SoR logo

Short Courses On

Computational Rheology via LAMMPS / Using Large Amplitude Oscillatory Shear (LAOS)

[85th Annual Meeting Home Page]


bullet_blue.GIF (262 bytes)  Date and Location
bullet_blue.GIF (262 bytes)  Instructors
bullet_blue.GIF (262 bytes)  Course Description
bullet_blue.GIF (262 bytes)  Short Course Registration
bullet_blue.GIF (262 bytes)  Lodging Accommodations

Date and Location

Computational Rheology via LAMMPS (a two-day course)
          October 12 and 13, 2013 (Saturday and Sunday)
Using Large Amplitude Oscillatory Shear (LAOS) (a 1½-day course: 1 day of lecture and ½ day hands-on experience)
  October 12 and 13, 2013 (Saturday and Sunday)

All classes will begin at 8:30 am in the Hilton Montréal Bonaventure.

The short courses are held in conjunction with the 85th Annual Meeting of The Society of Rheology (October 13- 17, 2013)

Return to Contents


Computational Rheology via LAMMPS
     Jeremy Lechman
Reactive and Nanoscale Processes Department
Sandia National Laboratories

     Matt Lane
Materials Science and Engineering department
Sandia National Laboratories
  Steve Plimpton
Computational Sciences Center
Sandia National Laboratories

Using Large Amplitude Oscillatory Shear (LAOS)
  Randy H. Ewoldt, Assistant Professor
Department of Mechanical Science and Engineering
University of Illinois at Urbana-Champaign

  A. Jeffrey Giacomin, Professor
Department of Chemical Engineering
Queen’s University

Instructor Biosketches

Jeremy Lechman is a staff member in the Reactive and Nanoscale Processes department at Sandia National Laboratories. His technical work includes coarse-grained and meso-scale computational mechanics with applications to multiphase, particulate, and composite materials. His current interests are in developing macro-scale, continuum governing equations and constitutive models for transport processes in reactive heterogeneous materials.

Matt Lane  is a staff member in the Materials Science and Engineering department at Sandia National Laboratories. He earned his doctorate in Physics at the University of Texas at Austin, but was educated at the University of Virginia. His computational research interests are in atomistic study of nanoscale soft condensed matter and far-from-equilibrium systems and his approaches are influenced heavily by training in nonlinear dynamics.

Steve Plimpton is a staff member in the computational sciences center at Sandia. He is one of the principal developers of LAMMPS, as well as other open-source scientific simulation codes which he supports. His background is in solid-state physics and materials science.

Professor Randy H. Ewoldt is Assistant Professor of Mechanical Science and Engineering at the University of Illinois at Urbana-Champaign. With a combination of experiment and theory, his research group studies nonlinear rheology, non-Newtonian fluid mechanics, mathematical modeling, and engineering design involving soft materials and complex fluids. Prior to joining Urbana-Champaign, he performed his doctoral research at MIT and postdoctoral work at Minnesota.

Professor A. Jeffrey Giacomin is President of The Society of Rheology, Professor of Chemical Engineering at Queen’s University, Kingston, Ontario, Canada. He teaches polymer processing and rheology to senior undergraduate and graduate students every semester, and his research focuses on the role of rheology in plastics processing. Professor Giacomin is an expert on the measurement of the nonlinear viscoelastic properties of molten plastics, and on interpreting these measurements.

Return to Contents

Course Description

Computational Rheology via LAMMPS / Using Large Amplitude Oscillatory Shear (LAOS)

Computational Rheology via LAMMPS (Saturday and Sunday)

Instructors: Jeremy Lechman, Matt Lane, and Steve Plimpton

Particle-based simulation has, in recent years, made great strides toward closing the gaps in understanding the rheological behavior of complex, multi-constituent and multiphase systems. Due to advances in both computational infrastructure and techniques, macroscopic rheological models can now be extracted from numerical simulations of individual interacting components at ever-finer length and time resolutions (e.g. grains, colloids , macromolecule, and atoms). Obtaining and analyzing this detailed information is crucial for prediction and designed control of the rheological behavior of complex fluids in countless manufacturing/industrial, biological and environmental processes.

In this course we will introduce participants to the relevant methods and techniques for numerical simulation of complex fluids for rheological applications using LAMMPS, an open-source molecular dynamics package. Mathematical and numerical tools for gaining physical understanding will be emphasized. Particle based simulations, both classical molecular dynamics and coarse-grained methods, will be discussed. Hence, the participant will receive an introduction to the basics of particle-based numerical simulation using LAMMPS. This will include writing and running LAMMPS input scripts and using the code to compute rheological properties of both atomic-scale and coarse-grained systems. Lectures on the technical basics will be interleaved with hands-on tutorial sessions. Rheological applications will be emphasized with a number of case studies and group discussions. Short-course participants will have an opportunity to discuss their particular research interests and applications.

Although some coding experience would be helpful, it is not required to use the LAMMPS package. Some familiarity with molecular modeling would also be helpful, though not required. Students should come with personal laptop, running Windows, MacOS, or Linux. A pre-built Windows executable version is available on the LAMMPS download site. Mac and Linux users should download and install LAMMPS prior to the course. Detailed instructions are given at http://lammps.sandia.gov in the 2nd chapter of the manual.

Course Outline

Session 1: LAMMPS overview
  1. Molecular Dynamics basics
    1. Newton’s Equations of motion for many-particle systems
    2. The pair potential
    3. Numerical integration – the Velocity Verlet algorithm
    4. Advanced techniques
  2. How LAMMPS is structured
    1. Atoms
    2. Pairs
    3. Fixes
    4. Computes and Thermo
    5. Dumps and restarts
  3. Movies, images of published work done in LAMMPS
Session 2: Getting started with LAMMPS
  1. Website and resources
  2. Downloading and installing/compiling
  3. LAMMPS out of the box – building a simple script
  4. Visualization of results – VMD?
    1. Other pre and post processing issues
  5. Examples from the LAMMPS distribution
Session 3: Hands-on applications lab I
Session 4: Atomistic representations
  1. Background/Foundations
    1. Strengths and weaknesses of atomistic study
    2. Representations and relevant potentials/theory
      1. Fully atomistic (Lennard-Jones, water, polymer)
      2. Coarse-grained (bead-spring, implicit solvent, united atom)
    3. Thermostats and ensembles – some statistical mechanics background
    4. Creating Initial configurations
Session 5: Coarse-grain representations
  1. Overview of coarse graining concepts and techniques
  2. Effective potentials for large particles
    1. DLVO models for colloidal particles
      1. van der Waals and Yukawa potentials
      2. Integrated Lennard-Jones model for colloids
    2. Numerically calculated complex interactions
    3. Granular potentials – noncolloidal particles
      1. Models based on Hertz theory for contact of elastic solids
      2. Models based on JKR/DMT adhesive contact theory for “sticky” particles
    4. Dissipative Particle Dynamics
  3. Coarse-grained solvent models
    1. Navier-Stokes (“Implicit Solvent”) methods
      1. Classical NS methods
      2. Stokesian Dynamics
      3. Lattice-Boltzmann, etc.
      4. Stochastic techniques
        1. Brownian Dynamics
        2. Dissipative Particle Dynamics
        3. Multi-particle Collision Dynamics
Session 6: Hands-on application lab II
Session 7: Common calculations and measurements
  1. Simple thermodynamic quantities - pressure, temperature, etc.
  2. Microstructure - radial distribution functions and structure factors
  3. Diffusion, displacement, velocity distributions and correlation functions
  4. Bulk viscosity (Green-Kubo)
  5. Issues and validation
  6. Non-equilibrium quantities – stress tensor
  7. Mueller-Plathe viscosity method
  8. Nonequilibrium MD viscosity method
  9. Issues and validation
Session 8: Post-processing, visualization and data handling
Session 9: Hands-on applications Lab III
  1. Set up and run simple example problem to calculate distributions, correlations, and equilibrium viscosity
  2. Set up and run simple example problem to calculate shear viscosity
  3. Stress/viscosity for water in nanoconfinement
  4. Forces between nanoparticles in suspension
  5. Set up and run simple example problem to calculate g(r), and MSD of suspension of hard-sphere colloids
  6. Set up and run simple example problem to calculate shear viscosity of hard-sphere colloids
Session 10: Recent development and future additions
  1. Microrheological Approach
    1. Generalized Langevin Equation
      1. Memory kernel for colloids in incompressible, Newtonian fluid
  2. Macrorheology of Non-Newtonian materials
    1. Peri-dynamics of visco-elastic solid

Course Schedule

Day 1
8:30        Introduction and course agenda
8:45-10:15   Overview of Molecular/Particulate Dynamics via LAMMPS (Plimpton)
10:15-10:30   Break
10:30-12:00   Getting started with LAMMPS (Lane)
12:00-1:30   Lunch Break
1:30-3:00   Hands-on applications lab I (Plimpton, Lane, Lechman)
3:00-3:45   Atomistic Applications (Lane)
3:45-4:00   Break
4:00-4:45   Coarse-grain Applications (Lechman)
Day 2
8:30-9:15   Common equilibrium calculations (Lechman)
9:15-10:15   Hands-on applications lab II (Plimpton, Lane, Lechman)
10:15-10:30   Break
10:30-11:15   Common non-equilibrium calculations (Lechman)
11:15-12:15   Hands-on applications lab III (Plimpton, Lane, Lechman)
12:15-1:45   Lunch Break
1:45-2:30   Getting under the hood – Making Changes to LAMMPS (Lane)
2:30-3:15   Recent development and future additions (Plimpton)
3:15-3:30   Break
3:30-4:30   Hands-on applications lab IV, Discussion/Consultations (Plimpton, Lane, Lechman)
4:30-4:45   Wrap-up discussion and feedback

Using Large Amplitude Oscillatory Shear (LAOS) (Saturday [1-day of lecture] and Sunday [½-day of hands-on experience])

Instructors: Prof. Randy H. Ewoldt and Prof. A. Jeffrey Giacomin

A popular use for commercial rheometers is the large amplitude oscillatory shear (LAOS) experiment, or oscillatory strain sweep. Rheologists have always used this to prepare for a linear viscoelastic frequency sweep. Beyond linear viscoelasticity, this nonlinear LAOS experiment generates rich data related to material structure, processing, in-use conditions, and function; nonlinear rheology is also a strong guide to the development of constitutive models. This course addresses the unique challenges of experimentally generating, analyzing, and interpreting data from LAOS, and other large amplitude oscillatory techniques. Of the various nonlinear deformation protocols, oscillatory techniques are powerful in that they systematically survey the broad range of deformation timescales and amplitudes (the Pipkin space), and quantify both elastic and viscous components simultaneously. Oscillatory techniques can also probe nonlinearity more gradually than step inputs, which is valuable for probing shear sensitive materials such as biological gels. This course will offer a comprehensive introduction to those industrial researchers, graduate students, and faculty that seek to probe microstructure, develop constitutive models, or simply fingerprint the nonlinear behavior of viscoelastic materials. Enrolled students will receive software for analyzing raw oscillatory data, along with a playbook for acquiring and analyzing data from LAOS.

Course Outline

  1. Rheological Material Functions Review
    1. Load input (compliance, fluidity)
    2. Deformation input (modulus, viscosity)
    3. Shear stress and normal stress difference responses
    4. Pipkin diagram
    5. Oscillatory deformation possibilities – not just LAOS
  2. Small Amplitude Oscillatory Shear (SAOS) Material Functions
    1. Complex viscosities and complex moduli
    2. Complex normal stress difference coefficients
    3. Linear viscoelasticity and discrete spectra
    4. Predictions from complex material functions (Cox-Merz relation, Laun relation, etc.)
  3. Large Amplitude Oscillatory Shear (LAOS) Material Functions
    1. The standard Strain Sweep analysis (first-harmonic moduli)
    2. Lissajous curves – the visualization playground
    3. Time domain analysis – Fourier-transform framework
    4. Deformation domain analysis – Chebyshev coefficients & nonlinear moduli
    5. Relaxing the typical symmetry assumptions (even harmonics, local moduli, sequence of physical processes,…)
  4. Rheometers
    1. Rectilinear flow
      1. Sliding plate
      2. Sandwich geometry
    2. Rotational
      1. Cone-plate
      2. Concentric cylinder
      3. Parallel plate
  5. Experimental Errors
    1. Total force versus shear stress
    2. Slip
    3.  Edge failure
    4. Viscous heating
    5. Fluid inertia
    6. Start up
    7. Electrical interference
    8. Noise
  6. Signal Processing
    1. How to calculate G’ and G” ? (sine regression, Fourier, and other options)
    2. Fourier transforms (DFT vs. FFT, underlying assumptions, performance sensitivity)
    3. Noise removal
    4. Software distribution and tutorial
  7. Interpretation of Results
    1. Common LAOS signatures (simple analysis)
    2. Common LAOS signatures (advanced analysis)
    3. Identifying bad data (edge failure, shear-banding, …)
    4. Constitutive model fingerprints
  8. Examples of Using LAOS
    1. Probing microstructure
    2. Constitutive model development
    3. Nonlinear viscoelastic model parameters for POLYFLOW
    4. Design of viscous dampers
  9. Beyond LAOS: Examples of Oscillatory Deformation to Probe Nonlinearities
    1.  Superposed steady flow + oscillations (fluid limit)
    2. Superposed stress or strain + oscillations (elastic limit)
    3. LAO-Extension, LAO-Bending, LAO-Microrheology, LAO-Flow
    4. Other reciprocating material functions

Return to Contents

Short Course Registration

Short course registration includes a complete set of course notes. Payment can be made on line with MasterCard, Visa, Discover, or American Express.

Registration Fee for Through 9/6/2013 After 9/6/2013
Computational Rheology via LAMMPS (Two-day Course)    
   Member* $750 $850
(includes membership for 2014)
$810 $910
   Student Member* $425 $525
   Student Non-Member**
(includes student membership for 2014)
$455 $555
Using Large Amplitude Oscillatory Shear (LAOS) (1½-day Course)    
  Member* $625 $725
(includes membership for 2014)
$685 $785
  Student Member* $350 $450
  Student Non-Member**
(includes student membership for 2014)
$380 $480
  * Member rates are available only to registrants who are members in good standing as of June 30, 2013 or who are registered to attend the 85th Annual Meeting.
  ** Non-members who are registered to attend the 85th Annual Meeting may register for the short course at the member rates.


Cancellations for the short course received by electronic mail (c/o The Local Arrangements Chair, Marie-Claude Heuzey, marie-claude.heuzey@polymtl.ca) by September 6, 2013 will be refunded minus a $50 administrative charge.  No refunds will be granted after that date. Each class is limited to 40 students.

Return to Contents

Questions can be directed to Anne Mary Grillet, Sandia National Laboratories, current chair of the SOR Education Committee, at amgrill@sandia.gov.

[85thAnnual Meeting Home Page]

Updated 02 August 2013