1. Molecular Dynamics Simulations and the Importance of
Advanced Cyberinfrastructure Resources
Douglas E. Spearot
Assistant Professor of Mechanical Engineering
Faculty Campus Champion for Cyberinfrastructure
University of Arkansas
Fayetteville, AR 72701
Cyberinfrastructure Days – Marshall University
April 7th, 2011

2. What is Molecular Dynamics?
Molecular dynamics (MD) involves the explicit simulation of atomic scale particles – including atoms and molecules
Example: DNA
Molecular mechanics (statics)
Athermal calculation used to find minimum energy configuration
Uses numerical algorithm such as steepest decent or conjugate gradients
Molecular dynamics
Simulate motion of atoms in time at desired temperature / pressure
Uses numerical integration to solve equations of motion for each atom
Monte Carlo methods
Sample equilibrium configurations of atoms via random displacements
Uses random number generators to perturb system from current state
Rokadia et al. (2010)

3. Why Molecular Dynamics?
Exploration of the unknown or misunderstood
Experiments often do not provide sufficient resolution to study discrete atomic motions in response to a set of boundary conditions
Simulations allow exploration of material behavior under boundary conditions that can not be easily tested experimentally
Example: Defects in Carbon Nanotubes
Image by N. Chopra
Stone-Wales transformation
Zhang et al. (2005; 2007)

4. How Does Molecular Dynamics Work?
In the molecular dynamics method, each atom is treated as a point mass in space
Once the force on each atom is computed, atomic motion is determined through application of Newton’s Laws of Motion
Simplify
Second-order ordinary differential equation which can be numerically integrated to find new atomic positions! i

5. How Does Molecular Dynamics Work?
Interatomic potential provides the “constitutive law” that defines how atoms interact with each other
Accuracy of a molecular dynamics simulation is dependent on the accuracy of U
Example: Polymers / Biomolecules

6. Need for Advanced Cyberinfrastructure
Problem 1: Materials are made up of lots of atoms
Forces and atom positions have to be updated at each integration time step
Solution 1: Parallel decomposition techniques
Example: Small cube of FCC Cu
1 mm
Core 1
Core 2
Core 3
Core 4
Core 5
Core 6
Core 7
Core 8
“Star of Arkansas”
Current world record: 320 billion atoms with EAM potential
(T. Germann et al., using 131,072 cores on IBM BlueGene/L at LLNL)

7. Need for Advanced Cyberinfrastructure
Other “scale” issues related to physical size
Microstructure related statistics may not be captured with small systems
Atomistic model of a nanocrystalline metal
Small Simulation Model
(<20 grains)
Large Simulation Model
(>400 grains)

8. Exploration of Material Properties
With an “appropriate” microstructure models, mechanical properties can be explored
Maximum stress
Flow stress
The “inverse” Hall-Petch relationship can be captured via atomistic simulations
Rajgarhia, Spearot, et al. (2010) Journal of Materials Research, 25, 411.

9. Need for Advanced Cyberinfrastructure
Problem 2: Atoms vibrate at very high frequencies
Requires integration time steps on the order of 1 fs
Limits molecular dynamics simulations to ns of material behavior
Solution 2: Parallel-replica dynamics (minor but measurable benefit)
Idea is to replicate entire system on N cores and run N independent simulations until a specific “event” occurs – at that point all simulations are stopped and updated to the “event” configuration

10. Need for Advanced Cyberinfrastructure
Problem 3: What do I do with all of this data?
Need visualization tools to sort, view and analyze a large amount of temporal and spatial data!

11. Need for Advanced Cyberinfrastructure
Solution 3: Data visualization and analysis
Commercial: Ensight, Materials Studio, etc.
Open Source: VMD, Ovito, AtomEye, ParaView, VisIT, etc.
Paul Navratil, TACC
For atomistic/molecular simulations, geometric primitives are “spheres” meant to represent each atom in the system

12. Open-Source General Visualization
ParaView:

13. Open-Source General Visualization
VisIt:

14. Open-Source Atomistic Visualization
VMD:

15. Open-Source Atomistic Visualization
Ovito:

17. Generate Bonds

18. Select a specific polymer chain

19. Remove all other polymer chains to study behavior of the selected chain

20. “Slice” through the system to study a specific phenomenon
Polymer/nanoparticle interface; impact of nanoparticle on chain dynamics

21. Conclusions and Acknowledgements
Students
Rahul Rajgarhia (Ph.D. 2009)
Alex Sudibjo (MS, 2010)
Shawn Coleman (Ph.D., current)
Varun Ullal (MS, current)
James Stewart (MS, current)
Support
National Science Foundation
CMMI CAREER (PI Spearot)
CMMI (PI Spearot)
EPS ; CNS (PI Apon)
ORAU Powe Junior Faculty Enhancement Award
University of Arkansas
For atomistic/molecular simulations, cyberinfrastructure must include HPC hardware, atomistic software, visualization software, and support personnel!