Molecular Dynamics Simulations and the Importance of
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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

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Molecular dynamics simulations and the importance of advanced cyberinfrastructure resources

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


What is molecular dynamics

What is Molecular Dynamics?

  • 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)


Why molecular dynamics

Image by N. Chopra

www.nano-lab.com

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

Stone-Wales transformation

Zhang et al. (2005; 2007)


How does molecular dynamics work

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


How does molecular dynamics work1

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


Need for advanced cyberinfrastructure

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)


Need for advanced cyberinfrastructure1

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

Large Simulation Model

(>400 grains)

Small Simulation Model

(<20 grains)


Exploration of material properties

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.


Need for advanced cyberinfrastructure2

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


Need for advanced cyberinfrastructure3

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!


Need for advanced cyberinfrastructure4

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


Open source general visualization

Open-Source General Visualization

  • ParaView: http://www.paraview.org


Open source general visualization1

Open-Source General Visualization

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


Open source atomistic visualization

Open-Source Atomistic Visualization

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


Open source atomistic visualization1

Open-Source Atomistic Visualization

  • Ovito: http://www.ovito.org/


Molecular dynamics simulations and the importance of advanced cyberinfrastructure resources

Generate Bonds


Molecular dynamics simulations and the importance of advanced cyberinfrastructure resources

Select a specific polymer chain


Molecular dynamics simulations and the importance of advanced cyberinfrastructure resources

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


Molecular dynamics simulations and the importance of advanced cyberinfrastructure resources

“Slice” through the system to study a specific phenomenon

Polymer/nanoparticle interface; impact of nanoparticle on chain dynamics


Conclusions and acknowledgements

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 0954505 CAREER (PI Spearot)

      • CMMI 1000912 (PI Spearot)

      • EPS 0918970; CNS 0959124 (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!


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