August 2011 LAMMPS Users' Workshop and Symposium

The second LAMMPS workshop and symposium for users and developers was held in Albuquerque, NM on August 9-11, 2011. Slides for most of the talks can be downloaded through the click-able links below. A list of attendees can be found here: attendees.

Tuesday August 9, 2011

1 – 4:30 p.m. Session I (auditorium) chaired by Paul Crozier

1:00 LAMMPS plans, Steve Plimpton, Sandia National Laboratories
1:30 Charge optimized many body (COMB) potential in LAMMPS, Tzu-Ray Shan, University of Florida
1:45 Coarse-grain modeling of lipid membranes, Mario Orsi, University of Southampton
2:00 15 minute break
2:15 H-bonding and Mechanics in Epoxy-Amine Polymer Networks from Atomistic Simulations, Craig Knox, US Army Research Laboratory
2:30 Analytical bond-order potential for cadmium telluride system, Xiaowang Zhou, Sandia National Laboratories
2:45 Using LAMMPS with the Knowledgebase of Interatomic Models (KIM), Ryan Elliott, University of Minnesota
3:00 Calculate pharmaceutical solubility using classical simulation tools, Joseph Tucker, Scienomics GmbH
3:15 15 minute break
3:30 Enhancing LAMMPS Capabilities: Granular Models, Coding Concepts, CAD Interoperability and Coupling to Continuum Methods, Christoph Kloss, JKU Linz
4:00 Molecular Simulations of Metal-Organic Frameworks, Jeffery Greathouse, Sandia National Laboratories
4:15 Inelastic Deformation in Shock-Loaded Pentaerythritol Tetranitrate (PETN), Reilly Eason, University of Missouri

6:00 p.m. no-host dinner @ Sandiagos and tram ride (both at 40 Tramway Rd NE) event led by Matt Lane

Wednesday August 10, 2011

8:30 – 12:00 Session II (auditorium) chaired by Stephanie Teich-McGoldrick

8:30 Enhanced sampling methods for biomolecular systems and self assembly
Michael Crowley, NREL
9:00 Using LAMMPS to map potential energy surfaces for forcefield development, Craig Tenney, Sandia National Labs
9:15 Effects of surface charge density and distribution on the nanochannel electro-osmotic flow, Bohumir Jelinek, Mississippi State University
9:30 15 minute break
9:45 Interatomic potentials in LAMMPS, Aidan Thompson, Sandia National Laboratories
10:00 Shock Simulations on Embedded-Atom-Method Copper with GPU acceleration
Steven Valone, LANL
10:15 Studies of the Molecular Weight Dependence of the Glass Transition Temperature of Oligomers Obtained using Molecular Dynamics Simulations, David Rigby, Materials Design, Inc.
10:30 GPU accelerated life and material science applications directions, Mark Berger, Nvidia, Inc.
10:45 15 minute break
11:00 GPU Acceleration in LAMMPS, W. Michael Brown, ORNL
11:30 Evaporation-induced nanoparticle self-assembly
Shengfeng Cheng, Sandia National Labs
11:45 Computing the Melting Points for Ionic Liquids Using Molecular Dynamics Simulations
Yong Zhang, University of Notre Dame

12 – 1 p.m. catered lunch (lobby/auditorium), courtesy of Sandia National Laboratories, organized by Rachel Leyba


1 – 2:45 p.m. Breakout Session A

Option A1 (room D): Tutorial session: getting started with LAMMPS, part 1, chaired by Craig Tenney

A two part 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 computer, there will be opportunities for discussion, hands-on work, and questions at the end of each tutorial.

1:00 Introduction to LAMMPS, Paul Crozier, Sandia National Laboratories
1:40 Overview of LAMMPS scripting, Craig Tenney and Matt Lane, Sandia National Laboratories
2:05 Real-world LAMMPS scripting
Matt Lane and Craig Tenney, Sandia National Laboratories
2:30 Group discussion

Option A2 (room G): Advanced interatomic potentials (ReaxFF, COMB, eFF, etc.), chaired by Aidan Thompson

1:00 Knowledgebase of Interatomic Models Application Program Interface, Valeriu Smirichinski, University of Minnesota
1:30 Development and application of ReaxFF reactive force field to the study of oxidation on complex Fe-based nanoalloys
Yun Kyung Shin, Pennsylvania State University
1:45 Performance Evaluation of USER-REAXC Package, Hasan Metin Aktulga, Lawrence Berkeley Lab
2:00 Group discussion

Option A3 (room H): Developers / hackers, chaired by Steve Plimpton

1:00 How to modify LAMMPS to meet your own needs, Steve Plimpton, Sandia National Laboratories
1:30 Support for LAMMPS in VMD: Setup, Monitoring, and Analysis
Axel Kohlmeyer, Temple University
1:45 Your requests for new LAMMPS features, capabilities, and improvements (group discussion)
2:00 Group discussion

Option A4 (room I): Soft materials (biomolecules, polymers, colloids), chaired by Stephanie Teich-McGoldrick

1:00 Coarse graining for soft materials in LAMMPS
Jay Oswald, Arizona State University
1:15 Effect of ion shape on dynamics of ionic liquids
Hongjun Liu, University of Notre Dame
1:30 Entanglements and Mechanical Strength of Polymer Welds, Ting Ge, Johns Hopkins University
1:45 Group discussion

3 – 4:45 p.m. Breakout Session B

Option B1 (room D): Tutorial session: getting started with LAMMPS, part 2, chaired by Matt Lane

A two part introduction to LAMMPS designed to get attendees up and running with LAMMPS quickly. This second session will include a panel discussion. Beginning with downloading and building, these tutorials will highlight major components of the code with an emphasis on examples and demos. Bring your computer, there will be opportunities for discussion, hands-on work, and questions at the end of each tutorial.

3:00 Welcome and panelist introductions (including panelists research area intro)
3:15 Pre-processing: creating system configurations
3:40 Post-processing and runtime analysis
4:05 Visualization methods
4:30 First steps toward customizing LAMMPS code
Matt Lane, Sandia National Laboratories

Option B2 (room G): GPUs / threading / faster simulation, chaired by Axel Kohlmeyer

3:00 LAMMPS Code and Script Development on a Two Node GPU and ManyCore Cluster
and EStella - a GPU and ManyCore Cloud Cluster for LAMMPS System Profiling
Greg Scantlen, Creative Consultants LLC
3:30 Autogenerating GPU-accelerated LAMMPS pair styles, Catherine O'Sullivan, Imperial College
3:45 Demonstration: Using LAMMPS with GPUs and OpenMP
Axel Kohlmeyer, Temple University
4:00 What is your best trick to run LAMMPS fast? (group discussion)

Option B3 (room H): Solid state materials (metals, ceramics, semiconductors), chaired by Todd Zeitler

3:00 Dislocation-Interface Interactions in Silicon, Lucas Hale, Sandia National Laboratories
3:15 Atomistic Modeling of Memristive Switching Mechanisms in Transition Metal Oxides
Robert Bondi, Sandia National Laboratories
3:30 Group discussion

Option B4 (room I): Coarse-grained, mesoscopic, granular, continuum systems, chaired by Mike Parks

3:00 Coarse Graining in Peridynamics
Stewart Silling, Sandia National Laboratories
3:15 Physical Aspects of Polymer Fibers and Nanocomposites with MD and DPD Simulations and Visual-Analytic Tools, Melissa Pasquinelli, North Carolina State University
3:30 Overview of the Atomistic-to-Continuum Package in LAMMPS, Jeremy Templeton, Sandia National Laboratories
4:00 Group discussion

5 – 6:30 p.m. Poster Session (lobby) chaired by Stephanie Teich-McGoldrick

P1. A Coarse-Graining Procedure for Mapping Atomistic Models, Chia-Chun Fu, U.C. Santa Barbara
P2. Atomistic Modeling of Iron and Steel
Jørn Skogsrud, Norwegian University of Science and Technology, NTNU
P3. Effect of Irradiation on Crack Propagation in Iron
Vijay Subramanian, Oklahoma State University
P4. Use of LAMMPS for the simulation of graphene
Sara Kadkhodaei, Brown University
P5. Segregation simulation using LAMMPS
Ram Chand, Beijing Institute of Technology, Beijing, China
P6. Implementation of the pressure profile calculation in spherical coordinates, Takenobu Nakamura, National Institute of Advanced Industrial Science and Technology
P7. Molecular dynamic simulation of glass formation in binary Co-W alloy using EAM
Ashish Singh, Oklahoma State University
P8. Molecular dynamics simulations of aggregation and structure in an ionomer melt
Lisa Hall, Sandia
P9. Overview of discrete element modelling in geomechanics
Catherine O'Sullivan, Imperial College
P10. Prediction of Thermal Conductivity of Colloidal Suspension via Molecular Dynamics Simulations
Hasan Babaei, Auburn University
P11. Stereoscopic Display of VMD visualized LAMMPS simulations
Greg Scantlen, Creative Consultants LLC
P12. Synchronous parallel kinetic Monte Carlo: Diffusion in Heterogeneous Systems, Enrique Martinez, LANL
P13. Equilibration of polymer melts
Gopinath Subramanian, LANL
P14. Toward more accurate simulations of CdTe semiconductor compounds
Donald Ward, Sandia National Lab Livermore
P15. The Relationship between Protein Diffusion and Protein Radius in the Lipid Bilayer
Allison Dickey, Sandia
P16. User interface of LAMMPS for calculation of actinide compound properties
Satoshi Minamoto, CTC
P17. Using simulated annealing coupled with parallel tempering in molecular dynamics simulations to create low-defect silica surfaces, Paul Norman, University of Minnesota
P18. Molecular dynamics simulation of fluid flow in confined systems
Anoosheh Niavarani, California Institute of Technology
P19. Parallel replica dynamic simulations of grain boundary motion
Shawn Coleman, University of Arkansas
P20. Molecular dynamics study of crack propagation behavior and mechanisms in Nickel
Jiaxi Zhang, The Johns Hopkins University
P21. Nanoparticle Diffusion into pores
Thiruvillamalai Mahadevan, TMHRI
P22. Combining locally optimized Interpolants with a multilevel QM/MM method for complex reactive simulations, Michael Salazar, Union University
P23. Microsolvation of Metal Ions in Water and Organic Solvents: QM/MM and MD-EXAFS Analyses
Srinivas Tulishetti, Indian Institute of Technology Kanpur

6:30 – 8:30 p.m. no-host dinner @ Tucanos (110 Central SW), organized by Paul Crozier

Thursday August 11, 2011

8:30 a.m. – 12:30 p.m. Session III (auditorium) chaired by Aidan Thompson

8:30 Challenges of Simulating Nanoparticles Suspensions, Gary Grest, Sandia National Laboratories
9:00 Simulation of Entangled Polymers with Dissipative Particle Dynamics, Timothy Sirk, Army Research Laboratory
9:15 The challenge of simulating the stressing of dense samples of sand, George Marketos, Imperial College, London
9:30 15 minute break
9:45 Large-scale Explicit Electron Molecular Dynamics and Applications to Materials/Phenomena in Extreme Conditions, Andres Jaramillo-Botero, California Institute of Technology
10:00 Molten salt eutectics from atomistic alchemical simulations, Saivenkataraman Jayaraman, Sandia National Laboratories
10:15 Granular Media Simulation in LAMMPS: Applications in Robotics, Open Issues and Desired Features
Rudranarayan Mukherjee, NASA JPL
10:30 Role of Interfaces in Spallation of a Multi-Layer Nanocomposite
Srinivasan Srivilliputhur, University of North Texas
10:45 15 minute break
11:00 Mesoscopic simulations of molten silicates using the LAMMPS code, and the use of LAMMPS at the UK National Nuclear Laboratory, Mark Bankhead, National Nuclear Laboratory, UK
11:30 Thermal transport in carbon nanotubes and graphene
Ajing Cao, Northwestern University
11:45 Resolving the Contribution of Deformation Mechanisms in Nanocrystalline Metals
Garritt Tucker, Sandia National Laboratories
12:00 Designing Tough Carbon Nanotube Fibers, Charles Cornwell, USACE
12:15 Workshop wrap-up, feedback, and follow-up, Paul Crozier, Sandia National Laboratories

Afternoon: workshop recreational events