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 - PowerPoint PPT PresentationTRANSCRIPT
Molecular Dynamics Simulations and the Importance of Advanced Cyberinfrastructure Resources
Douglas E. Spearot
Assistant Professor of Mechanical EngineeringFaculty Campus Champion for Cyberinfrastructure
University of ArkansasFayetteville, AR 72701
Cyberinfrastructure Days – Marshall UniversityApril 7th, 2011
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?
• 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
ww
w.n
ano-
lab.
com
Imag
e by
N. C
hopr
a
Stone-Wales transformation
Zhang et al. (2005; 2007)
Example: Defects in Carbon Nanotubes
• 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
How Does Molecular Dynamics Work?
Simplify
iNi
rrF
U
iF iiiiii raF mm
Second-order ordinary differential equation
which can be numerically integrated to find new
atomic positions!
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
612
2
2
)cos(12121
ij
ij
ij
ijbondednon
ijklijkltorsion
oijkijkijkbend
oijijijstretch
rB
rA
U
ndkU
kU
rrkU
Example: Polymers / Biomolecules
... bondednontorsionbendbonded UUUUU
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 m atomsCu billion 7.84cellunit 1
atoms 4 0.3615cellunit 1
1101
33
333
nmmnmm
Current world record: 320 billion atoms with EAM potential(T. Germann et al., using 131,072 cores on IBM BlueGene/L at LLNL)
Core 1Core 2
Core 3Core 4
Core 5Core 6
Core 7Core 8
“Star of Arkansas”
Need for Advanced Cyberinfrastructure
• Other “scale” issues related to physical size Microstructure related statistics may not be captured with small systems
Angle of Disorientation (degrees)0 10 20 30 40 50 60 70
Pro
babi
lity
Den
sity
0.00
0.02
0.04
0.06
0.08
0.10
0.12
Sample DODFMackenzie random DODF
Average grain diameter (nm)27 28 29 30 31 32 33Fr
eque
ncy
0
1
2
3
4
5
6 Grain size distributionLog normal distribution
Angle of Disorientation (degrees)0 10 20 30 40 50 60 70
Pro
babi
lity
Den
sity
0.00
0.01
0.02
0.03
0.04
0.05Sample DODFMackenzie random DODF
Average grain diameter (nm)8.5 9.0 9.5 10.0 10.5 11.0 11.5
Freq
uenc
y
0
20
40
60
80
100 Grain size distributionLog normal distribution
Small Simulation Model(<20 grains)
Large Simulation Model(>400 grains)
Atomistic model of a nanocrystalline metal
Exploration of Material Properties
• With an “appropriate” microstructure models, mechanical properties can be explored
d (nm)0 10 20 30 40 50 60
Flow
Stre
ss (G
Pa)
1.6
1.8
2.0
2.2
2.4Cu (Schiotz et al. 2003)Cu (present study)
7.5 nm 10 nm 15 nm 20 nm 25 nm 30 nm 35 nm 40 nm 45 nm
7.5 nm 10 nm 15 nm 20 nm 25 nm 30 nm 35 nm 40 nm 45 nm
7.5 nm 10 nm 15 nm 20 nm 25 nm 30 nm 35 nm 40 nm 45 nm
Pure Cus = 62nm, 20M atomsdeformation at 300K
Strain (%)0 2 4 6 8 10
Stre
ss (G
Pa)
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
7.5 nm 10 nm 15 nm 20 nm 25 nm 30 nm 35 nm 40 nm 45 nm
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 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 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 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
• VisIt: http://wci.llnl.gov/codes/visit
•
Open-Source Atomistic Visualization
• VMD: http://www.ks.uiuc.edu/Research/vmd/
•
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
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!