LAMMPS Workshop and Symposium

August 13-15, 2019


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

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

Here is the list of workshop attendees.

Click on a pic for a larger version, which can be downloaded.

The 1st place poster award was presented to Vaibhav Palkar (Clemson University).

The 2nd place poster award was presented to Felipe Perez (University of Oklahoma).

See details on these and other posters below.

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:

Here is more info on the LAMMPS-related tools these sponsors create and provide.

Invited speakers

Our workshop program included a keynote speaker and 5 invited talks:

Keynote speaker: Vasily Bulatov (Lawrence Livermore National Lab), bio
Crossing Materials Scales with LAMMPS, PDF
Susan Rempe (Sandia National Labs), bio
Assessing Biomolecular Hydration Mimicry for Ion Permeation through Membrane Channels, PDF
Niels Gronbech-Jensen (UC Davis), bio
Acquisition of Precise Statistics in Stochastic Langevin Molecular Dynamics
Ray Shan (Materials Design, Inc.), bio
High Value from High Throughput: Harness the Power of LAMMPS with MedeA, PDF
Alex Stukowski (Darmstadt University of Technology), bio
OVITO 3.0: A powerful data analysis and visualization solution for LAMMPS users, PDF
Xiang-Guo Li (UC San Diego), bio
Quantum-accurate Force Fields from Machine Learning of Large Materials Data, PDF


Tuesday August 13, 2019

All-day beginners tutorial

IMPORTANT: Instructions as to tutorial software you should download and/or install on your laptop before the workshop is posted at this tutorial site.

Note that final info may not be posted there until Fri, Aug 9. A couple of the LAMMPS developers are working through some last-minute glitches for this collection of software that may not be settled until Fri.

What you can and should do now is install the Virtual Box virtual machine software on your laptop. It can either be downloaded from for Windows, Mac, Linux. Or it is also available prepackaged for several popular Linux distributions; you can install it directly via your distribution's package manager.

Coffee and bagels will be available.

8:30-12:00 Beginners Tutorial Part I

8:30 Welcome and Tutorial Overview
Axel Kohlmeyer (Temple U)
8:45 A Brief Overview of Molecular Dynamics, Statistical Mechanics, Atomic Potentials
Stan Moore (Sandia)
9:30 A Quick Tour of LAMMPS
Steve Plimpton (Sandia)
Input scripts and output, classes of commands, basic & more advanced features, parallelism
10:15 Break
10:30 Self-Study Tutorial with Provided Exercises

12:00 Pizza lunch

1:00-5:30 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 Break
3:30 Compiling LAMMPS from Source
Richard Berger, Axel Kohlmeyer (Temple U)
4:00 OpenKIM Tutorial
Ryan Elliott and Ellad Tadmor (U Minnesota)

5:00 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.

Wednesday August 14, 2019

8:30-12:00 General Session of technical talks

Coffee and bagels will be available.

Session chair: Aidan Thompson (Sandia)

8:30 Steve Plimpton, (Sandia National Labs)
"Welcome and what's new in LAMMPS", PDF
9:00 (keynote) Vasily Bulatov (Lawrence Livermore National Lab)
Crossing Materials Scales with LAMMPS, PDF
9:45 (invited) Alex Stukowski (Darmstadt University of Technology)
OVITO 3.0: A powerful data analysis and visualization solution for LAMMPS users, PDF

10:15 Break

10:30 Mitch Wood, Sandia National Labs
Top-Down versus Bottom-Up Multiscale Modeling of Energetic Materials, PDF
10:45 Remi Dingreville, Sandia National Labs
Insights into modeling radiation damage using atomistic simulations
11:00 Julien Tranchida, Sandia National Labs
SPIN, a package for coupled spin and lattice simulations in LAMMPS, PDF
11:15 Javier Rojas, Universidad de Santiago de Chile
Modulated strength on FeNi nanowires, PDF
11:30 Sungkwang Mun, Mississippi State University
Modified Embedded Atom Method with Bond Order Implementation in LAMMPS, PDF
11:45 Andrew Rohskopf, MIT
Vibrationally Accurate Interatomic Potentials, PDF

12:00 Box lunches from UNM catering

1:00-5:30 General Session of technical talks

Coffee and cookies will be available.

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
Many-GPU Simulation of Nanopore Flow on the Summit Supercomputer, PDF
2:15 Stan Moore, Sandia National Labs
LAMMPS KOKKOS Package: The quest for performance portable MD, PDF
2:30 Lucas Hale, NIST
Interatomic Potentials Repository and iprPy, PDF
2:45 Ellad Tadmor, University of Minnesota
OpenKIM: A Repository of Tested Interatomic Potentials for use with LAMMPS, PDF
3:00 Ryan Elliott, University of Minnesota
A How-To Tutorial on Using OpenKIM with LAMMPS, PDF

3:15 Break

3:30 Dan Bolintineanu, Sandia National Labs
Granular simulations with LAMMPS: enhanced contact models and applications to powder rheology, PDF
3:45 Huilin Ye, University of Connecticut
A highly efficient and portable fluid-structure simulation package implemented in LAMMPS, PDF
4:00 Adrian Diaz, University of Florida
CAC simulation with LAMMPS, PDF
4:15 Ketan Khare, NIST
Quantitative Integration of Atomistic Simulation and Experiment for Cross-linked Epoxy Network, PDF
4:30 Allan Avila, Aimdyn Inc.
Modeling Hydrogen-Oxygen Combustion via Programmable Potentials
4:45 Jacob Gissinger, University of Colorado
DisARMMD: Distance-Actuated Reaction Mechanisms in Molecular Dynamics, PDF
5:00 (invited) Susan Rempe (Sandia National Labs)
Assessing Biomolecular Hydration Mimicry for Ion Permeation through Membrane Channels, PDF

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 elevetion) 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).

Thursday August 15, 2019

Coffee and bagelswill be available.

8:30-10:30 General Session of technical talks

Session chair: Stan Moore (Sandia)

8:30 (invited) Ray Shan (Materials Design Inc.)
High Value from High Throughput: Harness the Power of LAMMPS with MedeA, PDF
9:00 Christoph Kloss, DCS Computing
Marketplace - towards an online gateway to materials modelling, PDF
9:15 Kosuke Ohata, JSOL Corporation
Integrated simulation system for soft materials, J-OCTA, PDF
9:30 Andrew Jewett, The Scripps Research Institute
General Agent Based Modeling in LAMMPS, PDF
9:45 Godehard Sutmann, Juelich Supercomputing Centre, Forschungszentrum Juelich
A Load Balancing Library for Particle Simulation Codes, PDF
10:00 (invited) Xiang-Guo Li (UC San Diego)
Quantum-accurate Force Fields from Machine Learning of Large Materials Data, PDF

10:30 Group photo (Matt Lane)

10:35-12:00 Poster Session

Session chair: Julien Tranchida (Sandia)

For the first time this year, we had awards for the best posters, judged by a sophisticated machine learning algorithm (with possible human intervention).

10:35 One-minute poster advertisements

11:00 Posters in lobby

NOTE: You may setup your posters anytime on Wed, so attendees can browse them in advance.

(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 modelling of Kerogen Wettability
(20) John Karnes, Lawrence Livermore National Lab
Toward Photopolymer Resin Design for Additive Manufacturing
(21) Katsumi Hagita, National Defense Academy of Japan
"Coarse-Grained MD Simulations of Nanovoids in Elongated Polymer Nano-Composites"
(22) Cameron Shock, Michigan Technological University
"Solvation Energy of Ions in a Stockmayer Fluid"

12:00 Box lunches from UNM catering

12:55 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. Ahmed passed away earlier this year.

The 2st place poster award was presented to Vaibhav Palkar (Clemson University).

The 1st place poster award was presented to Felipe Perez (University of Oklahoma).

See photos at the top of this page.

1:00-5:30 Breakout Sessions (two parallel tracks A and B)

Coffee and cookies will be available.

Session chair: Aidan Thompson (Sandia)

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

Track A

1:15-2:15 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 Adding features to LAMMPS (tutorial)

Presented by Richard Berger (Temple U) and Axel Kohlmeyer (Temple U)

Topics: code structure, git, Github, best practices

3:15 Break

3:30-4:30 Machine-learned interatomic potentials (contributed)

Session chair: Thomas O'Connor (Sandia)

3:30 Ying Li, University of Connecticut
Machine learning force field for polymer modeling
3:45 Chun-Wei Pao, Research Center for Applied Sciences, Academia Sinica, Taiwan
Neural Network Potential of Complex Perovskite Materials and Their Implementation to LAMMPS, PDF
4:00 James Hickman, NIST
Development of physically informed neural network (PINN) interatomic potentials, PDF
4:15 Mary Alice Cusentino, Sandia National Labs
Machine Learned Interatomic Potentials for Modeling Plasma Material Interactions, PDF

4:30-5:30 Solid-state and soft materials (contributed)

Chaired by Amalie Frischknecht (Sandia)

4:30 Tuan Ho, Sandia National Labs
Molecular Simulation of the Multicomponent Interaction in Shale Nanopores
4:45 Rafael Gonzalez, Center for Applied Nanotechnology, Universidad Mayor
Molecular simulations of carbon allotropes in processes with creation and destruction of chemical bonds, PDF
5:00 Omar Almahmoud, University of North Texas
Water vapor diffusion in polyurethane silica nano-composite
5:15 Samuel Baltazar, Universidad de Santiago de Chile
Nanostructurated systems for water remediation process, PDF

Track B

1:15-2:15 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:

2:15-3:15 VOTCA and LAMMPS for electronic spectroscopy and transport: Part II (tutorial)

Chaired by Christoph Junghans (LANL)

See the previous breakout for description.

3:15 Break

3:30-4:30 Coarse grained systems (atomistic, meso, continuum) (contributed)

Chaired by Dan Bolintineanu (Sandia)

3:30 Yu-Hang Tang, Lawrence Berkeley National Lab
Marginalized Graph Kernel for Molecular Property Prediction
3:45 David Rosenberger, Los Alamos National Laboratory
Coarse grained molecular dynamics simulations in the isothermal,isobaric ensemble, PDF
4:00 Ishan Srivastava, Sandia National Labs
Discrete Element Simulations of Li-ion Electrodes using Brownian and Granular Dynamics
4:15 Christoph Kloss, DCS Computing
"Modelling of flow of viscoelastic materials with DEM and CFD"

4:30-5:30 Simulation setup via EMC (tutorial)

Presented by Pieter in 't Veld (BASF)

6:00 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.

Associated Software Tools and Projects

These are products from sponsors or tools that will be discussed during breakouts and tutorials: