August 2019 LAMMPS Users’ Workshop and Symposium Program
The sixth LAMMPS Workshop and Symposium will be held in Albuquerque, NM, at the University of New Mexico (UNM) Continuing Education Building (1634 University Blvd NE, map).
Thanks to our funders
We thank the DOE/NNSA ASC program for support in hosting this workshop. We also thank these partners for graciously providing additional financial support:
• Materials Design Inc., Tues lunch and coffee/snacks • JSOL Corp., Wed and Thurs lunches • Center for Non-Linear Studies (CNLS) at Los Alamos National Laboratory, travel expenses for several presenters
Day 1: Tuesday August 13th, 2019
8:30 AM – 12:00 PM Beginners Tutorial Part I
Coffee and bagels will be available
8:30 AM Welcome and Tutorial Overview, Axel Kohlmeyer (Temple U)
8:45 AM A Brief Overview of Molecular Dynamics, Statistical Mechanics, Atomic Potentials, Stan Moore (Sandia)
9:30 AM A Quick Tour of LAMMPS, Steve Plimpton (Sandia) Input scripts and output, classes of commands, basic & more advanced features, parallelism
10:15 AM Break
10:30 AM Self-Study Tutorial with Provided Exercises 12:00 PM - 1:00 PM Lunch in lobby (pizza, salad, lemonade and water)
1 PM - 5:30 PM Beginners Tutorial Part II, with 3 optional Intermediate Sessions
1:00 Continued Self-Study Tutorial with Provided Exercises or LAMMPS Examples
2:00 Advanced System building using VMD/TopoTools and LAMMPS, Axel Kohlmeyer (Temple U)
3:15 PM Break: Coffee and cookies will be available.
3:30 Compiling LAMMPS from Source, Richard Berger, Axel Kohlmeyer (Temple U)
4:00 OpenKIM Tutorial, Ryan Elliot and Ellad Tadmor (U Minnesota)
5:00 PM Dinner
We will provide info and coordinate at the end of the tutorial on 2-3 nearby restaurants where we can gather and socialize for dinner. Car pooling is encouraged.
• Matanza, 3225 Central Ave NE • Range Cafe, 2200 Menaul Blvd NE • Los Cuates, 4901 Lomas Blvd NE
Day 2: Wednesday August 14th, 2019
8:30 AM – 12:00 PM General session of technical talks Session chair: Aidan Thompson (Sandia)
Coffee and bagels will be available
8:30 Steve Plimpton, (Sandia National Labs) "Welcome and what's new in LAMMPS"
9:00 (keynote) Vasily Bulatov (Lawrence Livermore National Lab) Crossing Materials Scales with LAMMPS
9:45 (invited) Alex Stukowski (Darmstadt University of Technology) OVITO 3.0: A powerful data analysis and visualization solution for LAMMPS users
10:15 AM Break
10:30 Mitch Wood, Sandia National Labs Top-Down versus Bottom-Up Multiscale Modeling of Energetic Materials
10:45 Remi Dingreville, Sandia National Labs Insights into modeling radiation damage using atomistic simulations
10:30 Robert Elder, U.S. Army Research Laboratory Simulation studies of shock wave propagation and reflection in semi-crystalline polyethylene
11:00 Julien Tranchida, Sandia National Labs SPIN, a package for coupled spin and lattice simulations in LAMMPS
11:15 Javier Rojas, Universidad de Santiago de Chile Modulated strength on FeNi nanowires
11:30 Sungkwang Mun, Mississippi State University Modified Embedded Atom Method with Bond Order Implementation in LAMMPS
11:45 Andrew Rohskopf, MIT Vibrationally Accurate Interatomic Potentials
12:00 PM - 1:00 PM: Box lunches from UNM catering (lobby)
1:00 PM - 5:30 PM General Session of technical talks Session chair: Mitch Wood (Sandia)
1:00 (invited) Niels Gronbech-Jensen (UC Davis) Acquisition of Precise Statistics in Stochastic Langevin Molecular Dynamics
1:30 Kipton Barros, Los Alamos National Lab Building better datasets: active learning and transfer learning
1:45 Andrew Garmon, Clemson University Parallel Trajectory Splicing
2:00 Yidong Xia, Idaho National Laboratory Adaptive MPI for LAMMPS
2:15 Stan Moore, Sandia National Labs LAMMPS KOKKOS Package: The quest for performance portable MD
2:30 Lucas Hale, NIST Interatomic Potentials Repository and iprPy
2:45 Ellad Tadmor, University of Minnesota OpenKIM: A Repository of Tested Interatomic Potentials for use with LAMMPS
3:00 Ryan Elliott, University of Minnesota A How-To Tutorial on Using OpenKIM with LAMMPS
3:15 PM Break: Coffee and cookies will be available.
3:30 Dan Bolintineanu, Sandia National Labs Granular simulations with LAMMPS: enhanced contact models and applications to powder rheology
3:45 Huilin Ye, University of Connecticut A highly efficient and portable fluid-structure simulation package implemented in LAMMPS
4:00 Adrian Diaz, University of Florida CAC simulation with LAMMPS
4:15 Ketan Khare, NIST Quantitative Integration of Atomistic Simulation and Experiment for Cross-linked Epoxy Network
4:30 Allan Avila, University of California, Santa Barbara Modeling Hydrogen-Oxygen Combustion via Programmable Potentials
4:45 Jacob Gissinger, University of Colorado DisARMMD: Distance-Actuated Reaction Mechanisms in Molecular Dynamics
5:00 (invited) Susan Rempe (Sandia National Labs) Assessing Biomolecular Hydration Mimicry for Ion Permeation through Membrane Channels
6:00 No-host dinner and tram ride to top of Sandia Mountains
We have a group reservation at the County Line Barbecue, 9600 Tramway Blvd NE, which is 13 miles from the UNM conf center, at the foot of the Sandia mountains. Car pooling encouraged.
We've ordered the Cadillac family style menu (see page 2), which includes all-you-can-eat ribs, several other BBQ meats, sides, and homemade ice cream. Vegetarian options (e.g. kabobs) are also available. With tax and tip it comes to $38 per person. Pricey, but lunches are provided, and it's our one big workshop social event! After dinner, those who wish can join us to ride the ABQ Tram ($25) to the top of the mountain (6000 up to 10000 ft elevation) and see the city views and lights. Even in the summer it can be cool and windy on top, so it's a good idea to bring a light jacket or sweater. This is also a good test of whether you're scared of heights (1000 ft drop across the final canyon).
Day 3: Thursday August 15th, 2019
8:30 AM - 10:30 AM General Session of technical talks Session chair: Stan Moore (Sandia)
Coffee and bagels will be available
8:30 (invited) Ray Shan (Materials Design Inc.) High Value from High Throughput: Harness the Power of LAMMPS with MedeA
9:00 Christoph Kloss, DCS Computing Marketplace - towards an online gateway to materials modelling
9:15 Kosuke Ohata, JSOL Corporation Integrated simulation system for soft materials, J-OCTA
9:30 Andrew Jewett, The Scripps Research Institute General Agent Based Modeling in LAMMPS
9:45 Godehard Sutmann, Juelich Supercomputing Centre, Forschungszentrum Juelich A Load Balancing Library for Particle Simulation Codes
10:00 (invited) Xiang-Guo Li (UC San Diego) Quantum-accurate Force Fields from Machine Learning of Large Materials Data
10:30 AM Group photo (Matt Lane)
10:35 AM - 12:00 PM Poster Session Session chair: Julien Tranchida (Sandia)
For the first time this year, we will have an award for the best poster, judged by a sophisticated machine learning algorithm (with possible human intervention).
10:35 AM One-minute poster advertisements
11:00 AM Posters in lobby See the list of posters at the end of this document
12:00 PM Box lunches from UNM catering (lobby)
12:55 PM Presentation of best poster award. This is being given in honor of Ahmed Ismail, a former collaborator of many of us at Sandia, and a LAMMPS contributor and user, who passed away this year.
1:00-5:30 PM Breakout Sessions (two parallel tracks A and B) Session chair: Aidan Thompson (Sandia)
1:00-1:15: one-minute breakout advertisements
Track A
1:15-2:15 PM Pre- and post-processing tools & visualization (tutorial) Chaired by Mitch Wood (Sandia)
Alex Stukowski (Darmstadt University of Technology) This presentation will demonstrate how to use OVITO with LAMMPS.
Andrew Jewett (The Scripps Research Institute) "Creating molecular assemblies and force fields with Moltemplate" This presentation will demonstrate how to use Moltemplate, PACKMOL, and VIPSTER (time permitting).
2:15-3:15 PM Adding features to LAMMPS (tutorial)
Presented by Richard Berger and Axel Kohlmeyer (Temple U)
Topics: code structure, git, Github, best practices
3:15 PM Break: Coffee and cookies will be available.
3:30-4:30 PM Machine-learned interatomic potentials (contributed) Chaired by Thomas O'Connor (Sandia)
3:30 PM Ying Li, University of Connecticut Machine learning force field for polymer modeling
3:45 PM Chun-Wei Pao, Research Center for Applied Sciences, Academia Sinica Neural Network Potential of Complex Perovskite Materials and Their Implementation to LAMMPS
4:00 PM James Hickman, NIST Development of physically informed neural network (PINN) interatomic potentials
4:15 PM Mary Alice Cusentino, Sandia National Labs Machine Learned Interatomic Potentials for Modeling Plasma Material Interactions
4:30-5:30 PM Solid-state and soft materials (contributed) Chaired by Amalie Frischknecht (Sandia)
4:30 PM Tuan Ho, Sandia National Labs Molecular Simulation of the Multicomponent Interaction in Shale Nanopores
4:45 PM Rafael Gonzalez, Center for Applied Nanotechnology, Universidad Mayor Molecular simulations of carbon allotropes in processes with creation and destruction of chemical bonds
5:00 PM Omar Almahmoud, University of North Texas Water vapor diffusion in polyurethane silica nano-composite
5:15 PM Samuel Baltazar, Universidad de Santiago de Chile Nanostructurated systems for water remediation process
Track B
1:15-2:15 PM VOTCA and LAMMPS for electronic spectroscopy and transport: Part I (tutorial)
Chaired by Christoph Junghans (LANL)
In this breakout (and the following one) you will learn how to use VOTCA to simulate electron/hole/exciton transport and compute optical spectra for organic molecules using LAMMPS trajectories.
The 2 hours will start with a 25 min introduction and explanation of the theory and the implementation in VOTCA. This is followed by a hands-on session.
If you want to participate in the hands-on session, please have docker installed on your laptop:
• Windows: https://docs.docker.com/docker-for-windows/install/ • MacOs: https://docs.docker.com/docker-for-mac/ • Ubuntu: https://docs.docker.com/install/linux/docker-ce/ubuntu/
2:15-3:15 PM VOTCA and LAMMPS for electronic spectroscopy and transport: Part II (tutorial) Chaired by Christoph Junghans (LANL) See description in previous breakout.
3:15 PM Break
3:30-4:30 PM Coarse grained systems (atomistic, meso, continuum) (contributed) Chaired by Dan Bolintineanu (Sandia)
3:30 PM Yu-Hang Tang, Lawrence Berkeley National Lab Marginalized Graph Kernel for Molecular Property Prediction
3:45 PM David Rosenberger, Los Alamos National Laboratory Coarse grained molecular dynamics simulations in the isothermal,isobaric ensemble
4:00 PM Ishan Srivastava, Sandia National Labs Discrete Element Simulations of Li-ion Electrodes using Brownian and Granular Dynamics
4:15 PM Christoph Kloss, DCS Computing "Modelling of flow of viscoelastic materials with DEM and CFD"
4:30-5:30 PM Simulation setup via EMC (tutorial)
Presented by Pieter in 't Veld (BASF)
6:00 PM No-host dinner
Plans for this are TBD, since we don't yet know how many people are sticking around after the workshop ends. We'll likely head to ABQ's Old Town area where there are several good restaurants and some site seeing we can do.
And for those still here on Fri AM, Aidan is talking about organizing a group hike.
Map to County Line Barbeque Restaurant and Tram to Sandia Crest
Address: 9600 Tramway Blvd , Albuquerque, NM 87122
Head north on University Blvd NE Turn left onto N Frontage Rd (signs for I-40 W) Turn right onto Frontage Rd N Continue onto Pan American Frontage Rd N Use the left lane to take the ramp onto I-25 N Follow I-25 N to NM-556 E/tramway Rd NE – Exit 234
LAMMPS Posters Thursday August 15th, 2019
(1) John Clay (ERC, Inc.) "Using LAMMPS to Model Vapor-Liquid Equilibrium" (2) Yu-Hang Tang (Lawrence Berkeley National Lab) "Marginalized Graph Kernel for Molecular Property Prediction" (3) Kenji Nishimura (National Institute of Advanced Industrial Science and Technology) "Molecular dynamics study on defect formation in SiC film" (4) Rodolfo Aguirre (University of Texas at El Paso) "Using Molecular Dynamics to study polycrystalline interfaces and grain boundaries in CdTe heterostructures" (5) Chun-Yaung Lu, (Texas Advanced Computing Center, UT Austin) "A Notebook Based Platform for Computational Materials Science and Chemistry" (6) Michael DeLyser (Pennsylvania State University) "Bottom-up Open-source Coarse-graining Software" (7) Ryan Szukalo (Penn State University) "Investigating the State Point Dependence of Coarse-Grained Potentials Across a Glass Transition" (8) Dmitry Luchinsky (SGT Inc at NASA Ames Research Center) "Atomistic model of welding at polymer interfaces for aerospace applications" (9) Hideyo Yoshida (JSOL Corporation) "Creating Representative Volume Element by LAMMPS for Finite Element Analysis" (10) Felipe Perez (University of Oklahoma) "Molecular signatures of enhanced oil recovery in shale organic pores" (11) Naida Lacevic (Materials Design, Inc.) "Designing Atomistic Simulation Workflows with MedeA®, A Case Study: Viscoelasticity of Glycerol at Ultra-high Frequencies" (12) Manav Bhati (Rice University) "Multi-scale investigation of adhesion properties of Si/polymer interfaces using ReaxFF reactive force field" (13) Visal Subasinghege Don (Louisiana State University) "Computational Investigations of Structure and Dynamics at the Interface" (14) Vaibhav Palkar (Clemson University) "Development of a DPD framework for simulating tetra-PEG hydrogels with degradable crosslinks" (15) Hyungmook Kang (UC Berkeley) "Molecular Insight into the Lower Critical Solution Temperature Transition of Ionic Liquids" (16) Jan Lugowski (Purdue University) "Turbulence: Mathematics or Physics Problem?" (17) Kevin Hanley (University of Edinburgh) "Multi-level contact detection to enable efficient polydisperse DEM simulations using LAMMPS" (18) Arjun Valiya Parambathu (Rice University) "Computing NMR relaxation in alknae systems using Molecular Dynamics" (19) Mohamed Mehana (University of Oklahoma) "Molecular modeling of Kerogen Wettability" (20) John Karnes, Lawrence Livermore National Lab "Toward Photopolymer Resin Design for Additive Manufacturing" (21) Matthew Flamini, Rowan University "Modulating of the mechanical properties of electrospun Polycaprolactone nanofibers with heat treatment" (22) Katsumi Hagita, National Defense Academy of Japan "Coarse-Grained MD Simulations of Nanovoids in Elongated Polymer Nano- Composites" (23) Cameron Shock, Michigan Technological University "Solvation Energy of Ions in a Stockmayer Fluid"