Virtual LAMMPS Workshop and Symposium

About

The seventh LAMMPS Workshop and Symposium was held virtually on August 10-13, 2021 and was hosted by Temple University.

Recorded videos of the presentations and presentation slides (where available) can be accessed by clicking on the talk titles in the schedule below.

Invited Speakers

Gary Grest

Sandia National Laboratories

keynote A Brief History of Molecular Dynamics Simulations

Bio

Tim Germann

Los Alamos National Lab

MD: It’s Not Just For Atoms Any More

Bio

Gábor Csányi

University of Cambridge

First principles molecular dynamics on a large scale

Bio

Rommie Amaro

University of California San Diego

Computational Microscopy of SARS-CoV-2

Bio

Program

Schedule

Note: All times are in Eastern Daylight Time (EDT), which is UTC-4.

Day 1: Beginners Tutorial - Tuesday, August 10, 2021
Day 2: Symposium - Wednesday, August 11, 2021
Day 3: Symposium - Thursday, August 12, 2021
Day 4: Developers and Breakout Sessions - Friday, August 13, 2021

Day 1: Beginners Tutorial - Tuesday, August 10, 2021

Important: In advance of the tutorial, attendees should follow these instructions:
Beginners Tutorial Preparation Instructions

Time (EDT)	Type	Title	Presenter	Affiliation
9:55am	Introduction	Tutorial Welcome and Overview	Steve Plimpton	Sandia National Laboratories
10:00am	Lecture	Introduction to Molecular Dynamics	Stan Moore	Sandia National Laboratories
10:20am	Hands-on	Run a simulation, plot and visualize output	Steve Plimpton	Sandia National Laboratories
10:40am	Lecture	Ins and Outs of LAMMPS input scripts	Steve Plimpton	Sandia National Laboratories
11:00am	Hands-on	Editing input scripts	Steve Plimpton	Sandia National Laboratories
11:20am	Lecture	Styles, Styles, Styles	Steve Plimpton	Sandia National Laboratories
11:40am	Hands-on	Measuring material properties	Steve Plimpton	Sandia National Laboratories
12:00pm	Lunch Break
12:55pm	Introduction	Start of Afternoon Session	Steve Plimpton	Sandia National Laboratories
1:00pm	Lecture	How Ovito works	Mitchell Wood	Sandia National Laboratories
1:20pm	Hands-on	Using Ovito with LAMMPS	Mitchell Wood	Sandia National Laboratories
1:40pm	Lecture	How LAMMPS works internally	Steve Plimpton	Sandia National Laboratories
1:50pm	Lecture	Resources for LAMMPS info	Steve Plimpton	Sandia National Laboratories
2:00pm	Hands-on	Finding LAMMPS info	Steve Plimpton	Sandia National Laboratories
2:20pm	Lecture	Whirlwind tour of more advanced topics	Steve Plimpton	Sandia National Laboratories
2:40pm	Discussion	General Q&A with all attendees	Steve Plimpton	Sandia National Laboratories
3:00pm	End of Day 1

Day 2: Symposium - Wednesday, August 11, 2021

Time (EDT)	Type	Title	Presenter	Affiliation
9:50am	Introduction	Symposium Welcome and Session Intro	Session Chair Aidan Thompson	Sandia National Laboratories
9:55am	Keynote Invited Talk	A Brief History of Molecular Dynamics Simulations	Gary S. Grest	Sandia National Laboratories
10:30am	Contributed Talk	What’s New in LAMMPS	Steve Plimpton	Sandia National Laboratories
10:45am	Contributed Talk	Closed-Form Coexistence Equation for Phase Separation of Polymeric Mixtures in Dissipative Particle Dynamics	Pieter J. in ’t Veld	BASF
11:00am	Lightning Talks	New features in OVITO related to LAMMPS	Alexander Stukowski	OVITO GmbH
		Theoretical Approach to study structure of Water at the Solid-Water Interface	Vibhuti Taneja	Indian Institute of Technology
		Using controlled degradation to tailor interfacial spreading of nanogels at soft interfaces	Devanshu Thakar	Indian Institutes of Technology
		Surface Chemistry Implementation in SPPARKS	Enrique Mercado	University of California, Merced
		Extending and Modifying LAMMPS: Writing your own source code	Shafat Mubin	Valdosta State University
11:15am	Contributed Talk	Directional bonds for ellipsoids. A new style for coarse-grained molecular modelling	Otello M. Roscioni	MaterialX LTD
11:30am	Contributed Talk	Materials Square : How to Reduce The Barriers to Entry for LAMMPS?	Minkyu Park	Virtual Lab
11:45am	Contributed Talk	NUFEB - a LAMMPS user package for individual-based modelling of microbial communities	Bowen Li	Newcastle University
12:00pm	Lunch Break
12:50pm	Introduction	Symposium Session Intro	Session Chair Mary Alice Cusentino	Sandia National Laboratories
12:55pm	Invited Talk	MD: It’s Not Just For Atoms Any More	Tim Germann	Los Alamos National Lab
1:30pm	Contributed Talk	High-Fidelity Large-Scale Atomistic Simulations of Materials using Big Computers and Machine-Learning Interatomic Potentials	Aidan Thompson	Sandia National Laboratories
1:45pm	Contributed Talk	Interatomic Potentials for Materials Science and Beyond; Advances in Machine Learned Spectral Neighborhood Analysis Potentials	Mitchell Wood	Sandia National Laboratories
2:00pm	Lightning Talks	Modelling complex particles in LAMMPS using spherical harmonics	James Young	University of Edinburgh
		MD simulation of lattice damage in graphite and its effects on the material properties	Violetta Toto	Politecnico di Milano
		Simulation of surface abrasion in LAMMPS	Rosario Capozza	University of Edinburgh
		Concurrent Coupling of Kinetic Monte Carlo and Fluctuating Hydrodynamics (SPPARKS-MUI-FHDeX)	Changho Kim	University of California, Merced
		USER-MLMOD Package: Machine Learning Methods for Data-Driven Models in LAMMPS	Paul J. Atzberger	University of California, Santa Barbara
2:15pm	Contributed Talk	Interatomic Potentials Repository: Tools and Resources	Lucas Hale	National Insitute of Standards and Technology
2:30pm	Contributed Talk	A computational framework for studying normal mode dynamics	Andrew Rohskopf	MIT
2:45pm	Contributed Talk	The State of the LAMMPS KOKKOS Package	Stan Moore	Sandia National Laboratories
3:00pm	End of Day 2

Day 3: Symposium - Thursday, August 12, 2021

Time (EDT)	Type	Title	Presenter	Affiliation
9:50am	Introduction	Symposium Session Intro	Session Chair Mitchell Wood	Sandia National Laboratories
9:55am	Invited Talk	First principles molecular dynamics on a large scale	Gábor Csányi	University of Cambridge
10:30am	Contributed Talk	OpenKIM for the LAMMPS User	Ellad B. Tadmor	University of Minnesota
10:45am	Contributed Talk	LAMMPS implementation of rapid artificial neural network derived interatomic potentials	Christopher Barret	Mississippi State University
11:00am	Lightning Talks	AutoMapper: A Tool for Accelerating the Fix Bond/React Workflow	Matthew A. Bone	University of Bristol
		Nonequilibrium free-energy calculation of phase-boundaries using LAMMPS	Oscar Samuel Cajahuaringa Macollunco	IFGW/UNICAMP
		Pressure dependence of ice nucleation in coarse-grained water models	Elise Rosky	Michigan Technological University
		Double Hot Spots Mechanism in the crystalline RDX under the Overdriven Shock: A Reactive Molecular Dynamic Simulation Study	Ruqin Liu	Beijing Institute of Technology & China Academy of Engineering Physics (CAEP)
		Modeling of Nano-Projectile Impact Tests in LAMMPS	Nuwan Dewapriya	Carleton University
11:15am	Contributed Talk	LAMMPS-CONP2: Fast Simulations Of Constant Potential Difference Conductive Electrodes	Shern Ren Tee	University of Queensland
11:30am	Contributed Talk	Molecular dynamics simulation of localized electrochemical deposition	Anne Brant	University of Cincinnati
11:45am	Contributed Talk	What can you do with a polarizable force field?	Josh Rackers	Sandia National Laboratories
12:00pm	Lunch Break
12:50pm	Introduction	Symposium Session Intro	Session Chair Josh Rackers	Sandia National Laboratories
12:55pm	Invited Talk	Computational Microscopy of SARS-CoV-2	Rommie E. Amaro	University of California, San Diego
1:30pm	Contributed Talk	Mesoscale models for fluids and solids in LAMMPS	Joel T. Clemmer	Sandia National Laboratories
1:45pm	Contributed Talk	REACTER 2.0: Advanced Reaction Constraints and Automated Interaction Typing	Jacob R. Gissinger	NASA Langley Research Center
2:00pm	Lightning Talks	Updates and improvements in the Colvars package	Giacomo Fiorin	NIH
		Development of Native-Based Dissipative Particle Dynamics Approach for α-Helical Folding	Chandan Kumar Choudhury	Clemson University
		Conformation and ionization behavior of charge-regulating polyelectrolyte brushes in a poor solvent	Yanwei Wang	Nazarbayev University
		Thermal transport in Single Walled Carbon Nanotubes	Ama Tul Zahra	G.C University Faisalbad
		Strain Effect and the Li-ion Transport Mechanism in the Li6PS5Cl Superionic Conductor from Molecular Dynamics Simulations	Tridip Das	CalTech
2:15pm	Contributed Talk	Mesoscale modeling of erosion of polymer networks: characterizing mass loss via extent of reaction	Vaibhav Palkar	Clemson University
2:30pm	Contributed Talk	Development of SNAP potentials for fusion reactor materials	Mary Alice Cusentino	Sandia National Laboratories
2:45pm	Contributed Talk	Combining SNAP machine-learning potentials to the SPIN package for highly accurate magneto-elastic predictions	Julien Tranchida	Sandia National Laboratories
3:00pm	End of Day 3

Day 4: Developers and Breakout Sessions - Friday, August 13, 2021

Important: Some of the breakouts will use the Virtual Machine from the Beginners Tutorial. If you want to follow along, it is recommended you follow these steps before the workshop.
Beginners Tutorial Preparation Instructions

Time (EDT)	Type	Title	Presenter	Affiliation
9:55am	Introduction	Developers session Welcome and Overview	Axel Kohlmeyer	Temple University
10:00am	Developer	How to modify LAMMPS	Steve Plimpton	Sandia National Laboratories
10:30am	Developer	How to Use LAMMPS as a Library and from Python, How to call Python from LAMMPS	Richard Berger	Temple University
11:00am	Developer	Recent Changes in LAMMPS development: Coding style, Testing, Programmer Guide, GitHub Procedures, Common mistakes	Axel Kohlmeyer	Temple University
11:45am	Discussion	Group Discussion	Axel Kohlmeyer	Temple University
12:00pm	Lunch Break

12:50pm	Breakout Getting Things Done using OpenKIM in LAMMPS Ryan S. Elliott, University of Minnesota	Breakout EMC: An all-encompassing workflow to create input and run simulations with LAMMPS Pieter J. in 't Veld, BASF	Breakout Tutorial on using USER-SELM for fluctuating hydrodynamics models in LAMMPS Paul Atzberger, University of California, Santa Barbara
1:50pm	Break
2:00pm	Breakout Beginners tutorial for atomman Lucas Hale, National Insitute of Standards and Technology	Breakout Electronic Spectroscopy with VOTCA and LAMMPS Christoph Junghans, Los Alamos National Lab	Breakout Magneto-elastic material predictions with LAMMPS Julien Tranchida, Sandia National Laboratories
3:00pm	End of Day 4