LAMMPS Users’ Workshop

August 2013 LAMMPS Users' Workshop and Symposium

The third LAMMPS workshop and symposium for users and developers was held in Albuquerque, NM on August 7-8, 2013. A special session for beginners was held on August 6, 2013.

Abstracts for most of the posters and talks are available through click-able links below.

A list of workshop attendees can be found here: attendees.

All sessions were held in the UNM Continuing Education Building, (1634 University Blvd. NE, map).

More photos from the workshop.

Tuesday August 6, 2013

1 – 4:30 p.m. Beginners' Session (chaired by Paul Crozier)

"An introduction to LAMMPS designed to get attendees up and running with LAMMPS quickly. Beginning with downloading and building, these tutorials will highlight major components of the code with an emphasis on examples and demos. Bring your laptop computer with LAMMPS already installed if possible (and other relevant software already installed if possible: VMD,, a movie maker software package, and Cygwin might be useful if you've got a Windows laptop, MPICH). There will be opportunities for discussion, hands-on work, and questions at the end of each tutorial."

1:00 General LAMMPS overview, Aidan Thompson, Sandia
1:15 Download, build, and run LAMMPS, Paul Crozier, Sandia
1:35 Post-processing and visualization of results, Paul Crozier, Sandia
2:00 LAMMPS input script syntax and important commands, Steve Plimpton, Sandia
2:20 LAMMPS parallelization and efficiency issues, Steve Plimpton, Sandia
2:25 Big picture survey (force fields, minimizer, load-balancer, ensembles, electrostatics, GPUs, etc.), Steve Plimpton, Sandia
2:55 break
3:05 Case study 1: Simple examples that come with LAMMPS, Steve Plimpton, Sandia
3:35 Case study 2: Rheology calculations with LAMMPS, Matt Lane, Sandia
4:05 Case study 3: Build, run, and visulatize an SiO2 example, Christian Trott, Sandia

5:00 – 7:00 p.m. no-host dinner @ Tucanos (110 Central SW), organized by Paul Crozier

Wednesday August 7, 2013

8:30 – 11:50 Session I: New capabilities, (chaired by Aidan Thompson)

8:30 "LAMMPS and High Performance Computing at Sandia", Rob Leland, Computing Research Center Director, Sandia
8:40 LAMMPS status, Steve Plimpton, Sandia
9:10 "LAMMPS implementation of the Multilevel Summation Method (MSM) for long-range electrostatics calculations", (abstract), Stan Moore, Sandia
9:30 The Hidden Gem of LAMMPS, (movies), (abstract), Axel Kohlmeyer, International Centre for Theoretical Physics, Trieste
9:42 Numerical methods for the Extended Variable Generalized Langevin Equation, (abstract), Stephen Bond, Sandia
9:54 break
10:10 A new method for calculating the pressure profile by LAMMPS, (abstract), Takenobu Nakamura, Tohoku University WPI-AIMR
10:30 The Knowledgebase of Interatomic Models (KIM), (abstract), Ryan Elliott, University of Minnesota
10:50 Atom-to-Continuum (ATC) user package for LAMMPS, (abstract), Reese Jones, Sandia
11:02 Evaluating Continuum Mechanical Quantities at the Atomic Scale, (abstract), Jonathan Zimmerman, Sandia
11:20 LIGGGHTS and CFDEM coupling - Modelling of macroscopic particle processes based on LAMMPS technology, (abstract), Christoph Kloss, Johannes Kepler University Linz

11:50 a.m. – 12:30 p.m. Boxed Lunch, courtesy of Materials Design , (lobby/auditorium)


12:30 – 2:30 p.m. Breakout Session A


Option A1 (room B): Advanced interatomic potentials (ReaxFF, COMB, eFF, etc.), chaired by Ray Shan

12:30 Using Third Generation of Charge Optimization Many-Body Potentials in LAMMPS, (abstract), Tao Liang, University of Florida
1:00 "A screened environment-dependent reactive empirical bond-order (SED-REBO) potential for simulations of carbon materials", (abstract), Romain Perriot, University of South Florida
1:30 Streitz-Mintmire potential, QEq charge equilibration, and on-the-fly chemical species analysis, (abstract), Ray Shan, Sandia
2:00 Group discussion

Option A2 (room C): Developers / hackers, chaired by Axel Kohlmeyer

12:30 Modifying LAMMPS, Steve Plimpton, Sandia
12:45 Group discussion of the following topics (more details here):
---New physics features
---Input/output, pre-/post-processing features
---Improved efficiency and accuracy
---Build system
---Documentation, training and outreach
---Project management and software engineering

Option A3 (room D): Soft materials (biomolecules, polymers, colloids), chaired by Tim Sirk

12:30 "Mechanical Properties of Polymer Networks using LAMMPS", (abstract), Timothy Sirk, U.S. Army Research Laboratory
1:00 "Self-propelled soft-core dumbbells for the simulation of active suspensions --- application to self-motile bacterial suspensions", (abstract), Denis F. Hinz, McGill University
1:20 Molecular Simulation of Carbon Dioxide and Mineral Surface Interactions in Deep Saline Aquifers, (abstract), Craig Tenney, Sandia
1:50 "Thermodynamics of NaCl-KCl-ZnCl2 Molten Mixtures from Molecular Dynamics Simulations", (abstract), Venkateswara Rao Manga, University of Arizona
2:05 Group discussion

2:45 – 4:45 p.m. Breakout Session B


Option B1 (room B): Useful tools, (chaired by Christian Trott)

2:45 Moltemplate: a coarse-grained molecule builder for LAMMPS, (abstract), Andrew Jewett, Broad Institute
3:15 Integrating Open Source Software Applications for Building Molecular Dynamics Systems, (abstract), Bruce Allen, University of Denver
3:30 "Lammpsfe - user interface for LAMMPS", (abstract), Valeriu Smiricinschi, Scifes Inc.
3:50 Building LAMMPS Input Structures by Monte Carlo Means, (abstract), Pieter in 't Veld, BASF SE
4:15 MedeA instrument integrated into HPC Clouds and how this benefits LAMMPS users worldwide, (abstract), Timothy L. Thomas
4:30 Group discussion

Option B2 (room C): Solid state materials (metals, ceramics, semiconductors), (chaired by Jonathan Zimmerman)

2:45 "Nanomechanical and Nanotribological Responses of SiO2 Thin Films", (abstract), Fang-Yin Lin, University of Florida
3:00 "SiC Bicrystals Containing Intergranular Graphene", Stefan Bringuier, University of Arizona
3:15 "Thermal conductivity enhancement of paraffins by increasing the alignment of molecules through adding CNT/Graphene", (abstract), Hasan Babaei, Auburn University
3:30 Atomic scale investigation of grain boundary structure role on deformation and crack growth dynamics in Aluminum, (abstract), Ilaksh Adlakha, Arizona State University
3:45 Model-free test of local density mean-field behavior in electric double layers, (abstract), Brian Giera, UC Santa Barbara
4:00 Group discussion

Option B3 (room D): Coarse-grained, mesoscopic, granular, continuum systems, (chaired by Jeremy Lechman)

2:45 "Introduction to coarse-graining of liquids and soft matter", (abstract), Christoph Junghans, LANL
3:00 "Prediction of viscoelastic properties of polyurea using coarse gained molecular dynamics", (abstract), Vipin Agrawal, Arizona State University
3:20 Coarse-Grained Molecular Dynamics Simulations of Thermal Annealing of P3HT:PCBM Bulk Heterojunctions for Organic Photovoltaic Applications, (abstract), Jan Michael Carrillo, Oak Ridge National Laboratory
3:35 Performance Evaluation of Multi-Threaded Granular Force Kernels in LIGGGHTS, (abstract), Richard Berger, Johannes Kepler University Linz
3:50 Alternative fix rigid for small particles, (abstract), Trung Nguyen, Oak Ridge National Laboratory
4:05 Group discussion

5:30 – 7:00 p.m. no-host dinner @ Sandiagos (organized by Steve Plimpton)

7:00 - 8:00 p.m. optional Sandia Peak Tram ride, approx. $20 per person (organized by Steve Plimpton)

Thursday August 8, 2013

8:30 a.m. – 11:30 a.m. Session II: Faster, more accurate (chaired by Matt Lane)

8:30 Applications of LAMMPS GPU to soft matter simulations, (abstract), Trung Nguyen, Oak Ridge National Laboratory
8:50 Kepler GPUs and NVIDIA's Life and Material Science Applications Roadmap, (abstract), Mark Berger, NVIDIA Corporation
9:10 A next generation LAMMPS: preparing for the many-core future with Kokkos, Christian Trott, Sandia
9:30 Computational Science at the Argonne Leadership Computing Facility, (abstract), Nichols Romero, Argonne
9:50 break
10:03 LAMMPS strong scaling performance optimizations on Blue Gene/Q, (abstract), Paul Coffman, IBM
10:15 "The environment dependent dynamic charge potential", Krishna Muralidharan, University of Arizona
10:35 SNAP: Automated Generation of Quantum Accurate Potentials for Large-Scale Atomistic Materials Simulation, (abstract), Aidan Thompson, Sandia
11:00 Development and application of the ReaxFF reactive force field method, (abstract), Adri van Duin, Penn State

11:30 – 1:30 p.m. Poster Session (lobby), (chaired by Stephanie Teich-McGoldrick)

and Boxed Lunch, courtesy of Materials Design , (lobby/auditorium)

P01. "TBD", Baig Abdullah Al Muhit, University of Central Florida
P02. "Application of a Bottom-Up Approach to Study Bio-Adhesives’ Molecular Conformation", (abstract), Elham Fini and Kassu Gebresellasie, North Carolina A&T State University
P03. "Brownian dynamics simulations of adsorption and ordering of charged colloidal nanoparticles on an oppositely charged surface", (abstract), Jennifer Luna Singh, Rice University / AFRL
P04. Understanding 112 Slip in Tantalum, (abstract), Jonathan Zimmerman, Sandia
P05. Hybrid MD-continuum Simulation Methodology with Capability of Handling Two-Phase Flows, (abstract), Kasra Fattah-Hesary, Louisiana State University
P06. "Recent Developments in the Parallelization of Dissipative Particle Dynamics using Shardlow Splitting Algorithms", (abstract), James Larentzos, Dynamics Research Corporation (DRC)
P07. "Brief reviews of combined simulations of polymer nano composite systems by using LAMMPS", (abstract), Katsumi Hagita, National Defense Academy of JAPAN
P08. "A study of vibrational properties of twisted bilayer graphene system", (abstract), Mahesh Neupane, University of California, Riverside
P09. "Accurate and fast interpolations of quantum mechanical energy and force surfaces for large molecular systems", (abstract), Michael Salazar, Union University
P10. "Fluctuating Hydrodynamics Thermostats for Dynamic Implicit-Solvent Coarse-Grained Simulations", (abstract), Paul Atzberger, UC Santa Barbara
P11. "The effect of molecular length on the values of thermal conductivity and interfacial thermal conductance between the layers of long chain n-alkanes", (abstract), Rouzbeh Rastgar, Auburn University
P12. Indentation and Scratch Tests with LAMMPS in Nanoscale, (abstract), Sadri Sen, Ataturk University and Turgay Korkut, Agri Ibrahim Cecen University
P13. "Atomistic Investigations of Size and Strain Rate Dependence on the Mechanical Response of Nanoscaled Metallic Glass Structures", (abstract), Sara Adibi Sedeh, NUS
P14. Connectivity-based parallel replica dynamics method for simulating chemically reactive systems using ReaxFF reactive force field method, (abstract), Sumathy Raman, ExxonMobil Research and Engineering
P15. Multi-scale simulation of soft materials by using LAMMPS and OCTA/J-OCTA, (abstract), Taku Ozawa, JSOL Corporation
P16. "Multiscale Computational Polymer Research at the Army Research Laboratory", (abstract), Timothy Sirk, Army Research Laboratory
P17. Seamless elastic boundaries for lattices in molecular dynamics simulation, (abstract), Tristan Sharp, Johns Hopkins University
P18. Molecular Dynamics Simulations of Radiation Damage in Amorphous Silica: Effects of Hyperthermal Atomic Oxygen, (abstract), Vanessa Oklejas, The Aerospace Corporation
P19. Molecular Dynamics Simulations Require Sophisticated Software - Molecular Dynamics Studio is Delivering, Bruce Allen, University of Denver
P20. Building LAMMPS Input Structures by Monte Carlo Means, (abstract), Pieter in 't Veld, BASF SE
P21. "A LAMMPS based Virtual Workspace", (abstract), Greg Scantlen, CreativeC

1:30 p.m. – 4:15 p.m. Session III: Materials science, (chaired by Stan Moore)

1:30 Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid, (abstract), Colin Denniston, University of Western Ontario
1:50 Force-controlled walls and their application for shear tester simulations, (abstract), Andreas Aigner, Johannes Kepler University Linz
2:02 Using Ray Casting to Model Thermal Radiation in LIGGGHTS, Stefan Amberger, Johannes Kepler University Linz
2:14 Multiscale modeling of PECVD generated Silicon films with Kinetic Monte Carlo and LAMMPS molecular dynamics, (abstract), Andreas Bick, Scienomics SARL
2:26 LAMMPS Simulation in the Investigation of Dimensional Changes in Zirconium in the Presence of Alloying Elements and Hydrogen, (abstract), Clive Freeman, Materials Design, Inc.
2:46 break
3:00 Molecular Simulations of Repellant Surfaces for Chemical Biological Defense, QuickTime movies: ((movie_flat), (movie_2cones), (movie_6cones)), (abstract), Craig Knox, SAIC/Leidos, Inc. at US Army Edgewood Chemical Biological Center
3:12 "Green-Kubo simulations of Li+ transport in organic solvents", (abstract), Donald Ward, Sandia
3:24 "Self-assembly of Model Microtubules", (abstract), Mark Stevens, Sandia
3:44 Mechanical Properties of Glassy Polymer Blends and Thermosets, (abstract), David Rigby, Materials Design, Inc
4:10 "Request for feedback about LAMMPS and this workshop", Jonathan Zimmerman, Sandia

Evening: workshop recreational events