; Denniston, C. Computer Physics Communications, Vol. 184, Issue 8 https://doi.org/10.1016/j.cpc.2013.03.024	journal	August 2013
Development and application of a particle-particle particle-mesh Ewald method for dispersion interactions Isele-Holder, Rolf E.; Mitchell, Wayne; Ismail, Ahmed E. The Journal of Chemical Physics, Vol. 137, Issue 17 https://doi.org/10.1063/1.4764089	journal	November 2012
Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins Shi, Yue; Xia, Zhen; Zhang, Jiajing Journal of Chemical Theory and Computation, Vol. 9, Issue 9 https://doi.org/10.1021/ct4003702	journal	August 2013
Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants Shinoda, W.; DeVane, R.; Klein, M. L. Molecular Simulation, Vol. 33, Issue 1-2 https://doi.org/10.1080/08927020601054050	journal	January 2007
ReaxFF _SiO Reactive Force Field for Silicon and Silicon Oxide Systems van Duin, Adri C. T.; Strachan, Alejandro; Stewman, Shannon The Journal of Physical Chemistry A, Vol. 107, Issue 19 https://doi.org/10.1021/jp0276303	journal	May 2003
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals Daw, Murray S.; Baskes, M. I. Physical Review B, Vol. 29, Issue 12 https://doi.org/10.1103/PhysRevB.29.6443	journal	June 1984
A reactive potential for hydrocarbons with intermolecular interactions Stuart, Steven J.; Tutein, Alan B.; Harrison, Judith A. The Journal of Chemical Physics, Vol. 112, Issue 14 https://doi.org/10.1063/1.481208	journal	April 2000
Application of atomic stress to compute heat flux via molecular dynamics for systems with many-body interactions Surblys, Donatas; Matsubara, Hiroki; Kikugawa, Gota Physical Review E, Vol. 99, Issue 5 https://doi.org/10.1103/PhysRevE.99.051301	journal	May 2019
A Computational Algorithm to Produce Virtual X-ray and Electron Diffraction Patterns from Atomistic Simulations Coleman, Shawn P.; Sichani, Mehrdad M.; Spearot, Douglas E. JOM, Vol. 66, Issue 3 https://doi.org/10.1007/s11837-013-0829-3	journal	January 2014
A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity Müller-Plathe, Florian The Journal of Chemical Physics, Vol. 106, Issue 14 https://doi.org/10.1063/1.473271	journal	April 1997
Interaction potentials for soft and hard ellipsoids Everaers, R.; Ejtehadi, M. R. Physical Review E, Vol. 67, Issue 4 https://doi.org/10.1103/PhysRevE.67.041710	journal	April 2003
Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces Behler, Jörg; Parrinello, Michele Physical Review Letters, Vol. 98, Issue 14 https://doi.org/10.1103/PhysRevLett.98.146401	journal	April 2007
Automated scientific software scripting with SWIG Beazley, D. M. Future Generation Computer Systems, Vol. 19, Issue 5 https://doi.org/10.1016/S0167-739X(02)00171-1	journal	July 2003
Systematic analysis of local atomic structure combined with 3D computer graphics Faken, Daniel; Jónsson, Hannes Computational Materials Science, Vol. 2, Issue 2 https://doi.org/10.1016/0927-0256(94)90109-0	journal	March 1994
Perspective: Coarse-grained models for biomolecular systems Noid, W. G. The Journal of Chemical Physics, Vol. 139, Issue 9 https://doi.org/10.1063/1.4818908	journal	September 2013
Gaussian Approximation Potentials: The Accuracy of Quantum Mechanics, without the Electrons Bartók, Albert P.; Payne, Mike C.; Kondor, Risi Physical Review Letters, Vol. 104, Issue 13 https://doi.org/10.1103/PhysRevLett.104.136403	journal	April 2010
Group-theoretical high-order rotational invariants for structural representations: Application to linearized machine learning interatomic potential Seko, Atsuto; Togo, Atsushi; Tanaka, Isao Physical Review B, Vol. 99, Issue 21 https://doi.org/10.1103/PhysRevB.99.214108	journal	June 2019
Constant-stress Hugoniostat method for following the dynamical evolution of shocked matter Ravelo, R.; Holian, B.; Germann, T. Physical Review B, Vol. 70, Issue 1 https://doi.org/10.1103/PhysRevB.70.014103	journal	July 2004
Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids Müller-Plathe, Florian Physical Review E, Vol. 59, Issue 5 https://doi.org/10.1103/PhysRevE.59.4894	journal	May 1999
Phonon dispersion measured directly from molecular dynamics simulations Kong, Ling Ti Computer Physics Communications, Vol. 182, Issue 10 https://doi.org/10.1016/j.cpc.2011.04.019	journal	October 2011
The Design and Implementation of FFTW3 Frigo, M.; Johnson, S. G. Proceedings of the IEEE, Vol. 93, Issue 2 https://doi.org/10.1109/JPROC.2004.840301	journal	February 2005
A multiscale coarse-grained model of the SARS-CoV-2 virion Yu, Alvin; Pak, Alexander J.; He, Peng Biophysical Journal, Vol. 120, Issue 6 https://doi.org/10.1016/j.bpj.2020.10.048	journal	March 2021
A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons Brenner, Donald W.; Shenderova, Olga A.; Harrison, Judith A. Journal of Physics: Condensed Matter, Vol. 14, Issue 4 https://doi.org/10.1088/0953-8984/14/4/312	journal	January 2002
Performance and Cost Assessment of Machine Learning Interatomic Potentials Zuo, Yunxing; Chen, Chi; Li, Xiangguo The Journal of Physical Chemistry A, Vol. 124, Issue 4 https://doi.org/10.1021/acs.jpca.9b08723	journal	October 2019
Simulating Microscopic Hydrodynamic Phenomena with Dissipative Particle Dynamics Hoogerbrugge, P. J.; Koelman, J. M. V. A. Europhysics Letters (EPL), Vol. 19, Issue 3 https://doi.org/10.1209/0295-5075/19/3/001	journal	June 1992
Fast and robust algorithm for energy minimization of spin systems applied in an analysis of high temperature spin configurations in terms of skyrmion density Ivanov, A. V.; Uzdin, V. M.; Jónsson, H. Computer Physics Communications, Vol. 260 https://doi.org/10.1016/j.cpc.2020.107749	journal	March 2021
Modeling chemical reactions in classical molecular dynamics simulations Gissinger, Jacob R.; Jensen, Benjamin D.; Wise, Kristopher E. Polymer, Vol. 128 https://doi.org/10.1016/j.polymer.2017.09.038	journal	October 2017
P3M algorithm for dipolar interactions Cerdà, Juan J.; Ballenegger, V.; Lenz, O. The Journal of Chemical Physics, Vol. 129, Issue 23 https://doi.org/10.1063/1.3000389	journal	December 2008
Uncertainty quantification in molecular simulations with dropout neural network potentials Wen, Mingjian; Tadmor, Ellad B. npj Computational Materials, Vol. 6, Issue 1 https://doi.org/10.1038/s41524-020-00390-8	journal	August 2020
Temperature-Dependent Elasticity of a Semicrystalline Interphase Composed of Freely Rotating Chains in 't Veld, Pieter J.; Rutledge, Gregory C. Macromolecules, Vol. 36, Issue 19 https://doi.org/10.1021/ma0346658	journal	September 2003
The Amber biomolecular simulation programs Case, David A.; Cheatham, Thomas E.; Darden, Tom Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20290	journal	January 2005
Using metadynamics to explore complex free-energy landscapes Bussi, Giovanni; Laio, Alessandro Nature Reviews Physics, Vol. 2, Issue 4 https://doi.org/10.1038/s42254-020-0153-0	journal	March 2020
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation Ren, Pengyu; Ponder, Jay W. The Journal of Physical Chemistry B, Vol. 107, Issue 24 https://doi.org/10.1021/jp027815+	journal	May 2003
How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines Deserno, Markus; Holm, Christian The Journal of Chemical Physics, Vol. 109, Issue 18 https://doi.org/10.1063/1.477414	journal	November 1998
Analytic bond-order potentials beyond Tersoff-Brenner. I. Theory Pettifor, D. G.; Oleinik, I. I. Physical Review B, Vol. 59, Issue 13 https://doi.org/10.1103/PhysRevB.59.8487	journal	April 1999
Neural network potential from bispectrum components: A case study on crystalline silicon Yanxon, Howard; Zagaceta, David; Wood, Brandon C. The Journal of Chemical Physics, Vol. 153, Issue 5 https://doi.org/10.1063/5.0014677	journal	August 2020
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation Chenoweth, Kimberly; van Duin, Adri C. T.; Goddard, William A. The Journal of Physical Chemistry A, Vol. 112, Issue 5 https://doi.org/10.1021/jp709896w	journal	February 2008
Peridynamic model for microballistic perforation of multilayer graphene Silling, Stewart A.; Fermen-Coker, Müge Theoretical and Applied Fracture Mechanics, Vol. 113 https://doi.org/10.1016/j.tafmec.2021.102947	journal	June 2021
Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials Thompson, A. P.; Swiler, L. P.; Trott, C. R. Journal of Computational Physics, Vol. 285 https://doi.org/10.1016/j.jcp.2014.12.018	journal	March 2015
Reversible multiple time scale molecular dynamics Tuckerman, M.; Berne, B. J.; Martyna, G. J. The Journal of Chemical Physics, Vol. 97, Issue 3 https://doi.org/10.1063/1.463137	journal	August 1992
Models, algorithms and validation for opensource DEM and CFD-DEM Kloss, Christoph; Goniva, Christoph; Hager, Alice Progress in Computational Fluid Dynamics, An International Journal, Vol. 12, Issue 2/3 https://doi.org/10.1504/PCFD.2012.047457	journal	January 2012
Structural characterization of deformed crystals by analysis of common atomic neighborhood Tsuzuki, Helio; Branicio, Paulo S.; Rino, José P. Computer Physics Communications, Vol. 177, Issue 6 https://doi.org/10.1016/j.cpc.2007.05.018	journal	September 2007
Mesoscopic model for solvent dynamics Malevanets, Anatoly; Kapral, Raymond The Journal of Chemical Physics, Vol. 110, Issue 17 https://doi.org/10.1063/1.478857	journal	May 1999
A Gay–Berne potential for dissimilar biaxial particles Berardi, Roberto; Fava, Carlo; Zannoni, Claudio Chemical Physics Letters, Vol. 297, Issue 1-2 https://doi.org/10.1016/S0009-2614(98)01090-2	journal	November 1998
Evidence for percolation diffusion of cations and reordering in disordered pyrochlore from accelerated molecular dynamics Perriot, Romain; Uberuaga, Blas P.; Zamora, Richard J. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00708-z	journal	September 2017
Empirical variable-charge models for titanium oxides: A study in transferability Thomas, B. S.; Marks, N. A.; Begg, B. D. Physical Review B, Vol. 69, Issue 14 https://doi.org/10.1103/PhysRevB.69.144122	journal	April 2004
Comparison of modern Langevin integrators for simulations of coarse-grained polymer melts Finkelstein, J.; Fiorin, G.; Seibold, B. Molecular Physics, Vol. 118, Issue 6 https://doi.org/10.1080/00268976.2019.1649493	journal	August 2019
Implementing molecular dynamics on hybrid high performance computers – short range forces Brown, W. Michael; Wang, Peng; Plimpton, Steven J. Computer Physics Communications, Vol. 182, Issue 4 https://doi.org/10.1016/j.cpc.2010.12.021	journal	April 2011
Efficient particle labeling in atomistic simulations Meloni, Simone; Rosati, Mario; Colombo, Luciano The Journal of Chemical Physics, Vol. 126, Issue 12 https://doi.org/10.1063/1.2719690	journal	March 2007
REACTER: A Heuristic Method for Reactive Molecular Dynamics Gissinger, Jacob R.; Jensen, Benjamin D.; Wise, Kristopher E. Macromolecules, Vol. 53, Issue 22 https://doi.org/10.1021/acs.macromol.0c02012	journal	November 2020
Accurate and efficient methods for modeling colloidal mixtures in an explicit solvent using molecular dynamics in 't Veld, Pieter J.; Plimpton, Steven J.; Grest, Gary S. Computer Physics Communications, Vol. 179, Issue 5 https://doi.org/10.1016/j.cpc.2008.03.005	journal	September 2008
Electric and antiferromagnetic chiral textures at multiferroic domain walls Chauleau, J. -Y.; Chirac, T.; Fusil, S. Nature Materials, Vol. 19, Issue 4 https://doi.org/10.1038/s41563-019-0516-z	journal	November 2019
Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA Mashayak, S. Y.; Jochum, Mara N.; Koschke, Konstantin PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0131754	journal	July 2015
Anomalous collapses of Nares Strait ice arches leads to enhanced export of Arctic sea ice Moore, G. W. K.; Howell, S. E. L.; Brady, M. Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-020-20314-w	journal	January 2021
Robust structural identification via polyhedral template matching Larsen, Peter Mahler; Schmidt, Søren; Schiøtz, Jakob Modelling and Simulation in Materials Science and Engineering, Vol. 24, Issue 5 https://doi.org/10.1088/0965-0393/24/5/055007	journal	May 2016
Direct simulation Monte Carlo investigation of the Richtmyer-Meshkov instability Gallis, M. A.; Koehler, T. P.; Torczynski, J. R. Physics of Fluids, Vol. 27, Issue 8 https://doi.org/10.1063/1.4928338	journal	August 2015
On the nature of the magnetocaloric effect of the first-order magnetostructural transition Gschneidner, K. A.; Mudryk, Y.; Pecharsky, V. K. Scripta Materialia, Vol. 67, Issue 6 https://doi.org/10.1016/j.scriptamat.2011.12.042	journal	September 2012
DFTB+, a software package for efficient approximate density functional theory based atomistic simulations Hourahine, B.; Aradi, B.; Blum, V. The Journal of Chemical Physics, Vol. 152, Issue 12 https://doi.org/10.1063/1.5143190	journal	March 2020
Molecular dynamics of polymeric systems Bishop, Marvin; Kalos, M. H.; Frisch, H. L. The Journal of Chemical Physics, Vol. 70, Issue 3 https://doi.org/10.1063/1.437567	journal	February 1979
The potential of atomistic simulations and the knowledgebase of interatomic models Tadmor, E. B.; Elliott, R. S.; Sethna, J. P. JOM, Vol. 63, Issue 7 https://doi.org/10.1007/s11837-011-0102-6	journal	July 2011
LAMMPS implementation of rapid artificial neural network derived interatomic potentials Dickel, D.; Nitol, M.; Barrett, C. D. Computational Materials Science, Vol. 196 https://doi.org/10.1016/j.commatsci.2021.110481	journal	August 2021
Dynamical fluctuating charge force fields: Application to liquid water Rick, Steven W.; Stuart, Steven J.; Berne, B. J. The Journal of Chemical Physics, Vol. 101, Issue 7 https://doi.org/10.1063/1.468398	journal	October 1994
A method for accelerating the molecular dynamics simulation of infrequent events Voter, Arthur F. The Journal of Chemical Physics, Vol. 106, Issue 11 https://doi.org/10.1063/1.473503	journal	March 1997
A smooth particle mesh Ewald method Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L. The Journal of Chemical Physics, Vol. 103, Issue 19 https://doi.org/10.1063/1.470117	journal	November 1995
Correlations in the Motion of Atoms in Liquid Argon Rahman, A. Physical Review, Vol. 136, Issue 2A https://doi.org/10.1103/PhysRev.136.A405	journal	October 1964
Nonlinear-response theory for steady planar Couette flow Evans, Denis J.; Morriss, G. P. Physical Review A, Vol. 30, Issue 3 https://doi.org/10.1103/PhysRevA.30.1528	journal	September 1984
Spin dynamics in magnets: Equation of motion and finite temperature effects Antropov, V. P.; Katsnelson, M. I.; Harmon, B. N. Physical Review B, Vol. 54, Issue 2 https://doi.org/10.1103/PhysRevB.54.1019	journal	July 1996
Energy surface and lifetime of magnetic skyrmions Uzdin, V. M.; Potkina, M. N.; Lobanov, I. S. Journal of Magnetism and Magnetic Materials, Vol. 459 https://doi.org/10.1016/j.jmmm.2017.10.100	journal	August 2018
Optimizing legacy molecular dynamics software with directive-based offload Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin Computer Physics Communications, Vol. 195 https://doi.org/10.1016/j.cpc.2015.05.004	journal	October 2015
Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions Fattebert, J. -L.; Richards, D. F.; Glosli, J. N. Computer Physics Communications, Vol. 183, Issue 12 https://doi.org/10.1016/j.cpc.2012.07.013	journal	December 2012
Aspherical particle models for molecular dynamics simulation Nguyen, Trung Dac; Plimpton, Steven J. Computer Physics Communications, Vol. 243 https://doi.org/10.1016/j.cpc.2019.05.010	journal	October 2019
Charge Regulation Effects in Nanoparticle Self-Assembly Curk, Tine; Luijten, Erik Physical Review Letters, Vol. 126, Issue 13 https://doi.org/10.1103/PhysRevLett.126.138003	journal	March 2021
General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions Thompson, Aidan P.; Plimpton, Steven J.; Mattson, William The Journal of Chemical Physics, Vol. 131, Issue 15 https://doi.org/10.1063/1.3245303	journal	October 2009
Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics Jewett, Andrew I.; Stelter, David; Lambert, Jason Journal of Molecular Biology, Vol. 433, Issue 11 https://doi.org/10.1016/j.jmb.2021.166841	journal	May 2021
Smooth particle hydrodynamics simulation of damage induced by a spherical indenter scratching a viscoplastic material Leroch, S.; Varga, M.; Eder, S. J. International Journal of Solids and Structures, Vol. 81 https://doi.org/10.1016/j.ijsolstr.2015.11.025	journal	March 2016
Beryllium-driven structural evolution at the divertor surface Cusentino, M. A.; Wood, M. A.; Thompson, A. P. Nuclear Fusion, Vol. 61, Issue 4 https://doi.org/10.1088/1741-4326/abe7bd	journal	March 2021
Scalable molecular dynamics on CPU and GPU architectures with NAMD Phillips, James C.; Hardy, David J.; Maia, Julio D. C. The Journal of Chemical Physics, Vol. 153, Issue 4 https://doi.org/10.1063/5.0014475	journal	July 2020
Prebiotic Chemistry within a Simple Impacting Icy Mixture Goldman, Nir; Tamblyn, Isaac The Journal of Physical Chemistry A, Vol. 117, Issue 24 https://doi.org/10.1021/jp402976n	journal	May 2013
Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble Panagiotopoulos, Athanassios Z. Molecular Physics, Vol. 61, Issue 4 https://doi.org/10.1080/00268978700101491	journal	July 1987
Molecular simulation of flow-enhanced nucleation in n -eicosane melts under steady shear and uniaxial extension Nicholson, David A.; Rutledge, Gregory C. The Journal of Chemical Physics, Vol. 145, Issue 24 https://doi.org/10.1063/1.4972894	journal	December 2016
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
The effect of electron–ion interactions on radiation damage simulations Rutherford, A. M.; Duffy, D. M. Journal of Physics: Condensed Matter, Vol. 19, Issue 49 https://doi.org/10.1088/0953-8984/19/49/496201	journal	November 2007
DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics Wang, Han; Zhang, Linfeng; Han, Jiequn Computer Physics Communications, Vol. 228 https://doi.org/10.1016/j.cpc.2018.03.016	journal	July 2018
Charge optimized many-body potential for the $Si ∕ {SiO}_{2}$ system Yu, Jianguo; Sinnott, Susan B.; Phillpot, Simon R. Physical Review B, Vol. 75, Issue 8 https://doi.org/10.1103/PhysRevB.75.085311	journal	February 2007
SEM++: A particle model of cellular growth, signaling and migration Milde, Florian; Tauriello, Gerardo; Haberkern, Hannah Computational Particle Mechanics, Vol. 1, Issue 2 https://doi.org/10.1007/s40571-014-0017-4	journal	May 2014
Adaptive machine learning framework to accelerate ab initio molecular dynamics Botu, Venkatesh; Ramprasad, Rampi International Journal of Quantum Chemistry, Vol. 115, Issue 16 https://doi.org/10.1002/qua.24836	journal	December 2014
Large-scale simulation of the spin-lattice dynamics in ferromagnetic iron Ma, Pui-Wai; Woo, C. H.; Dudarev, S. L. Physical Review B, Vol. 78, Issue 2 https://doi.org/10.1103/PhysRevB.78.024434	journal	July 2008
PLUMED 2: New feathers for an old bird Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide Computer Physics Communications, Vol. 185, Issue 2 https://doi.org/10.1016/j.cpc.2013.09.018	journal	February 2014
Versatile Object-Oriented Toolkit for Coarse-Graining Applications Rühle, Victor; Junghans, Christoph; Lukyanov, Alexander Journal of Chemical Theory and Computation, Vol. 5, Issue 12 https://doi.org/10.1021/ct900369w	journal	November 2009
Electronegativity-equalization method for the calculation of atomic charges in molecules Mortier, Wilfried J.; Ghosh, Swapan K.; Shankar, S. Journal of the American Chemical Society, Vol. 108, Issue 15 https://doi.org/10.1021/ja00275a013	journal	July 1986
Unified Approach for Molecular Dynamics and Density-Functional Theory Car, R.; Parrinello, M. Physical Review Letters, Vol. 55, Issue 22 https://doi.org/10.1103/PhysRevLett.55.2471	journal	November 1985
Adaptive dynamic load-balancing with irregular domain decomposition for particle simulations Begau, Christoph; Sutmann, Godehard Computer Physics Communications, Vol. 190 https://doi.org/10.1016/j.cpc.2015.01.009	journal	May 2015
Particle shape effects in discrete element modelling of cohesive angular particles Wang, J.; Yu, H. S.; Langston, P. Granular Matter, Vol. 13, Issue 1 https://doi.org/10.1007/s10035-010-0217-4	journal	October 2010
Modified charge transfer–embedded atom method potential for metal/metal oxide systems Zhou, X. W.; Wadley, H. N. G.; Filhol, J. -S. Physical Review B, Vol. 69, Issue 3 https://doi.org/10.1103/PhysRevB.69.035402	journal	January 2004
Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems Pollock, E. L.; Glosli, Jim Computer Physics Communications, Vol. 95, Issue 2-3 https://doi.org/10.1016/0010-4655(96)00043-4	journal	June 1996
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model Ouldridge, Thomas E.; Louis, Ard A.; Doye, Jonathan P. K. The Journal of Chemical Physics, Vol. 134, Issue 8 https://doi.org/10.1063/1.3552946	journal	February 2011
Magnetostructural Transition Kinetics in Shocked Iron Surh, Michael P.; Benedict, Lorin X.; Sadigh, Babak Physical Review Letters, Vol. 117, Issue 8 https://doi.org/10.1103/PhysRevLett.117.085701	journal	August 2016
Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh Brown, W. Michael; Kohlmeyer, Axel; Plimpton, Steven J. Computer Physics Communications, Vol. 183, Issue 3 https://doi.org/10.1016/j.cpc.2011.10.012	journal	March 2012
Implementing peridynamics within a molecular dynamics code Parks, Michael L.; Lehoucq, Richard B.; Plimpton, Steven J. Computer Physics Communications, Vol. 179, Issue 11 https://doi.org/10.1016/j.cpc.2008.06.011	journal	December 2008
DEM simulations of polydisperse media: efficient contact detection applied to investigate the quasi-static limit Shire, Tom; Hanley, Kevin J.; Stratford, Kevin Computational Particle Mechanics, Vol. 8, Issue 4 https://doi.org/10.1007/s40571-020-00361-2	journal	September 2020
Explicit Multielement Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems Cusentino, M. A.; Wood, M. A.; Thompson, A. P. The Journal of Physical Chemistry A, Vol. 124, Issue 26 https://doi.org/10.1021/acs.jpca.0c02450	journal	May 2020
The Kokkos EcoSystem: Comprehensive Performance Portability For High Performance Computing Trott, Christian; Berger-Vergiat, Luc; Poliakoff, David Zoeller Computing in Science & Engineering https://doi.org/10.1109/MCSE.2021.3098509	journal	January 2021
Simulation of low index rutile surfaces with a transferable variable-charge Ti–O interatomic potential and comparison with ab initio results Swamy, Varghese; Muscat, Joseph; Gale, Julian D. Surface Science, Vol. 504 https://doi.org/10.1016/S0039-6028(01)01925-2	journal	April 2002
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems Darden, Tom; York, Darrin; Pedersen, Lee The Journal of Chemical Physics, Vol. 98, Issue 12 https://doi.org/10.1063/1.464397	journal	June 1993
Dynamics of Radiation Damage Gibson, J. B.; Goland, A. N.; Milgram, M. Physical Review, Vol. 120, Issue 4 https://doi.org/10.1103/PhysRev.120.1229	journal	November 1960
Computational aspects of many-body potentials Plimpton, Steven J.; Thompson, Aidan P. MRS Bulletin, Vol. 37, Issue 5 https://doi.org/10.1557/mrs.2012.96	journal	May 2012
Viscoplasticity using peridynamics Foster, J. T.; Silling, S. A.; Chen, W. W. International Journal for Numerical Methods in Engineering https://doi.org/10.1002/nme.2725	journal	January 2009
Parallel Multistream Training of High-Dimensional Neural Network Potentials Singraber, Andreas; Morawietz, Tobias; Behler, Jörg Journal of Chemical Theory and Computation, Vol. 15, Issue 5 https://doi.org/10.1021/acs.jctc.8b01092	journal	April 2019
PANNA: Properties from Artificial Neural Network Architectures Lot, Ruggero; Pellegrini, Franco; Shaidu, Yusuf Computer Physics Communications, Vol. 256 https://doi.org/10.1016/j.cpc.2020.107402	journal	November 2020
ReaxFF: A Reactive Force Field for Hydrocarbons van Duin, Adri C. T.; Dasgupta, Siddharth; Lorant, Francois The Journal of Physical Chemistry A, Vol. 105, Issue 41 https://doi.org/10.1021/jp004368u	journal	October 2001
Rendezvous algorithms for large-scale modeling and simulation Plimpton, Steven J.; Knight, Christopher Journal of Parallel and Distributed Computing, Vol. 147 https://doi.org/10.1016/j.jpdc.2020.09.001	journal	January 2021
Algorithm for Molecular Dynamics Simulations of Spin Liquids Omelyan, I. P.; Mryglod, I. M.; Folk, R. Physical Review Letters, Vol. 86, Issue 5 https://doi.org/10.1103/PhysRevLett.86.898	journal	January 2001
A Partitioning Strategy for Nonuniform Problems on Multiprocessors IEEE Transactions on Computers, Vol. C-36, Issue 5 https://doi.org/10.1109/TC.1987.1676942	journal	May 1987
Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques Aktulga, H. M.; Fogarty, J. C.; Pandit, S. A. Parallel Computing, Vol. 38, Issue 4-5 https://doi.org/10.1016/j.parco.2011.08.005	journal	April 2012
DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism Todorov, Ilian T.; Smith, William; Trachenko, Kostya Journal of Materials Chemistry, Vol. 16, Issue 20, p. 1911-1918 https://doi.org/10.1039/b517931a	journal	January 2006
Catastrophic depolymerization of microtubules driven by subunit shape change Bollinger, Jonathan A.; Stevens, Mark J. Soft Matter, Vol. 14, Issue 10 https://doi.org/10.1039/C7SM02033C	journal	January 2018
Atomic cluster expansion of scalar, vectorial, and tensorial properties including magnetism and charge transfer Drautz, Ralf Physical Review B, Vol. 102, Issue 2 https://doi.org/10.1103/PhysRevB.102.024104	journal	July 2020
Vibration induced flow in hoppers: DEM 2D polygon model Fraige, Feras Y.; Langston, Paul A.; Matchett, Andrew J. Particuology, Vol. 6, Issue 6 https://doi.org/10.1016/j.partic.2008.07.019	journal	December 2008
Use of a variable-charge interatomic potential for atomistic simulations of bulk, oxygen vacancies, and surfaces of rutile ${TiO}_{2}$ Hallil, A.; Tétot, R.; Berthier, F. Physical Review B, Vol. 73, Issue 16 https://doi.org/10.1103/PhysRevB.73.165406	journal	April 2006
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
Dislocation nucleation and defect structure during surface indentation Kelchner, Cynthia L.; Plimpton, S. J.; Hamilton, J. C. Physical Review B, Vol. 58, Issue 17 https://doi.org/10.1103/PhysRevB.58.11085	journal	November 1998
Dynamic magnetocaloric effect in bcc iron and hcp gadolinium Ma, Pui-Wai; Dudarev, S. L. Physical Review B, Vol. 90, Issue 2 https://doi.org/10.1103/PhysRevB.90.024425	journal	July 2014
Computer simulations of bilayer membranes: Self-assembly and interfacial tension Goetz, Rüdiger; Lipowsky, Reinhard The Journal of Chemical Physics, Vol. 108, Issue 17 https://doi.org/10.1063/1.476160	journal	May 1998
Multiscale modeling of shock wave localization in porous energetic material Wood, M. A.; Kittell, D. E.; Yarrington, C. D. Physical Review B, Vol. 97, Issue 1 https://doi.org/10.1103/PhysRevB.97.014109	journal	January 2018
Characteristics of dynamic brittle fracture captured with peridynamics Ha, Youn Doh; Bobaru, Florin Engineering Fracture Mechanics, Vol. 78, Issue 6 https://doi.org/10.1016/j.engfracmech.2010.11.020	journal	April 2011
Modeling shockwaves and impact phenomena with Eulerian peridynamics Silling, Stewart A.; Parks, Michael L.; Kamm, James R. International Journal of Impact Engineering, Vol. 107 https://doi.org/10.1016/j.ijimpeng.2017.04.022	journal	September 2017
Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules Verlet, Loup Physical Review, Vol. 159, Issue 1 https://doi.org/10.1103/PhysRev.159.98	journal	July 1967
Energy-conserving dissipative particle dynamics with temperature-dependent properties Li, Zhen; Tang, Yu-Hang; Lei, Huan Journal of Computational Physics, Vol. 265 https://doi.org/10.1016/j.jcp.2014.02.003	journal	May 2014
Analytic bond-order potential for the gallium arsenide system Murdick, D. A.; Zhou, X. W.; Wadley, H. N. G. Physical Review B, Vol. 73, Issue 4 https://doi.org/10.1103/PhysRevB.73.045206	journal	January 2006
Charge equilibration for molecular dynamics simulations Rappe, Anthony K.; Goddard, William A. The Journal of Physical Chemistry, Vol. 95, Issue 8 https://doi.org/10.1021/j100161a070	journal	April 1991
Size- and temperature-dependent magnetization of iron nanoclusters Dos Santos, G.; Aparicio, R.; Linares, D. Physical Review B, Vol. 102, Issue 18 https://doi.org/10.1103/PhysRevB.102.184426	journal	November 2020
Particle dynamics modeling methods for colloid suspensions Bolintineanu, Dan S.; Grest, Gary S.; Lechman, Jeremy B. Computational Particle Mechanics, Vol. 1, Issue 3 https://doi.org/10.1007/s40571-014-0007-6	journal	May 2014
Electronegativity equalization: application and parametrization Mortier, Wilfried J.; Van Genechten, Karin; Gasteiger, Johann Journal of the American Chemical Society, Vol. 107, Issue 4 https://doi.org/10.1021/ja00290a017	journal	February 1985
Long-Time Dynamics through Parallel Trajectory Splicing Perez, Danny; Cubuk, Ekin D.; Waterland, Amos Journal of Chemical Theory and Computation, Vol. 12, Issue 1 https://doi.org/10.1021/acs.jctc.5b00916	journal	December 2015
Periodic boundary conditions for long-time nonequilibrium molecular dynamics simulations of incompressible flows Dobson, Matthew The Journal of Chemical Physics, Vol. 141, Issue 18 https://doi.org/10.1063/1.4901276	journal	November 2014
Performant implementation of the atomic cluster expansion (PACE) and application to copper and silicon Lysogorskiy, Yury; Oord, Cas van der; Bochkarev, Anton npj Computational Materials, Vol. 7, Issue 1 https://doi.org/10.1038/s41524-021-00559-9	journal	June 2021
Coarse-grained simulation of DNA using LAMMPS: An implementation of the oxDNA model and its applications Henrich, Oliver; Gutiérrez Fosado, Yair Augusto; Curk, Tine The European Physical Journal E, Vol. 41, Issue 5 https://doi.org/10.1140/epje/i2018-11669-8	journal	May 2018
Piezomagnetism and magnetoelastic memory in uranium dioxide Jaime, M.; Saul, A.; Salamon, M. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00096-4	journal	July 2017
Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length scales Padding, J. T.; Louis, A. A. Physical Review E, Vol. 74, Issue 3 https://doi.org/10.1103/PhysRevE.74.031402	journal	September 2006
Molecular-dynamics simulations of void collapse in shocked model-molecular solids Mintmire, J. W.; Robertson, D. H.; White, C. T. Physical Review B, Vol. 49, Issue 21 https://doi.org/10.1103/PhysRevB.49.14859	journal	June 1994
Markov State Models: From an Art to a Science Husic, Brooke E.; Pande, Vijay S. Journal of the American Chemical Society, Vol. 140, Issue 7 https://doi.org/10.1021/jacs.7b12191	journal	February 2018
Coarse-grained simulations of lipid bilayers Stevens, Mark J. The Journal of Chemical Physics, Vol. 121, Issue 23 https://doi.org/10.1063/1.1814058	journal	December 2004
Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations Andersen, Hans C. Journal of Computational Physics, Vol. 52, Issue 1 https://doi.org/10.1016/0021-9991(83)90014-1	journal	October 1983
Smoothed dissipative particle dynamics Español, Pep; Revenga, Mariano Physical Review E, Vol. 67, Issue 2 https://doi.org/10.1103/PhysRevE.67.026705	journal	February 2003
Mapping Atomistic Simulations to Mesoscopic Models: A Systematic Coarse-Graining Procedure for Vinyl Polymer Chains Milano, Giuseppe; Müller-Plathe, Florian The Journal of Physical Chemistry B, Vol. 109, Issue 39 https://doi.org/10.1021/jp0523571	journal	October 2005
Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems Klein, M. L.; Shinoda, W. Science, Vol. 321, Issue 5890 https://doi.org/10.1126/science.1157834	journal	August 2008
Electrostatic potentials for metal-oxide surfaces and interfaces Streitz, F. H.; Mintmire, J. W. Physical Review B, Vol. 50, Issue 16 https://doi.org/10.1103/PhysRevB.50.11996	journal	October 1994
Developing community codes for materials modeling Plimpton, Steven J.; Gale, Julian D. Current Opinion in Solid State and Materials Science, Vol. 17, Issue 6 https://doi.org/10.1016/j.cossms.2013.09.005	journal	December 2013
Semiempirical modified embedded-atom potentials for silicon and germanium Baskes, M. I.; Nelson, J. S.; Wright, A. F. Physical Review B, Vol. 40, Issue 9 https://doi.org/10.1103/PhysRevB.40.6085	journal	September 1989
A Method for Molecular Dynamics on Curved Surfaces Paquay, Stefan; Kusters, Remy Biophysical Journal, Vol. 110, Issue 6 https://doi.org/10.1016/j.bpj.2016.02.017	journal	March 2016
Software components for parallel multiscale simulation: an example with LAMMPS FrantzDale, Benjamin; Plimpton, Steven J.; Shephard, Mark S. Engineering with Computers, Vol. 26, Issue 2 https://doi.org/10.1007/s00366-009-0156-z	journal	December 2009
Structural Relaxation Made Simple Bitzek, Erik; Koskinen, Pekka; Gähler, Franz Physical Review Letters, Vol. 97, Issue 17 https://doi.org/10.1103/PhysRevLett.97.170201	journal	October 2006
Implementing molecular dynamics on hybrid high performance computers—Three-body potentials Brown, W. Michael; Yamada, Masako Computer Physics Communications, Vol. 184, Issue 12 https://doi.org/10.1016/j.cpc.2013.08.002	journal	December 2013
Physically informed artificial neural networks for atomistic modeling of materials Pun, G. P. Purja; Batra, R.; Ramprasad, R. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10343-5	journal	May 2019
Classical Pauli repulsion: An anisotropic, atomic multipole model Rackers, Joshua A.; Ponder, Jay W. The Journal of Chemical Physics, Vol. 150, Issue 8 https://doi.org/10.1063/1.5081060	journal	February 2019
The MolSSI Driver Interface Project: A framework for standardized, on-the-fly interoperability between computational molecular sciences codes Barnes, Taylor A.; Marin-Rimoldi, Eliseo; Ellis, Samuel Computer Physics Communications, Vol. 261 https://doi.org/10.1016/j.cpc.2020.107688	journal	April 2021
Electronegativity and bond energy Sanderson, R. T. Journal of the American Chemical Society, Vol. 105, Issue 8 https://doi.org/10.1021/ja00346a026	journal	April 1983
Massively parallel symplectic algorithm for coupled magnetic spin dynamics and molecular dynamics Tranchida, J.; Plimpton, S. J.; Thibaudeau, P. Journal of Computational Physics, Vol. 372 https://doi.org/10.1016/j.jcp.2018.06.042	journal	November 2018
Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations Nguyen, Trung Dac; Carrillo, Jan-Michael Y.; Matheson, Michael A. Nanoscale, Vol. 6, Issue 6 https://doi.org/10.1039/C3NR05413F	journal	January 2014
Using collective variables to drive molecular dynamics simulations Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme Molecular Physics, Vol. 111, Issue 22-23 https://doi.org/10.1080/00268976.2013.813594	journal	December 2013
Method for finding mechanism and activation energy of magnetic transitions, applied to skyrmion and antivortex annihilation Bessarab, Pavel F.; Uzdin, Valery M.; Jónsson, Hannes Computer Physics Communications, Vol. 196 https://doi.org/10.1016/j.cpc.2015.07.001	journal	November 2015
Efficient optimization method for finding minimum energy paths of magnetic transitions Ivanov, A. V.; Dagbartsson, D.; Tranchida, J. Journal of Physics: Condensed Matter, Vol. 32, Issue 34 https://doi.org/10.1088/1361-648X/ab8b9c	journal	May 2020
Highly scalable discrete-particle simulations with novel coarse-graining: accessing the microscale Mattox, Timothy I.; Larentzos, James P.; Moore, Stan G. Molecular Physics, Vol. 116, Issue 15-16 https://doi.org/10.1080/00268976.2018.1471532	journal	May 2018
Monte Carlo simulation of multicomponent equilibria in a semigrand canonical ensemble Kofke, David A.; Glandt, Eduardo D. Molecular Physics, Vol. 64, Issue 6 https://doi.org/10.1080/00268978800100743	journal	August 1988
Analytical bond-order potential for the cadmium telluride binary system Ward, D. K.; Zhou, X. W.; Wong, B. M. Physical Review B, Vol. 85, Issue 11 https://doi.org/10.1103/PhysRevB.85.115206	journal	March 2012
Including the effects of electronic stopping and electron–ion interactions in radiation damage simulations Duffy, D. M.; Rutherford, A. M. Journal of Physics: Condensed Matter, Vol. 19, Issue 1 https://doi.org/10.1088/0953-8984/19/1/016207	journal	December 2006

Similar Records

Towards Microsecond Biological Molecular Dynamics Simulations on Hybrid Processors

Conference · Fri Jan 01 00:00:00 EST 2010 · OSTI ID:1821775

Hampton, Scott S; Agarwal, Pratul K

Implementation of metal-friendly EAM/FS-type semi-empirical potentials in HOOMD-blue: A GPU-accelerated molecular dynamics software

Journal Article · Fri Jan 12 00:00:00 EST 2018 · Journal of Computational Physics · OSTI ID:1821775

Yang, Lin; Zhang, Feng; Wang, Cai-Zhuang; +2 more

Machine Learning Classical Interatomic Potentials for Molecular Dynamics from First-Principles Training Data

Journal Article · Thu Jan 03 00:00:00 EST 2019 · Journal of Physical Chemistry. C · OSTI ID:1821775

Chan, Henry; Narayanan, Badri; Cherukara, Mathew J.; +5 more

Related Subjects

74 ATOMIC AND MOLECULAR PHYSICS
97 MATHEMATICS AND COMPUTING
molecular dynamics
materials modeling
parallel algorithms
LAMMPS

Title: LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Citation Formats

References (195)

Similar Records

Related Subjects