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Molecular Dynamics Simulations and the Importance of Advanced Cyberinfrastructure Resources

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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

- Molecular dynamics (MD) involves the explicit simulation of atomic scale particles – including atoms and molecules

- 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

Example: DNA

Rokadia et al. (2010)

Image by N. Chopra

www.nano-lab.com

- 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

Stone-Wales transformation

Zhang et al. (2005; 2007)

- 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

- 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

- 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)

- Other “scale” issues related to physical size
- Microstructure related statistics may not be captured with small systems

Atomistic model of a nanocrystalline metal

Large Simulation Model

(>400 grains)

Small Simulation Model

(<20 grains)

- 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.

- 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

- 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!

- 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

- ParaView: http://www.paraview.org

- VisIt: http://wci.llnl.gov/codes/visit

- VMD: http://www.ks.uiuc.edu/Research/vmd/

- Ovito: http://www.ovito.org/

Generate Bonds

Select a specific polymer chain

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

“Slice” through the system to study a specific phenomenon

Polymer/nanoparticle interface; impact of nanoparticle on chain dynamics

- 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 0954505 CAREER (PI Spearot)
- CMMI 1000912 (PI Spearot)
- EPS 0918970; CNS 0959124 (PI Apon)

- ORAU Powe Junior Faculty Enhancement Award
- University of Arkansas

- National Science Foundation

For atomistic/molecular simulations, cyberinfrastructure must include HPC hardware, atomistic software, visualization software, and support personnel!