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

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

(2021) Andrew I. Jewett et al.   JOURNAL OF MOLECULAR BIOLOGY

Peridynamic Model for Microballistic Perforation of Multilayer Graphene

(2021) Stewart A. Silling et al.   THEORETICAL AND APPLIED FRACTURE MECHANICS

Automated discovery of a robust interatomic potential for aluminum

(2021) Justin S. Smith et al.   Nature Communications

GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP

(2021) Nikolay Kondratyuk et al.   INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS

Beryllium-driven structural evolution at the divertor surface

(2021) M.A. Cusentino et al.   NUCLEAR FUSION

Charge Regulation Effects in Nanoparticle Self-Assembly

(2021) Tine Curk et al.   PHYSICAL REVIEW LETTERS

LAMMPS implementation of rapid artificial neural network derived interatomic potentials

(2021) D. Dickel et al.   COMPUTATIONAL MATERIALS SCIENCE

Performant implementation of the atomic cluster expansion (PACE) and application to copper and silicon

(2021) Yury Lysogorskiy et al.   npj Computational Materials

Kokkos 3: Programming Model Extensions for the Exascale Era

(2021) Christian R. Trott et al.   IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS

Performance and Cost Assessment of Machine Learning Interatomic Potentials

(2020) Yunxing Zuo et al.   JOURNAL OF PHYSICAL CHEMISTRY A

PANNA: Properties from Artificial Neural Network Architectures

(2020) Ruggero Lot et al.   COMPUTER PHYSICS COMMUNICATIONS

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations

(2020) B. Hourahine et al.   JOURNAL OF CHEMICAL PHYSICS

Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems

(2020) Mary Alice Cusentino et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Efficient optimization method for finding minimum energy paths of magnetic transitions

(2020) A V Ivanov et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Neural network atomic potential to investigate the dislocation dynamics in bcc iron

(2020) Hideki Mori et al.   Physical Review Materials

Parallel algorithms for hyperdynamics and local hyperdynamics

(2020) Steven J. Plimpton et al.   JOURNAL OF CHEMICAL PHYSICS

Neural network potential from bispectrum components: A case study on crystalline silicon

(2020) Howard Yanxon et al.   JOURNAL OF CHEMICAL PHYSICS

Scalable molecular dynamics on CPU and GPU architectures with NAMD

(2020) James C. Phillips et al.   JOURNAL OF CHEMICAL PHYSICS

The MolSSI QCA rchive project: An open‐source platform to compute, organize, and share quantum chemistry data

(2020) Daniel G. A. Smith et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Uncertainty quantification in molecular simulations with dropout neural network potentials

(2020) Mingjian Wen et al.   npj Computational Materials

DEM simulations of polydisperse media: efficient contact detection applied to investigate the quasi-static limit

(2020) Tom Shire et al.   Computational Particle Mechanics

Rendezvous algorithms for large-scale modeling and simulation

(2020) Steven J. Plimpton et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

A multiscale coarse-grained model of the SARS-CoV-2 virion

(2020) Alvin Yu et al.   BIOPHYSICAL JOURNAL

The MolSSI Driver Interface Project: A framework for standardized, on-the-fly interoperability between computational molecular sciences codes

(2020) Taylor A. Barnes et al.   COMPUTER PHYSICS COMMUNICATIONS

Classical Pauli repulsion: An anisotropic, atomic multipole model

(2019) Joshua A. Rackers et al.   JOURNAL OF CHEMICAL PHYSICS

Incorporating surface polarization effects into large-scale coarse-grained Molecular Dynamics simulation

(2019) Trung Dac Nguyen et al.   COMPUTER PHYSICS COMMUNICATIONS

Aspherical particle models for molecular dynamics simulation

(2019) Trung Dac Nguyen et al.   COMPUTER PHYSICS COMMUNICATIONS

Parallel Multistream Training of High-Dimensional Neural Network Potentials

(2019) Andreas Singraber et al.   Journal of Chemical Theory and Computation

Physically informed artificial neural networks for atomistic modeling of materials

(2019) G. P. Purja Pun et al.   Nature Communications

Enhanced sampling in molecular dynamics

(2019) Yi Isaac Yang et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of modern Langevin integrators for simulations of coarse-grained polymer melts

(2019) J. Finkelstein et al.   MOLECULAR PHYSICS

Direct simulation Monte Carlo on petaflop supercomputers and beyond

(2019) S. J. Plimpton et al.   PHYSICS OF FLUIDS

HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations

(2019) Joshua A. Anderson et al.   COMPUTATIONAL MATERIALS SCIENCE

Electric and antiferromagnetic chiral textures at multiferroic domain walls

(2019) J.-Y. Chauleau et al.   NATURE MATERIALS

DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics

(2018) Han Wang et al.   COMPUTER PHYSICS COMMUNICATIONS

Coarse-grained simulation of DNA using LAMMPS

(2018) Oliver Henrich et al.   EUROPEAN PHYSICAL JOURNAL E

Extending the accuracy of the SNAP interatomic potential form

(2018) Mitchell A. Wood et al.   JOURNAL OF CHEMICAL PHYSICS

Massively parallel symplectic algorithm for coupled magnetic spin dynamics and molecular dynamics

(2018) J. Tranchida et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Energy surface and lifetime of magnetic skyrmions

(2018) V.M. Uzdin et al.   JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Highly scalable discrete-particle simulations with novel coarse-graining: accessing the microscale

(2018) Timothy I. Mattox et al.   MOLECULAR PHYSICS

Catastrophic depolymerization of microtubules driven by subunit shape change

(2018) Jonathan A. Bollinger et al.   Soft Matter

Achieving DFT accuracy with a machine-learning interatomic potential: Thermomechanics and defects in bcc ferromagnetic iron

(2018) Daniele Dragoni et al.   PHYSICAL REVIEW MATERIALS

Relating Chain Conformations to Extensional Stress in Entangled Polymer Melts

(2018) Thomas C. O’Connor et al.   PHYSICAL REVIEW LETTERS

Importance of corners in fracture of highly crosslinked polymeric adhesives

(2018) Mark J. Stevens   JOURNAL OF CHEMICAL PHYSICS

Direct observations of shape fluctuation in long-time atomistic simulations of metallic nanoclusters

(2018) Rao Huang et al.   PHYSICAL REVIEW MATERIALS

Modeling shockwaves and impact phenomena with Eulerian peridynamics

(2017) Stewart A. Silling et al.   INTERNATIONAL JOURNAL OF IMPACT ENGINEERING

The atomic simulation environment—a Python library for working with atoms

(2017) Ask Hjorth Larsen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Probing the limits of metal plasticity with molecular dynamics simulations

(2017) Luis A. Zepeda-Ruiz et al.   NATURE

Modeling chemical reactions in classical molecular dynamics simulations

(2017) Jacob R. Gissinger et al.   POLYMER

Evidence for percolation diffusion of cations and reordering in disordered pyrochlore from accelerated molecular dynamics

(2017) Romain Perriot et al.   Nature Communications

Piezomagnetism and magnetoelastic memory in uranium dioxide

(2017) M. Jaime et al.   Nature Communications

Probing eukaryotic cell mechanics via mesoscopic simulations

(2017) Kirill Lykov et al.   PLoS Computational Biology

A Method for Molecular Dynamics on Curved Surfaces

(2016) Stefan Paquay et al.   BIOPHYSICAL JOURNAL

Smooth particle hydrodynamics simulation of damage induced by a spherical indenter scratching a viscoplastic material

(2016) S. Leroch et al.   INTERNATIONAL JOURNAL OF SOLIDS AND STRUCTURES

A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization

(2016) Zhen Li et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular simulation of flow-enhanced nucleation in n-eicosane melts under steady shear and uniaxial extension

(2016) David A. Nicholson et al.   JOURNAL OF CHEMICAL PHYSICS

Robust structural identification via polyhedral template matching

(2016) Peter Mahler Larsen et al.   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Magnetostructural Transition Kinetics in Shocked Iron

(2016) Michael P. Surh et al.   PHYSICAL REVIEW LETTERS

Adaptive dynamic load-balancing with irregular domain decomposition for particle simulations

(2015) Christoph Begau et al.   COMPUTER PHYSICS COMMUNICATIONS

Method for finding mechanism and activation energy of magnetic transitions, applied to skyrmion and antivortex annihilation

(2015) Pavel F. Bessarab et al.   COMPUTER PHYSICS COMMUNICATIONS

Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

(2015) Zhen Li et al.   JOURNAL OF CHEMICAL PHYSICS

Long-Time Dynamics through Parallel Trajectory Splicing

(2015) Danny Perez et al.   Journal of Chemical Theory and Computation

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

(2015) A.P. Thompson et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Direct simulation Monte Carlo investigation of the Richtmyer-Meshkov instability

(2015) M. A. Gallis et al.   PHYSICS OF FLUIDS

Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA

(2015) S. Y. Mashayak et al.   PLoS One

Adaptive machine learning framework to accelerateab initiomolecular dynamics

(2014) Venkatesh Botu et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

A Computational Algorithm to Produce Virtual X-ray and Electron Diffraction Patterns from Atomistic Simulations

(2014) Shawn P. Coleman et al.   JOM

Periodic boundary conditions for long-time nonequilibrium molecular dynamics simulations of incompressible flows

(2014) Matthew Dobson   JOURNAL OF CHEMICAL PHYSICS

Extension and evaluation of the multilevel summation method for fast long-range electrostatics calculations

(2014) Stan G. Moore et al.   JOURNAL OF CHEMICAL PHYSICS

Energy-conserving dissipative particle dynamics with temperature-dependent properties

(2014) Zhen Li et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Dynamic magnetocaloric effect in bcc iron and hcp gadolinium

(2014) Pui-Wai Ma et al.   PHYSICAL REVIEW B

Models, algorithms and validation for opensource DEM and CFD-DEM

(2014) Christoph Kloss et al.   PROGRESS IN COMPUTATIONAL FLUID DYNAMICS

SEM++: A particle model of cellular growth, signaling and migration

(2014) Florian Milde et al.   Computational Particle Mechanics

Particle dynamics modeling methods for colloid suspensions

(2014) Dan S. Bolintineanu et al.   Computational Particle Mechanics

Implementing molecular dynamics on hybrid high performance computers—Three-body potentials

(2013) W. Michael Brown et al.   COMPUTER PHYSICS COMMUNICATIONS

Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

(2013) F.E. Mackay et al.   COMPUTER PHYSICS COMMUNICATIONS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Developing community codes for materials modeling

(2013) Steven J. Plimpton et al.   CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE

Local hyperdynamics

(2013) Soo Young Kim et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Prebiotic Chemistry within a Simple Impacting Icy Mixture

(2013) Nir Goldman et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Classical atomistic simulations of surfaces and heterogeneous interfaces with the charge-optimized many body (COMB) potentials

(2013) Tao Liang et al.   MATERIALS SCIENCE & ENGINEERING R-REPORTS

Using collective variables to drive molecular dynamics simulations

(2013) Giacomo Fiorin et al.   MOLECULAR PHYSICS

Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations

(2013) Trung Dac Nguyen et al.   Nanoscale

Molecular Dynamics Simulations of Polymer Welding: Strength from Interfacial Entanglements

(2013) Ting Ge et al.   PHYSICAL REVIEW LETTERS

Three dimensional flow structures in a moving droplet on substrate: A dissipative particle dynamics study

(2013) Zhen Li et al.   PHYSICS OF FLUIDS

Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

(2012) J.-L. Fattebert et al.   COMPUTER PHYSICS COMMUNICATIONS

Sequence-dependent thermodynamics of a coarse-grained DNA model

(2012) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

Development and application of a particle-particle particle-mesh Ewald method for dispersion interactions

(2012) Rolf E. Isele-Holder et al.   JOURNAL OF CHEMICAL PHYSICS

Computational aspects of many-body potentials

(2012) Steven J. Plimpton et al.   MRS BULLETIN

Atomistic modeling of long-term evolution of twist boundaries under vacancy supersaturation

(2012) Enrique Martínez et al.   PHYSICAL REVIEW B

Analytical bond-order potential for the cadmium telluride binary system

(2012) D. K. Ward et al.   PHYSICAL REVIEW B

On the nature of the magnetocaloric effect of the first-order magnetostructural transition

(2012) K.A. Gschneidner et al.   SCRIPTA MATERIALIA

Smoothed Particle Hydrodynamics and Its Diverse Applications

(2011) J.J. Monaghan   Annual Review of Fluid Mechanics

Phonon dispersion measured directly from molecular dynamics simulations

(2011) Ling Ti Kong   COMPUTER PHYSICS COMMUNICATIONS

Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh

(2011) W. Michael Brown et al.   COMPUTER PHYSICS COMMUNICATIONS

The potential of atomistic simulations and the knowledgebase of interatomic models

(2011) E. B. Tadmor et al.   JOM

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques

(2011) H.M. Aktulga et al.   PARALLEL COMPUTING

Implementing molecular dynamics on hybrid high performance computers – short range forces

(2010) W. Michael Brown et al.   COMPUTER PHYSICS COMMUNICATIONS

Characteristics of dynamic brittle fracture captured with peridynamics

(2010) Youn Doh Ha et al.   ENGINEERING FRACTURE MECHANICS

Particle shape effects in discrete element modelling of cohesive angular particles

(2010) J. Wang et al.   GRANULAR MATTER

A two-temperature model of radiation damage in α-quartz

(2010) Carolyn L. Phillips et al.   JOURNAL OF CHEMICAL PHYSICS

Large-scale, long-term nonadiabatic electron molecular dynamics for describing material properties and phenomena in extreme environments

(2010) Andres Jaramillo-Botero et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Charge-optimized many-body potential for the hafnium/hafnium oxide system

(2010) Tzu-Ray Shan et al.   PHYSICAL REVIEW B

Second-generation charge-optimized many-body potential forSi/SiO2and amorphous silica

(2010) Tzu-Ray Shan et al.   PHYSICAL REVIEW B

Origins of the anomalous stress behavior in charged colloidal suspensions under shear

(2010) Amit Kumar et al.   PHYSICAL REVIEW E

Gaussian Approximation Potentials: The Accuracy of Quantum Mechanics, without the Electrons

(2010) Albert P. Bartók et al.   PHYSICAL REVIEW LETTERS

VORO++: A three-dimensional Voronoi cell library in C++

(2009) Chris H. Rycroft   CHAOS

Software components for parallel multiscale simulation: an example with LAMMPS

(2009) Benjamin FrantzDale et al.   ENGINEERING WITH COMPUTERS

Viscoplasticity using peridynamics

(2009) J. T. Foster et al.   INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING

General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions

(2009) Aidan P. Thompson et al.   JOURNAL OF CHEMICAL PHYSICS

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

(2009) Victor Rühle et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool

(2009) Alexander Stukowski   MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING

Accurate and efficient methods for modeling colloidal mixtures in an explicit solvent using molecular dynamics

(2008) Pieter J. in 't Veld et al.   COMPUTER PHYSICS COMMUNICATIONS

Implementing peridynamics within a molecular dynamics code

(2008) Michael L. Parks et al.   COMPUTER PHYSICS COMMUNICATIONS

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

P3M algorithm for dipolar interactions

(2008) Juan J. Cerdà et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation

(2008) Kimberly Chenoweth et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Vibration induced flow in hoppers: DEM 2D polygon model

(2008) Feras Y. Fraige et al.   Particuology

Embedded-ion method: An analytical energy-conserving charge-transfer interatomic potential and its application to the La-Br system

(2008) X. W. Zhou et al.   PHYSICAL REVIEW B

Large-scale simulation of the spin-lattice dynamics in ferromagnetic iron

(2008) Pui-Wai Ma et al.   PHYSICAL REVIEW B

Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems

(2008) M. L. Klein et al.   SCIENCE