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August 2015 LAMMPS Users' Workshop and Symposium


The fourth LAMMPS workshop and symposium for users and developers was held in Albuquerque, NM on August 5-7, 2015, at the UNM Continuing Education Building, (1634 University Blvd. NE, map).

We thank the DOE/NNSA ASC program for financial support in hosting the workshop and industrial partners Materials Design and Scienomics for graciously providing lunches, snacks, and drinks for the attendees.

PDFs for most of the talks, posters, and tutorial presentations can be viewed or downloaded via the links below.

Video of most of the main sessions talks are available on Moodle, and can be accessed as follows:

A list of workshop attendees can be found here: attendees

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Click here for full-size image


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

There were also display booths from these industrial partners:



Wednesday August 5, 2015

8:30 AM - 12 PM Beginners' Tutorial (chaired by Matt Lane)

An introduction to LAMMPS designed to get attendees running and using LAMMPS quickly.

Overview: This tutorial is an introduction to LAMMPS designed to get attendees up and using LAMMPS quickly. Beginning with downloading and building, these tutorials will highlight major features of the code with an emphasis on examples and demos. Bring your laptop computer with LAMMPS already installed if at all possible. Also have other relevant software already installed if you wish to use it: MPI (MPICH or OpenMPI), VMD or AtomEye or Ovito, Pizza.py, a movie making software (e.g. QuickTime or ImageMagick). If you have a Windows laptop, Cygwin will be useful. There will be opportunities for discussion, hands-on work, and questions.

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)

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

9:25 Visualization of results: Matt Lane, Sandia (PDF)

9:40 break

9:50 LAMMPS input scripts, syntax and rules: Steve Plimpton, Sandia (PDF)

10:15 LAMMPS capabilities - force fields, ensembles, electrostatics, fixes and computes, load-balancing, on-the-fly viz, GPU acceleration: Steve Plimpton, Sandia

10:45 Hands-on activity - run the simple examples that come with LAMMPS: Steve Plimpton, Sandia

11:00 break

11:10 Case study 1 - Interatomic potentials and KIM: Ryan Elliott, Univ of Minnesota (PDF)

11:40 Case study 2 - Monitoring chemical reactions using on-the-fly molecular species analysis: Ray Shan, Sandia (PDF)


12 PM - 1 PM Boxed lunches in lobby


Official start of workshop

1 PM - 5 PM General session of technical talks (chaired by Aidan Thompson)

1:00 Steve Plimpton, Sandia
Welcome and what's new in LAMMPS (PDF)
1:30 (keynote) Eduardo Bringa, Universidad Nacional de Cuyo (Mendoza, Argentina)
Computational and modeling challenges to model materials under extreme conditions (PDF)
2:00 Enrique Saez, Los Alamos National Lab
Sublattice parallel replica dynamics (PDF)
2:15 Ray Shan, Sandia
Charge equilibration for many-body potentials (PDF)
2:30 Hengjia Wang, Clemson University
Calculations of lattice vibrational mode lifetimes using Jazz: a new Python wrapper for LAMMPS (PDF)
2:45 Matt Lane, Sandia
Molecular modeling of high-pressure ramp waves in tantalum (PDF)

3:00 break

3:15 Mike Brown, Intel
Faster Simulations with LAMMPS - Advancing Performance on Intel(r) Xeon(r) and Xeon Phi(tm) Processors (PDF)
3:30 Andreas Bick, Scienomics
Properties of Mixed-Matrix Composites predicted by Molecular Dynamics and Dissipative particle Dynamics
3:45 Paul Saxe, Materials Design
Thoughts on Challenges for Molecular Modeling (PDF)
4:00 Greg Scantlen, CreativeC LLC
The LAMMPS Instrument for Material Science
4:15 Mark Berger, NVIDIA Corporation
GPU-Accelerated Molecular Dynamics and Quantum Chemistry Applications are Changing Research (PDF)
4:30 (invited) Stephen Foiles, Sandia
Complexity of Grain Boundary Motion: Insights from Molecular Dynamics (PDF)

5 PM - 7 PM No-host dinner at El Pinto, details TBA


Thursday August 6, 2015

8:30 AM - 12 PM General session of technical talks (chaired by Matt Lane)

8:30 (invited) Andres Jaramillo-Botero, Caltech
Quantum Electron Dynamics of Large-Scale, Highly-Excited Systems using the Gaussian Hartree Approximated eFF kernel (eFF-GHA) (PDF)
9:00 Xiaowang Zhou, Sandia
Bond Order Potentials for AlCuH and C (PDF)
9:15 Matthew Wander, Brigham Young University
The Valence Multipole Model, a New Pair Style (PDF)
9:30 Stan Moore, Sandia
Kokkos Package -- Targeting Next-Generation Platforms in LAMMPS
9:45 Shawn Coleman, U.S. Army Research Laboratory
Virtual Diffraction Using LAMMPS (PDF)
10:00 Lucas Hale, NIST
Comparing Property Predictions Across Interatomic Potentials (PDF)

10:15 break

10:30 Kyungjoo Kim, Sandia
Development of Scalable Parallel Implicit Smoothed Particle Hydrodynamics using LAMMPS and Trilinos (PDF)
10:45 Christoph Junghans, LANL
Coarse-graining using VOTCA and LAMMPS
11:00 (invited) Fabio Pavia, EPFL and ANSYS (Switzerland)
Parallel algorithm for multiscale atomistic/continuum simulations using LAMMPS (PDF)
11:30 Pieter in 't Veld, BASF
LAMMPS in an Industrial Environment
11:45 Ellad Tadmor, University of Minnesota
OpenKIM: An online suite of open source tools for molecular simulations of materials (PDF)

12 PM - 1 PM Boxed lunches (lobby)

1:00-3:00 PM - Breakout Session A

Option A1 (Room B): Advanced Interatomic Potentials (ReaxFF, COMB, eFF, etc.), chaired by Ray Shan

4 talks plus a general discussion - time schedule TBA

Tao Liang, University of Florida
Applications of Charge Optimized Many Body (COMB) Potentials in Multicomponent Systems (PDF)
Aidan Thompson, Sandia
SNAP: Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials for LAMMPS (PDF)
Xiaowang Zhou, Sandia
Stillinger-Weber (SW) Potential and Its Polymorphic Extension (PDF)

Option A2 (Room D): Initial Structure Generation (EMC Monte Carlo Builder), presented by Pieter in 't Veld

This is a hands-on tutorial for building complex initial structures using EMC. Participants should download and install EMC (https://montecarlo.sourceforge.net/) and LAMMPS on their machine 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 

Option A3 (Room C): Developers / Hackers, chaired by Stan Moore and Axel Kohlmeyer

Short(!) Overview on LAMMPS Development, by Steve Plimpton
  - Where to find info on how to extend/modify LAMMPS for your needs
  - How to adapt LAMMPS for your research:
    (New styles, Library interface, Python embedding)
  - How to contribute your features to main LAMMPS distro
Status of LAMMPS Regression Testing, by Stan Moore
Moderated discussion on the following topics (in this order):
  - New physics features
  - New input/output, pre-/post-processing features
  - Improved efficiency and accuracy
  - LAMMPS build system
  - LAMMPS documentation, training, & outreach
  - Project management and software engineering
  - Licencing, contracting, interfacing LAMMPS with commercial tools 

3:15-5:15 PM - Breakout Session B

Option B1 (Room C): Coarse-grained, Mesoscopic, Granular, Continuum Systems, chaired by Jeremy Lechman

3 talks plus a general discussion - time schedule TBA

Vipin Agrawal, Arizona State University
Pressure Transferable Coarse-Grained Potentials for Polymers under Isothermal and Shock Compression (PDF)
Christoph Junghans and Sikandar Mayashak, Los Alamos National Laboratory and U Illinois at Urbana/Champaign
Coarse-grained potentials for confined water from relative entropy minimization in VOTCA
Juan Vanegas, Sandia National Labs
Is the microscopic stress computed from molecular simulations in mechanical equilibrium? (PDF)

Option B2 (Room C): The KIM and OpenKIM system, presented by Ryan Elliott and Ellad Tadmor

0:30 Presentation: The KIM and OpenKIM system: Review and in-depth
0:45 Discussion: "Wish list for KIM and OpenKIM"
This discussion will focus on the improvements or new features
that the Molecular Modeling community would like to see in KIM
and OpenKIM.
0:45 Discussion: "How can I, personally, best contribute to KIM and OpenKIM?"
This discussion will focus on making connections between
specific development needs of KIM and OpenKIM and specific
members of the audience (or broader community) who are
interested in contributing to the KIM and OpenKIM system. 

5:30 PM - 7:30 PM no-host dinner at Sandiago's Mexican Grill with optional tram-ride to Sandia Crest (about $20), details TBA


Friday August 7, 2015

8:30 AM - 10:30 AM General session of technical talks (chaired by Ray Shan)

8:30 (invited) Jim Larentzos and Brian Barnes, Engility Corporation and U.S. Army Research Laboratory
Recent Extensions of Dissipative Particle Dynamics Methods and Application to Hierarchical Multiscale Simulation (PDF)
9:00 Greg Vernon, Honeywell FM&T
Utilization of LAMMPS in a Rapid-Response Production Environment to Solve Manufacturing Challenges (PDF)
9:15 Aidan Thompson, Sandia
Monte Carlo simulations with LAMMPS (PDF)
9:30 Rezwanur Rahman, The University of Texas at Austin
Peridynamic theory of solids from the perspective of classical statistical mechanics (PDF)
9:45 (invited) Gary Grest, Sandia
Nanoparticle Dynamics in Polymer Matrices (PDF)

10:15 AM 1 minute poster advertisements

10:30 AM - 11:30 AM Poster session (lobby)

Sara Adibi, University of Houston
Atomistic Simulations of Metallic Glass and Nanoglass (PDF)
Anupriya Agrawal, Clemson University and Washington University in St. Louis
Coarse Graining Atactic Polystyrene and its Analogues (PDF)
Dipak Aryal, Clemson University
Engineering Controlled Nano Systems: Understanding Aggregation of Structured Ionic Copolymers (PDF)
Pedro Alves da Silva Autreto, University of Campinas
Fully Atomistic Reactive Molecular Dynamics simulations of mechanical properties of Gold Nanotips Encapsulated with Carbon Nanocones (PDF)
Venkat Bala, University of Western Ontario
Shear Induced Adsorption of Polymers onto Neutral Surfaces (PDF)
Benjamin Cowen, University of New Mexico
Molecular Dynamics Simulations of Radiation-Induced Defects in Crystalline Silica
Kasra Fattah Hesary, Louisiana State University
Nanoparticle-Wall interactions for Implementation into Multi-scale MD-Continuum Simulations
Rafael Gonzalez, Universidad de Chile
Model for Self-Rolling of an Aluminosilicate Sheet into a Single-Walled Imogolite Nanotube (PDF)
Robert Latour, Clemson University
New LAMMPS Modules for the Simulation of Protein-Surface Interactions with CHARMM (PDF)
Katie Maerzke, Los Alamos National Laboratory
Deformation of Poly(amido amine) Dendrimers at Surfaces (PDF)
Manoharan Muruganathan, JAIST
Role of electric field in the carbon dioxide adsorption on the graphene nanoribbon
Mohammad Sadat, University of Arizona
Molecular dynamics simulation to better understand environmentally-friendly geopolymer from wastes (PDF)
Manjula Senanayake, Clemson University
On the Way to Transport Controlled Membranes: Solvent Effects on Structured Ionic Polymers (PDF)
Michael Skarlinski, University of Rochester
Determining the Mechanical Properties of Oxide-Coated Copper Nano-films using Reactive Molecular Dynamics (PDF)
Sidath Wijesinghe, Clemson University
Polydots, Soft Nanoparticles, at Membrane Interfaces (PDF)
Yi Zeng, Auburn University
An investigation of the size effect and molecular orientation on the values of thermal conductivity of long-chain n-alkane by molecular dynamics simulation (PDF)
11:30 AM (invited) Christoph Kloss, DCS Computing (Austria)
LIGGGHTS, CFDEMcoupling and ParScale - LAMMPS as part of an ecosystem for modelling macroscopic particle processes

12 noon - 12:30 PM Open discussion, Feedback, Group picture - led by Aidan Thompson

12:30 PM - 1:30 PM Boxed lunches (lobby)

1:30 PM onward Recreational events - 3 choices, see below


Abstracts on hiking the Tree Spring Trail in the Sandia Mountains:

For those who enjoy wilderness hiking, we will be hiking the Tree Spring Trail, which is on the cooler, shadier east side of the Sandia Mountains, 30-40 minutes from Albuquerque by car. From the trailhead, the trail climbs approximately 1000 feet in 2 miles to the main ridgeline. After exploring and admiring the views from the ridge, we'll return via the reverse route. For people in reasonable physical condition, this hike is 'moderate' in difficulty. The trail starts at 8500 feet above sea level, and anyone not accustomed to this altitude will notice the lack of oxygen. The total hike distance (there and back) is approximately 4 miles. We don't know exactly how long the hike will last, but a rough guess is three to four hours, including the drive.

Near the top; post-hike meal with survivors (click for larger images)


Abstracts on National Museum of Nuclear Science & History

http://www.nuclearmuseum.org


Abstracts on go-karting at Albuquerque Indoor Karting:

http://www.abqkarting.com Cost = $15/person