LAMMPS Workshop and Symposium

August 1-3, 2017

The fifth LAMMPS Workshop and Symposium was held in Albuquerque, NM, at the University of New Mexico (UNM) Continuing Education Building (1634 University Blvd NE, map).

We thank the DOE/NNSA ASC program for financial support in hosting the workshop. We also thank industrial partners JSOL, Materials Design, Inc., and Scienomics for graciously providing lunches, snacks, and drinks for the attendees. Here is more info on the LAMMPS-related tools these sponsors create and provide.

All the PDFs we receive for talks, posters, tutorials, and breakout sessions will be posted below, for viewing or download.

Video of the main session talks should be accessible on-line in the next few weeks. We will post the link here when it's available.

Here is the list of workshop attendees.

Click for a larger, downloadable version (4.5 MB)

The workshop program included a keynote speaker and 6 invited talks:

Keynote speaker: George Karniadakis (Brown University): The DPD Alphabet for Mesoscopic Modeling
Mike Chandross (Sandia National Labs): Understanding the Mechanisms of Metallic Friction from Atomistic Simulations
Amalie Frischknecht (Sandia National Labs): Molecular Dynamics Simulations of Ion-Containing Polymers, PDF
Nir Goldman (Lawrence Livermore National Lab): LAMMPS Driven Quantum Simulations of Prebiotic Chemistry in Impacting Icy Materials, PDF
Tim Mattox (Engility Corporation): Highly-Scalable Discrete-Particle Simulations with Novel Coarse-Graining: Accessing the Microscale, PDF
Danny Perez (Los Alamos National Lab): Long-timescale Simulations with Accelerated Molecular Dynamics and the EXAALT package
Ale Strachan (Purdue University): Use of molecular dynamics to uncover the operation of electrochemical nanodevices, design materials for shock energy absorption and metallic metamaterials with ultra-low stiffness, PDF

Program

Tuesday August 1, 2017

Tuesday AM: Two tutorials

LAMMPS Beginner tutorial: 8:30 AM to 12 noon

Organized by Matt Lane and Aidan Thompson (Sandia)

8:30 Welcome and agenda, Matt Lane (Sandia), PDF

8:35 General LAMMPS overview, Aidan Thompson, Sandia, PDF

8:50 Download, build, and run LAMMPS, Matt Lane (Sandia), PDF, PDF handout

9:10 Basic output post-processing, Aidan Thompson (Sandia), PDF

9:25 Visualization of results, Mitch Wood (Sandia), PDF

9:40 Break

9:50 Quick tour of LAMMPS, Steve Plimpton (Sandia), PDF

10:45 Hands-on activity with simple examples that come with LAMMPS, Aidan Thompson (Sandia), PDF

11:30 Unstructured one-on-one exploration (until noon)

GitHub tutorial: 9:30 AM to 12 noon

Organized by Richard Berger (Temple U) and Anders Hafreager (U Oslo)

9:30 LAMMPS GitHub Introduction / Continuous Integration, Richard Berger, PDF

10:00 Git Introduction, Anders Hafreager, PDF

10:45 GitHub Hands-on (until noon), Anders Hafreager & Richard Berger

12 noon to 1 PM: Lunch in lobby (pizza, salad, soft drinks)

1 PM - 5:30 PM General session of technical talks

Session chair: Amalie Frischknecht (Sandia)

1:00 Steve Plimpton, Sandia: Welcome and what's new in LAMMPS, PDF
1:30 (keynote) George Karniadakis (Brown University): The DPD Alphabet for Mesoscopic Modeling
2:15 Giacomo Fiorin, Temple University: Enhanced sampling simulations with the Colvars module
2:30 Jason Koski, Sandia National Laboratories: Effect of an electric field on capillary waves
2:45 Javier Rojas, Universidad de Santiago de Chile: Structure and energy properties of Fe(x)-Cu(1-x) nanoparticles: Morphology and size effects, PDF
3:00 Dan Bolintineanu, Sandia National Laboratories: Recent developments and applications of LAMMPS capabilities for simulations of granular media, PDF

3:15 PM break

3:30 Alexander Moore, Sandia National Laboratories: Understanding the Plastic Response of Tantalum in Quasi-Isentropic Compression using Atomistic Simulations
3:45 Ray Shan, Materials Design, Inc: Mechanical Properties of Glassy Polymer Blends and Thermosets from Atomistic Simulations, PDF
4:00 Pieter in 't Veld (BASF): Soft Matter simulations and workflows at BASF
4:15 Drew Rohskopf, Georgia Institute of Technology: Phonon Optimized Potentials
4:30 Julien Tranchida, Sandia National Laboratories: Parallel implementation of spin and spin-lattice simulations in LAMMPS, PDF
4:45 Jacob Gissinger, University of Colorado Boulder: Modeling Chemical Reactions in Classical Molecular Dynamics Simulations, PDF
5:00 (invited) Nir Goldman (Lawrence Livermore National Lab): LAMMPS Driven Quantum Simulations of Prebiotic Chemistry in Impacting Icy Materials, PDF

Tuesday dinner: No-host dinner at County Line Barbeque, 9600 Tramway Blvd NE, and optional tram-ride to top of Sandia Crest, meet up for rides in lobby at 5:30 PM. Dinner cost of ~$30, tram cost of ~$25.

Wednesday August 2, 2017

8:30 AM - 12 noon General session of technical talks

Session chair: Mark Stevens (Sandia)

8:30 (invited) Amalie Frischknecht (Sandia National Labs): Molecular Dynamics Simulations of Ion-Containing Polymers, PDF
9:00 Brandon Peters, Sandia National Laboratories: Dynamics in entangled polyethylene melts using coarse-grained models
9:15 Lucas Hale, National Institute of Standards and Technology: Interatomic Potentials Repository: interatomic potentials, property calculation scripts, and related resources, PDF
9:30 Ellad Tadmor, University of Minnesota: The OpenKIM testing framework for interatomic potentials, PDF
9:45 Ryan Elliott, University of Minnesota: A Brief User's Guide and Developer's Introduction to OpenKIM, PDF
10:00 Nikhil Chandra Admal, University of California Los Angeles: MDStressLab - Computing stress in atomistic simulations, PDF

10:15 PM break

10:30 Robert Elder, U.S. Army Research Laboratory: Simulation studies of shock wave propagation and reflection in semi-crystalline polyethylene
10:45 Aidan Thompson, Sandia National Laboratories: Large-Scale Reactive Simulations of Shocked Energetic Materials, PDF
11:00 (invited) Tim Mattox (Engility Corporation): Highly-Scalable">PDF Discrete-Particle Simulations with Novel Coarse-Graining: Accessing the Microscale
11:30 Richard Berger, Temple University: Using Python in LAMMPS, PDF
11:45 Anders Hafreager, University of Oslo: Atomify - increased productivity with live visualization, PDF

12 noon to 1 PM: Box lunches (lobby)

1 PM - 5:30 PM Breakout sessions

8 one-hour breakouts (two per hour in parallel)

1:00-1:15: one-minute breakout advertisements

Materials track: all in side ballroom

1:15-2:15 Solid-state: chaired by Ray Shan (Materials Design, Inc.), PDF

1:15 Potentials for solid state materials: Discussion and Q&A
1:30 Felipe Valencia, University of Chile: Confinement effects in irradiation of nanocrystalline diamond
1:45 Tahereh Majdi, McMaster University: Leveraging epitaxy to control thermal transport
2:00 Obtaining properties for solid state materials: Discussion and Q&A

2:15-3:15 Soft matter: chaired by Mark Stevens (Sandia), PDF

2:30 Qiang Wang, Colorado State University: Systematic and Simulation-Free Coarse Graining of Polymer Melts, PPT slideshow file
2:45 Minghao Liu, Arizona State University: A united atom model for polyurea elastomers

3:15 PM break

3:30-4:30 Coarse graining: chaired by Dan Bolintineanu (Sandia), PDF

3:45 Svetoslav Nikolov, Georgia Institute of Technology: Modeling non-linear micromechanics of hydrogels using dissipative particle dynamics

4:30-5:30 Interfaces (solid/liquid): chaired by Jeff Greathouse (Sandia), PDF

4:45 Rafael I Gonzalez, Universidad Mayor: Simulation of Aluminosilicate Nanotubes (Imogolite) Immersed in Water
5:00 Douglas Franz, University of South Florida: Simulations of Gas Sorption in rht-MOF-9, PDF

Software track: all in main auditorium

1:15-2:15 Simulation setup via EMC: chaired by Pieter in't Veld (BASF), PDF

This is a hands-on tutorial for building complex initial structures using EMC. If possible, participants should download and install EMC (https://montecarlo.sourceforge.net) and LAMMPS on their laptop beforehand, in order to maximize time devoted to working with EMC.

- Introduction
- Installation (see comment above)
- Treatment of provided examples
- Treatment of user-supplied examples

2:15-3:15 Visualization (Ovito, VMD): chaired by Mitch Wood (Sandia), PDF

3:15 PM break

3:30-4:30 Performance via accelerator packages: chaired by Stan Moore (Sandia), PDF, PDF2

4:30-5:30 Developers brainstorm: chaired by Steve Plimpton (Sandia), PDF

4:45 Christoph Junghans, Los Alamos National Laboratory: LAMMPS on CMake, PDF

Wednesday dinner: No-host dinner at Los Cuates, 4901 Lomas Blvd, meet up for rides in lobby at 5:30 PM. Dinner cost of ~$20.

Thursday August 3, 2017

8:30 AM - 12:30 PM General session of technical talks and posters

Session chair: Aidan Thompson (Sandia)

8:30 (invited) Ale Strachan (Purdue University)
Use of molecular dynamics to uncover the operation of electrochemical nanodevices, design materials for shock energy absorption and metallic metamaterials with ultra-low stiffness, PDF
9:00 Shawn Coleman, U.S. Army Research Laboratory: HCP Grain Boundary Motion Via Artificial Driving Force Methods
9:15 Remi Dingreville, Sandia National Laboratories: A primer on selecting grain boundary sets for comparison of interfacial fracture properties in molecular dynamics simulations, PDF
9:30 Mitchell Wood, Sandia National Laboratories: Linear Scaling, Quantum-Accurate Interatomic Potentials with SNAP; Reaching those Hard-to-Reach Places in Classical Molecular Dynamics
9:45 Christian Negre, Los Alamos National Laboratory: LAMMPS and the LATTE density functional tight-binding code, PDF
10:00 (invited) Danny Perez (Los Alamos National Laboratory): Long-timescale Simulations with Accelerated Molecular Dynamics and the EXAALT package

10:30 AM one-minute poster advertisements

10:45 AM to 11:45 AM Poster session (lobby)

Nathaniel Blevins, Arkansas State University: Molecular Dynamic Simulations: Estimating Engineering & Thermodynamic Properties of Asphaltene & Resin
Jonathan Bollinger, Sandia National Laboratories, CINT: Microscopic simulations show allosteric compaction in microtubules drives catastrophe
Jordan Campbell, University of California, San Diego: Diffusion Studies of Structurally Amorphous Metal Foils Using Molecular Dynamics Simulation
Kenta Chaki, JSOL Corporation: Dissipative particle dynamics simulations for dispersion of polymer grafted nanoparticles
Jennifer Clark, Sandia National Laboratories: Modeling the Impact of Sulfonate Concentration on Proton Diffusion in Hydrated SDAPP
Rachel Flanagan, University of California, San Diego: Non-equilibrium simulations of shock-induced horizontal defects and amorphization in 4H silicon carbide
Eric Hahn, Los Alamos National Laboratory: Towards Predicting a Microstructure's Susceptibility to Spall: Non-equilibrium Molecular Dynamics Simulations of Tantalum, PDF
Keith Jones, Sandia National Laboratories: Molecular dynamics study of shock compression in porous silica glass
Zhen Li, Brown University: Mesoscopic Modeling, Concurrent Coupling and Multiscale Framework, PDF
Aria Mansouri Tehrani, University of Houston: Effect of Point Defects on the Phase Transformation of NiTi Shape Memory Alloy, PDF
Ygor Morais Jaques, University of Campinas: Nanodroplets Behavior on Functionalized Nanopores, PDF
Ingrid Marcela Padilla Espinosa, North Carolina A&T State University: Molecular dynamics simulations of Calcium Silicate Hydrates under hydrostatic compression
Felipe Perez, University of Oklahoma: Methane and carbon dioxide adsorption in kerogen models using molecular simulations, PDF
Cristiano Woellner, University of Campinas / Rice University: Molecular Dynamics Investigation of energy absorption of crystalline 3D porous carbon-based structures
Mohammad Reza Zamani Kouhpanji, University of New Mexico: Molecular dynamic simulations of Lithium Cobalt Oxide cathode materials, PDF

11:45 (invited) Mike Chandross (Sandia National Labs): Understanding the Mechanisms of Metallic Friction from Atomistic Simulations

12:15 Workshop feedback, group photo - led by Aidan Thompson (Sandia)

Thursday 12:30 PM to 1:30 PM: Box lunches (lobby)

Thursday PM

Recreational actitivies

We held nice group dinners on Tuesday and Wednesday at the County Line BBQ and Los Quates.

After dinner on Tues, we went on a tram-ride up to the top of Sandia Crest (10500 ft).

After the workshop ended, we had two Thursday afternoon activities.

Hiking the Tree Spring Trail in the Sandia Mountains

Click for larger, downloadable versions of last two

For those who enjoy a pleasant hike, we will be walking up the Tree Spring Trail, which is on the cooler, shadier east side of the Sandia Mountains, 30-40 minutes from Albuquerque by car. We recommend everyone car pool as much as possible for the drive up and back. From the trailhead, the trail climbs approximately 1000 feet in 2 miles to a point on the ridgeline of the Sandia mountains. After exploring and admiring the views from the ridge, we'll return via the same route. This hike is 'moderate' in difficulty and the pace will be leisurely. The total walking distance (there and back) is approximately 4 miles. The trail starts at 8500 feet above sea level, going up to 9500 feet. The reduced fugacity of O2 will be somewhat noticeable, but that will be more than compensated for by the cooler temperatures. We don't know exactly how long the hike will last, but a rough guess is three to four hours, including the drive.

Visit to the Old Town section of ABQ, which included the Rattlesnake Musuem and some local history going back 300+ years.

Coporate sponsors

Here is more info on the companies who helped sponsor the workshop, their LAMMPS-related products, and contact info for who will be at the workshop. Two of the companies will also have display tables in the lobby during the conference.

JSOL Corporation

The JSOL Corporation has released the latest version of J-OCTA, v3.1, in July 2017. In v3.1, various new features and enhancements, such as new force field definitions and a force field optimizing functionality, have been added. The usability of the interface has been remarkably improved, an interface access to the job management system has been added, and the platform has been enhanced. Please try and explore the powerful and user-friendly J-OCTA v3.1 at our JSOL booth at the LAMMPS Workshop and Symposium 2017.

More details are available here.

Contact:

Dr. Taku Ozawa, Ph.D. taku.ozawa at jsol.co.jp Material Sciences Team Engineering Technology Division JSOL Corporation

Materials Design, Inc.

Materials Design is the leading atomistic simulation software and services company for materials. We help users across many diverse disciplines improve existing materials, design new materials, predict their properties, and generate value through innovation. MedeA-LAMMPS fully automates the use of LAMMPS, and unlocks its power for both experimental and theoretical groups seeking to increase their productivity. MedeA combines LAMMPS with a sophisticated GUI, databases, structure builders, and computation modules for tackling complex structures and labor-intensive property extractions. In addition, MedeA’s unique integration of ab initio and forcefield methods enables users to model each step during the research life cycle and allows them to understand the mechanism of physical processes. High-throughput and high-fidelity modeling enabled by MedeA provides guidance to screen large numbers of design options for materials before committing to experiments saving resources, and maximizing your productivity. Check out http://materialsdesign.com for more details.

Stop by the Materials Design table and say hello to Dr. Ray Shan (rshan at materialsdesign.com) and Dr. Naida Lacevic (nlacevic at materialsdesign.com), who will be happy to answer any questions you may have on our products.

Scienomics

Contact: Lalitha Subramanian (lalitha at scienomics.com)