From nano to macro: Introduction to atomistic

modeling techniques
Lecture series, CEE, Fall 2005, IAP, Spring 2006

Introduction to atomistic modelingxxx

techniques: Do we need atoms to
describe how materials behave?
Lecture 1
Markus J. Buehler
Room 1-272
Email: [email protected]
 Introduction: Lecture series

„ Introduce large-scale atomistic modeling techniques and motivate its

importance for solving problems in modern engineering sciences.

„ Demonstrate how atomistic modeling can be successfully applied to

understand dynamical materials failure of:
… Metals (Cu, Ni, Al, Fe…) and alloys (NiAl…),
… Semiconductors (Si),
… Thin films (of metals or other materials),
… Ceramics (Al2O3, SiC),
… and biological materials (e.g. collagen) as well as natural materials
(clay, C-S-H; ongoing and future studies).

„ Find potential collaborations and synergies within the CEE Department

and at MIT as a whole

„ Target group: Undergraduate / graduate students, postdocs, faculty

interested in atomistic methods and scale coupling
© 2005 Markus J. Buehler, CEE/MIT
 Format

„ Ca. 10 lectures 45-50 minutes each, with time for discussion and questions

„ Clustered lectures during IAP and workshop (course 1.978, for credit)

… Lectures (introduction and methods)

… Modeling and simulation of fracture and deformation of copper
(Dislocation nucleation, fracture, brittle versus ductile, comparion with
theory and experiment..)

„ Two UROP projects posted (fracture of silicon and modeling of collagen)

„ Course material posted on the website

(introductionary papers, books, etc.)

http://web.mit.edu/mbuehler/www/Teaching/LS/
Check for updates and supplementary material

© 2005 Markus J. Buehler, CEE/MIT

 Outline and content (Lecture 1)

„ The BIG challenge to couple nano with macro

„ Historical perspective: Understanding behavior of materials

„ How atomistic simulations are carried out, including:

… Definition and numerical issues
… Time scale dilemma
… Pre-processing and input parameters
… Atomic interactions (potential energy surface)
… Computing strategy: MD codes, parallelization, supercomputing
… Analysis and visualization, data extraction

„ Research examples using atomistic methods

„ Discussion and conclusion:

Are all atoms necessary to describe how materials behave?

„ Outlook
© 2005 Markus J. Buehler, CEE/MIT
Introduction

© 2005 Markus J. Buehler, CEE/MIT

 From nano to macro
„ Materials are made out of atoms
Crack „ Depending on the scale looked
dynamics at at materials, these atoms are
micrometers
(macroscale)
“visible” or not
„ Nevertheless, the atomic
structure always plays an
essential role in determining
material properties (in particular
Dynamics of under certain conditions)
fracture in
protein crystals
(mesoscale) „ Example: Structure of a
complex biological material
(levels of hierarchies)

Chemistry
Mechanics of (atomic
individual scale)
collagen
fibers/proteins
(nanoscale)
© 2005 Markus J. Buehler, CEE/MIT
 The BIG problem …

Want: Accuracy of quantum mechanics (QM) in 1023 atom systems…

This is impossible (today and in the foreseeable future)
Possible solution: ~1023 atoms
Multi-scale modeling techniques
based on hierarchies of overlapping Bridge
scales

MEMS

NEMS Concept:
“finer scales train coarser
Electronics scales by overlap”

100..2 atoms © 2005 Markus J. Buehler, CEE/MIT

 Historical perspective: Modeling of mechanics
(behavior) of materials
„ 1500-1600s: L. da Vinci, Galileo „ 20th century: Atoms discovered
Galilei (Jean Perrin)

Continuum
1700-1800: Euler, Bernoulli „ MD: First introduced by Alder and
Beam theories, rods (partial differential Wainwright in the late 1950's (interactions
equations, continuum theories) of hard spheres). Many important insights
concerning the behavior of simple liquids
„ Continuum mechanics theories emerged from their studies.
„ 1964, when Rahman carried out the first
„ Development of theories of fracture simulation using a realistic potential for
mechanics, theory of dislocations liquid argon (Rahman, 1964).
(1930s) „ Numerical methods like DFT
(Kohn-Sham, 1960s-80s)
„ 1960..70s: Development of FE „ First molecular dynamics simulation of a

Atomistic
theories and methods (engineers) realistic system was done by Rahman and
Stillinger in their simulation of liquid water
in 1974 (Stillinger and Rahman, 1974).
„ 1990s: Marriage of MD and FE via „ First fracture / crack simulations in the
Quasicontinuum Method (Ortiz, 1980s by Yip and others, 1990s Abraham
Tadmor, Phillips) and coworkers (large-scale MD)

„ Now: MD simulations of biophysics problems, fracture, deformation are routine

„ The number of simulation techniques has greatly expanded: Many specialized
techniques for particular problems, including mixed quantum mechanical -
classical simulations, that are being employed to study enzymatic reactions
(“QM-MM”) or fracture simulations (Kaxiras and others, Buehler and J.Goddard).
© 2005 Markus Buehler, CEE/MIT
 The problem to solve

„ In atomistic simulations, the goal is to understand and model the motion of

each atom in the material
„ The collective behavior of the atoms allows to understand how the material
undergoes deformation, phase changes or other phenomena, providing links
between the atomic scale to meso/macro phenomena

Vibration, change of location,

connectivity and others

“Spring”
connects http://www.sr.bham.ac.uk/xmm/images/structu
atoms… res/spherespring_300_248.jpg
http://www.freespiritproductions.com/pdatom.jpg © 2005 Markus J. Buehler, CEE/MIT
 Classical molecular dynamics (MD)
„ Classical MD calculates the time dependent behavior of a molecular system
by integrating their equations of motion (F=force vector, a=acceleration
vector)
F = ma

„ The word “classical” means that the core motion of the constituent particles
obeys the laws of classical mechanics
„ Molecular dynamics simulations generate information at the microscopic
level, which are: Atomic positions, velocities, forces
„ The conversion of this microscopic information to macroscopic observables
such as pressure, stress tensor, strain tensor, energy, heat capacities, etc.,
requires theories and strategies developed in the realm of statistical
mechanics
„ Statistical mechanics is fundamental to the study of many different atomistic
systems
Important: The Ergodic hypothesis states

Ensemble average = Time average (atomistic data usually not valid

instantaneously in time and space) © 2005 Markus J. Buehler, CEE/MIT
 Integrating the equations of motion

„ Verlet algorithm Update of positions

„ Leap-frog algorithm
„ Beeman’s algorithm

„ Velocity Verlet (popular) Update of velocities

„ Algorithms to control the temperature of a system, pressure, stress,

etc. exist (e.g. Nosé-Hoover, Berendson, etc.)
„ NVE, NVT, NPT calculations
„ Most calculations in mechanics field are NVE (nonequilibrium
phenomena such as fracture)
F (use a=F/m)
r, v, a
1
11 2
r, v, a
F © 2005 Markus J. Buehler, CEE/MIT
 Time scale dilemma…
¾ Calculate timely evolution of large number of particles
(integrate using Velocity Verlet, for example)
¾ Need to
F = ma resolve high
Build crystals,
Polycrystal components frequency
structure Nano
oscillations,
e.g. C-H bond
F (at nanoscale)

Time step:
0.1..3 fs

Macro

Time scale range of MD: Picoseconds to several nanoseconds

Timescale dilemma: No matter how many processors (how powerful the
computer), can only reach nanoseconds: can not parallelize time
© 2005 Markus J. Buehler, CEE/MIT
 Consequences of the time scale dilemma

„ Very high strain rates in fracture or deformation (displacement km/sec)

„ Limited accessibility to diffusional processes or any other slow
mechanisms
„ Unlike as for the scale problem (ability to treat more atoms in a
system) there is no solution in sight for the time scale dilemma
„ MD has to be applied very carefully while considering its range of
validity (window, niche: fracture ideal, since cracks move at km/sec)
„ When valid, MD is very powerful and nicely complements experiment
and theory, but it has limitations which need to be understood
km/sec

(Buehler, 2004)

http://www.fz-juelich.de/nic-series/volume23/frenkel.pdf
See also article by Art Voter et al. on the time scale dilemma © 2005 Markus J. Buehler, CEE/MIT
 Monte Carlo (MC) techniques

„ Monte Carlo (MC) techniques and alike have been developed to overcome
some of the limitations of dynamical (MD) atomistic calculations
„ Instead of integrating the EOM, MC performs a random walk to measure
properties: Randomly probing the geometry of the molecular system
(configuration space, acceptance depends on “cost function”)
„ MC enables modeling of diffusion and other “slow” processes (slow
compared to the time scale of atomic vibrations)
„ There exist many different flavors, including
… Classical MC (no information about dynamics, only about mechanisms and
steady state properties, e.g. thermodynamical variables)
… Kinetic MC (get information about dynamics)
… Advanced MD methods (marriage between MC and MD, e.g. Temp. Acc. Dyn.)
… Bias potentials (e.g. restraints) to facilitate specific events by reducing the
barriers

„ Generally, MC techniques require more knowledge about the system of

interest than MD
http://www.fz-juelich.de/nic-series/volume23/frenkel.pdf
D. Frenkel and B. Smit Understanding Molecular Simulations: from Algorithms to Applications, Academic Press, San Diego, 2nd
edition (2002).
http://www.ccl.net/cca/documents/molecular-modeling/node9.html © 2005 Markus J. Buehler, CEE/MIT
 Example: Measuring the average
depth of the Charles River

Classical grid-based
quadrature scheme:
Discretize problem and
perform measurements at
grid points

Monte Carlo:
Perform random walk through
the river; measurements are
performed only at accepted
locations

http://www.fz-juelich.de/nic-series/volume23/frenkel.pdf, http://maps.google.com/ © 2005 Markus J. Buehler, CEE/MIT

 Characteristics of MD (and MC)
„ Atomistic or molecular simulations (molecular dynamics, MD) is a
fundamental approach, since it considers the basic building blocks of
materials as its smallest entity: Atoms
„ At the same, time, molecular dynamics simulations allow to model materials
with dimensions of several hundred nanometers and beyond: Allows to
study deformation and properties, mechanisms etc. with a very detailed
“computational microscope”, thus bridging through various scales from
“nano” to “macro” possible by DNS
„ Sometimes, MD has been referred to as a “first principles approach to
understand the mechanics of materials” (e.g. dislocations are “made” out of
atoms…)
„ With the definition of the interatomic potentials (how atoms interact) all
materials properties are defined (endless possibilities & challenges…)
DFT or
Empirical or
?? Semi-empirical…

http://www.sr.bham.ac.uk/x
mm/images/structures/spher
espring_300_248.jpg
© 2005 Markus J. Buehler, CEE/MIT
 First principles description of mechanics:
Dislocations carry plasticity in metals

Dislocations
are made
out of atoms

© 2005 Markus J. Buehler, CEE/MIT

 The interatomic potential
„ The fundamental input into molecular simulations, in addition to structural
information (position of atoms, type of atoms and their
velocities/accelerations) is provided by definition of the interaction potential
(equiv. terms often used by chemists is “force field”)
„ MD is very general due to its formulation, but hard to find a “good” potential
(extensive debate still ongoing, choice depends very strongly on the
application)
„ Popular: Semi-empirical or empirical (fit of carefully chosen mathematical
functions to reproduce the energy surface…)
Parameters
Lennard-Jones
φ LJ 12:6
potential
~σ
??

r ε0 Or more sophisticated potentials

r (multi-body potentials EMT,
EAM, TB…)
Forces by dφ/dr
© 2005 Markus J. Buehler, CEE/MIT
 Training of Force Fields:
Hydrocarbon-Pt interactions
Concept: Enforce agreement
QC ReaxFF
between force field and
150 quantum mechanics
Hydrocarbon fragments on Pt35-
Binding energy (kcal/mol)

clusters
100

50

H2CCH2(II)
CCH3

CCH2
CH

HCCH
CH2

HCCH3

CHCH2

CH3

H2CCH2(I)
H2CCH3
C

CCH
C2

(van Duin, 2004)

ReaxFF can describe different C-Pt bonding modes © 2005 Markus J. Buehler, CEE/MIT
 Challenge: Coupling of various scales
From QM to Macroscale

Integration of various
scales is essential to Engineering
describe complex materials properties
and systems

Coupling to continuum
1E9 atoms
Meso-FF training
50 atoms
Concurrent coupling
FF training
FF training
Quantum
mechanics © 2005 Markus J. Buehler, CEE/MIT
Atomistic model of fracture (small-scale)

┴ LJ
2D
┴
Mode I
┴

© 2005 Markus J. Buehler, CEE/MIT

 Example: Potentials for metals

http://phycomp.technion.ac.il/~p
Pair potentials
hsorkin/thesis/node18.html Good for gases, but don’t
describe metallic bonding
well

Lennard-Jones 12-6

Morse

Electron density EAM potentials (1980s), Finnis-

Sinclair method, Effective
medium theory: All based on QM
arguments

Quality varies: Good for copper, nickel, to some extend for aluminum ...
M. S. Daw and M. I. Baskes, Phys. Rev. B 29, 6443 (1984); S. M. Foiles, M. I. Baskes, and M. S. Daw, Phys. Rev. B 33, 1986.
M. W. Finnis and J. E. Sinclair, Philos. Mag. A 50, 45 (1984).
K. W. Jacobsen, J. K. Nørskov and M. J. Puska, Phys. Rev. B 35, 7423 (1987).
© 2005 Markus J. Buehler, CEE/MIT
 Nano-meso-macro transition: Biopolymer

Fully atomistic (MD)

(based on QM)

+H2O skin
Elasticity,
Plasticity,..
of single fiber
assemblies
(cross-links)

Mesoscale (parametrization)
Long-range, short-range
interactions
(Buehler, to be published) © 2005 Markus J. Buehler, CEE/MIT
Nano-meso-macro transition: Biopolymer

(Buehler, to be published)
• Concept of hierarchical coupling
works well for some systems
• Challenge: “Which level of detail”
to leave out & what information to
transport (and how)?
© 2005 Markus J. Buehler, CEE/MIT
 Interatomic potential concepts, materials and
simulation codes
QM (not much material specific): DFT (electronic structure information),
codes: JAGUAR, GAUSSIAN, GAMES, CPMD…

Decrease in computational effort

Electron FF: Electrons as particles (Gaussians moving according to
classical EOMs), codes: CMDF
Tight binding: Orbitals, semi-empirical, has fitting parameter obtained from
QM (codes: EZTB and many more)

Increase in accuracy
ReaxFF: Bridge between QM and empirical FFs (charge flow)
EAM: Metals, alloys; semi-empirical expressions (QM derived); Codes:
IMD, LAMMPS, XMD and many others
MEAM: Silicon, metals and other covalently dominated materials (codes:
IMD, CMDF)
Tersoff: Bond order potentials (covalent systems), simple
Organic force fields (harmonic): Proteins, organics etc., CHARMM,
DREIDING, AMBER (codes: NAMD, GROMACS, CHARMM…)
Pair potentials: Noble gases (Ar) or model materials

Less accuracy does not mean less science can be done

© 2005 Markus J. Buehler, CEE/MIT
 Concurrent versus hierarchical
multi-scale simulations
(Molinero et al.) glucose
monomer unit DNA CMDF (Buehler et al.)

Glycosidic
bond
(Pascal et al.)
atomistic and M3B meso model of oligomer QC

Concurrent coupling
(QC-Tadmor, Ortiz, Phillips,…
MAAD-Abraham et al., Wagner et al.)

Hierarchical coupling “Spatial variation of resolution and accuracy“

“finer scales train coarser scales” © 2005 Markus J. Buehler, CEE/MIT
 The Quasi-Continuum (QC) Method

Thin copper
film

Combine atomistic regions embedded

in continuum region
(Buehler et al., 2006) © 2005 Markus J. Buehler, CEE/MIT
 Atomic stress tensor: Cauchy stress

Virial stress:

where ri is the projection of the interatomic distance vector r along

coordinate i.

• We only consider the force part, excluding the part containing the effect of
the velocity of atoms (the kinetic part).
• It was recently shown by Zhou et al. that the virial stress including the
kinetic contribution is not equivalent to the mechanical Cauchy stress.
• The virial stress needs to be averaged over space and time to converge to
the Cauchy stress tensor.
D.H. Tsai. Virial theorem and stress calculation in molecular-dynamics. J. of Chemical Physics, 70(3):1375–1382, 1979.
Min Zhou, A new look at the atomic level virial stress: on continuum-molecular system equivalence,
Royal Society of London Proceedings Series A, vol. 459, Issue 2037, pp.2347-2392 (2003)
Jonathan Zimmerman et al., Calculation of stress in atomistic simulation, MSMSE, Vol. 12, pp. S319-S332 (2004) and references in
those articles by Yip, Cheung, . © 2005 Markus J. Buehler, CEE/MIT
 Atomic strain tensor

Atomic virial strain

• The strain field is a measure of geometric deformation of the

atomic lattice
• The local atomic strain is calculated by comparing the local
deviation of the lattice from a reference configuration.
• Usually, the reference configuration is taken to be the
undeformed lattice.
• In the atomistic simulations, the information about the position
of every atom is readily available, either in the current or in the
reference configuration and thus calculation of the virial strain is
relatively straightforward.

• Unlike the virial stress, the atomic strain is valid

instantaneously in space and time. However, the expression is
only strictly applicable away from surfaces and interfaces.
Jonathan Zimmerman, Continuum and atomistic modeling of dislocation nucleation at crystal surface ledges.
PhD Thesis, Stanford University, 1999. © 2005 Markus J. Buehler, CEE/MIT
Stress versus strain from atomistics…

Harmonic potential
© 2005 Markus J. Buehler, CEE/MIT
Computation and numerical issues

© 2005 Markus J. Buehler, CEE/MIT

 Typical simulation procedure

1. Pre-processing
(define geometry, build
crystal etc.)
2. Energy relaxation
(minimization)
3. Annealing (equilibration F=ma
at specific temperature)
4. “Actual” calculation; e.g.
apply loading to crack
5. Analysis
(picture by J. Schiotz)

Real challenge:
Questions to ask and what to learn
© 2005 Markus J. Buehler, CEE/MIT
 Increase in computing power
Classical molecular dynamics

Focus

(Buehler et al., to appear 2006) © 2005 Markus J. Buehler, CEE/MIT

TOP500 List for November 2004

http://www.top500.org
© 2005 Markus J. Buehler, CEE/MIT
 Parallel Molecular Dynamics

Concept:
Divide the workload
No immediate long range
interaction (only via dynamics)

• Each CPU is responsible

for part of the problem
• Atoms can move into
other CPUs (migration)
• Need to know topology
or the geometric
environment on other
CPUs (green region)

(after Schiotz) © 2005 Markus J. Buehler, CEE/MIT

 Differential multi-scale modeling
„ The strength of MD is not its predictive power (time scale limitations…)
„ Rather use it in a differential way
„ Hypothesis: MD only gives relative differential information
„ Consequence: No quantitative number but only slope and thus additional
integration needed to make information useful, use model systems

“Taylor series”
to move information
property across scales

Parameter (physical)
E.g. potential shape
© 2005 Markus J. Buehler, CEE/MIT
 Atomistic methods in mechanics

„ Use MD methods to perform virtual experiments

„ Computational microscope

„ As long as valid, ideal method to gain fundamental understanding

about behavior of materials

„ Have intrinsic length scale given by the atomic scale (distance)

„ Handles stress singularities intrinsically

„ Ideal for deformation under high strain rate etc., not accessible by
other methods (FE, DDD..)

© 2005 Markus J. Buehler, CEE/MIT

 Experimental verification of intersonic cracking

„ Mike Marder’s group at Univ. of Texas verified the phenomenon of intersonic

cracking in a hyperelastic stiffening material (PRL, 2004)
„ Agreement and confirmation of our theoretical predictions

(Buehler et al., Nature, 2003) (Petersan et al., PRL, 2004)

Theory/MD experiment

Multiple-exposure photograph
of a crack propagating in a rubber sample
(λx = 1.2, λy = 2.4); speed of the crack, ~56
m/s (Petersan et al.).
© 2005 Markus J. Buehler, CEE/MIT
Some example applications

© 2005 Markus J. Buehler, CEE/MIT

How “stuff” deforms?

© 2005 Markus J. Buehler, CEE/MIT

Ductile versus brittle materials

(Buehler, 2004)

© 2005 Markus J. Buehler, CEE/MIT

 Geometry of fracture simulations

„ Large-scale atomistic models with up to 70,000,000 atoms

„ Simple model potential (next slide)

© 2005 Markus J. Buehler, CEE/MIT

 Strain field close to cracks

Atomic virial strain

(e.g. Freund, 1990)

Result: Reasonable
agreement

(Buehler, Gao, Huang; Theor. Appl. Fracture Mechanics, 2004) © 2005 Markus J. Buehler, CEE/MIT
 Stress field close to cracks

Shear stress near a crack

at a bimaterial interface
(Buehler et al., 2006)

Hoop stress near a

moving crack
(Buehler and Gao, Nature, to
appear)

© 2005 Markus J. Buehler, CEE/MIT

 Increase in computing power:
Parallelization

2000 2005 5 µm
1,000,000,000 70,000,000,000
particles particles
10 TFLOP 70 TFLOP
computers computers

0.3 µm

1.2 µm

2010
7,000,000,000,000 particles
1,000 TFLOP computers
© 2005 Markus J. Buehler, CEE/MIT
 A simulation with 1,000,000,000 particles

LJ
potential…
(simple
interaction
but VERY
complex
behavior!!)

(Abraham et a., 2002, Buehler, Hartmaier et al., 2004) © 2005 Markus J. Buehler, CEE/MIT
 LJ in 2D… model system
for brittle material

Why 30% versus 73%?

Does hyperelasticity play the
governing role?

Attempts of explanation:
LJ-solid
(similar to • Yoffe (linear elasticity, 1951)
Abraham
• Gao (purely hyperelastic, 1996)
et al.,
Instability
1994) speed • Marder (lattice models, 1992-
@ 30 % cr 2000)

• Abraham (lattice vibration, 1994)

Critical speed for onset of surface roughening=instability speed

(Buehler et al., Springer Lecture Notes, 2004) © 2005 Markus J. Buehler, CEE/MIT
Dynamical crack tip instabilities

• Developed
new model to
include material
nonlinearities
into instability
theory

Interface fracture

(Buehler and Gao, Nature, 2005 (to appear)) © 2005 Markus J. Buehler, CEE/MIT
 Supersonic interface cracking

• Shear dominated loading (Buehler et al., JCIE, 2005)

• Bimaterial interface (upper part: stiff, lower part: soft)

© 2005 Markus J. Buehler, CEE/MIT
 Cross-scale interactions: Brittle fracture
energy flow engineering
scale

cohesive laws quantum Supersonic fracture

(Buehler et al.)
mechanics
In brittle fracture, the macroscopic behavior of the materials depends on its
underlying atomic interaction across several hierarchies of scales
© 2005 Markus J. Buehler, CEE/MIT
 Concurrent multi-scale simulations

Concurrent
integration of
various scales
and paradigms

nonreactive
• Concurrent FE-atomistic-
atomistic ReaxFF scheme in a crack
FE (continuum)

problem (crack tip treated by

ReaxFF) and an interface
ReaxFF
Organic phase
problem (interface treated by
ReaxFF).
• Highlighted transition regions
as handshake domains between
nonreactive
atomistic
different scale and methods.
Inorganic phase
© 2005 Markus J. Buehler, CEE/MIT
 Example for code coupling:
Concept of mixed Hamiltonian

• Schematic
Computationally
showing the
(eV/Angstrom)

4.0
INEXPENSIVE
3.5
coupling of reactive
Force dE/dX/atom (eV/Angstrom)

Tersoff and nonreactive

3.0
Computationally
potentials
2.5 EXPENSIVE
2.0 ReaxFF • The simpler
nonreactive
Force/atom

1.5
potential is trained
1.0 to resemble the
0.5 reactive potential for
0.0
small deviations
1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 from the equilibrium
Uniaxial strain
Uniaxial strain in [110]-direction
in [110]-direction configuration.

Agreement at small deformation: LINK

© 2005 Markus J. Buehler, CEE/MIT
 Mixed Hamiltonians

wi
(eV/Angstrom)

4.0

3.5
Force dE/dX/atom (eV/Angstrom)

Tersoff
3.0 w2 w1
2.5 100%
2.0 ReaxFF
Force/atom

1.5

1.0

0.5

0.0
1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8
0%
R-Rbuf R R+Rtrans R+Rtrans+Rbuf
R
Uniaxial strain
Uniaxial strain in [110]-direction
in [110]-direction
transition
Capture ReaxFF
layer
Tersoff

QM Tersoff
ghost atoms
ReaxFF
ghost atoms
No QM
y
captured
x Tersoff
ReaxFF
• Bond breaking with QM
L
accuracy

L • Elasticity with inexpensive

potentials
© 2005 Markus J. Buehler, CEE/MIT
 Cracking in Silicon: Model within CMDF
• To model cracking in Silicon efficiently, we developed a multi-paradigm
scheme that combines the Tersoff potential and ReaxFF
• The ReaxFF region is moving with the crack tip (region determined based on
local atomic strain)
New hybrid scheme within CMDF
Reactive region is moving
(110) crack surface, 10 % strain with crack tip

ReaxFF • CMDF reproduces experimental results (e.g. Cramer,

Tersoff Wanner, Gumbsch, 2000) © 2005 Markus J. Buehler, CEE/MIT
Oxidation versus brittle fracture
Including complex chemistry
• Crack dynamics in
silicon without (subplots
(a) and
(c)) and with oxygen
molecules present
(subplots (b) and (d))
• Subplots (a) and (b)
show the results for 5
percent applied
strain, whereas subplots
(c) and (d) show the
results
for 10 percent applied
strain.
• The systems contain
13,000 atoms and
Lx ≈ 160Å and Ly ≈ 310Å.
© 2005 Markus J. Buehler, CEE/MIT
 Extension to large time scales: TAD*

Concept: Find state transitions at

high temperature, estimate times
at low temperature
Defect

• Long time dynamics at crack tip using * In collaboration with Art

TAD Voter, LANL

• Boundary conditions “elasticity”

provided by large background system © 2005 Markus J. Buehler, CEE/MIT
 Diffusion of H on Pt

(Collaboration with Art Voter, LANL)

ReaxFF interfaced with TAD through CMDF © 2005 Markus J. Buehler, CEE/MIT
 Diffusion of H on Pt

(Collaboration with Art Voter, LANL)

ReaxFF interfaced with TAD through CMDF © 2005 Markus J. Buehler, CEE/MIT
Summary and wrap-up

© 2005 Markus J. Buehler, CEE/MIT

 Do we need atoms to describe how materials
behave?
Atomic details needed for some applications and situations, including:
„ Small-scale materials: Miniaturization as a new engineering frontier and
potential (nanomaterials and small-scale structures)
… Thin films, IC technology
… Basis for modern technologies: Coatings
… New metals, alloys, composites, including structural applications

„ Interfaces between dissimilar materials (living systems and technologies,

bio-chips or N/MEMS)
“Interfacial materials” (incl. nanomaterials)

„ Quantum effects, confinement, size effects: Now important for engineers

and exploited for technologies

„ Thus: MD may play a critical role as engineering tool ( “new” engineers

trained in physics, chemistry, biology etc. and the intersections of
various scientific disciplines)
© 2005 Markus J. Buehler, CEE/MIT
 Size effects in materials

Property
Property B

Exploit scale effects

• Optimal size?
• Optimal structure?

Property A

size-1
macroscale nanoscale

This helps to define novel machine and materials design principles

© 2005 Markus J. Buehler, CEE/MIT

 Linkage of experiment-theory-simulation

9 Atomistic simulations is an increasingly important tool in materials science;

it can be used to…
- Advance theory and discover new physical phenomena
- Augment and explain experiment

9 With its limitations understood, MD simulation is an ideal tool to study

small-scale dynamics materials phenomena; gain insight into mechanisms

Experiment

Computer
Theory
simulation

© 2005 Markus J. Buehler, CEE/MIT

 Scales covered at CEE: From nano to
macro to help understand the “world”

“Cells” “City/region” Moshe Ben-Akiva

Traffic
DynaMIT

Dara

Penny Chisholm System Entekhabi

Space
Bacteria, viruses,
microbes perspective instruments

“Space”
“Nano/Micro- Interfaces
materials”
New frontiers
“Coastal areas” “Nano-macro”
Franz Ulm Heidi Nepf Markus Buehler
Materials (cement, Environmental Fracture, natural &
bone), Genoming fluid mechanics biological materials
© 2005 Markus J. Buehler, CEE/MIT
 Nanoscale at CEE
„ At CEE, we use a holistic approach to understand the scientific
concepts “how” the world works

„ A key focus is the “system perspective” and integration of dissimilar

hierarchies of materials, methods, and interactions of technology-
human/society

„ Genuine interest in multi-scale phenomena and their modeling,

experimental investigation and understanding

„ To develop deep understanding of scale problems we need different

perspectives and views, including nano-view (atomistic), systems
perspective, macroscale properties and many others

„ This involves a variety of numerical, theoretical and experimental

approaches across scales and disciplines, including atomistic and
mesoscale simulations

¾ Helps to understand the similarities in behavior across disciplines and

across the scales for development of new engineering concepts
© 2005 Markus J. Buehler, CEE/MIT
 Lecture topics: Outline
Fall 2005
„ Oct. 27, 1 PM, Room 1-134: Introduction to atomistic modeling techniques: Do we need atoms to describe
how materials behave?
„ Nov. 3, 1 PM, Room 1-134: Methods and techniques for modeling metals and their alloys and application to
the mechanics of thin metal films
„ Nov. 17, 1 PM, Room 1-134: Scale coupling techniques: From nano to macro
„ Dec. 5, 1 PM, Room 1-150: Reactive versus nonreactive potentials: Towards unifying chemistry and
mechanics in organic and inorganic systems

IAP 2006: From nano to macro: Introduction to atomistic modeling techniques and
application in a case study of modeling fracture of copper (1.978 PDF)
„ Jan. 9 (Monday): Introduction to classical molecular dynamics: Brittle versus ductile materials behavior
„ Jan. 11 (Wednesday): Deformation of ductile ma terials like metals using billion-atom simulations with
massively parallelized computing techniques
„ Jan. 13 (Friday): Dynamic fracture of brittle materials: How nonlinear elasticity and geometric confinement
governs crack dynamics
„ Jan. 16 (Monday): Size effects in deformation of materials: Smaller is stronger
„ Jan. 18 (Wednesday): Introduction to the problem set: Atomistic modeling of fracture of copper
„ The IAP activity can be taken for credit. Both undergraduate and graduate level students are welcome to
participate. Details will be posted on the IAP website (http://web.mit.edu/iap/).

Spring 2006
„ TBD. Atomistic modeling of biological and natural materials: Mechanics of protein crystals and collagen
„ TBD. Mechanical properties of carbon nanotubes: Scale effects and self-folding mechanisms
„ TBD. Atomistic and multi-scale modeling in civil and environmental engineering: Current status and future
development
http://web.mit.edu/mbuehler/www/Teaching/LS/ © 2005 Markus J. Buehler, CEE/MIT
 Additional references

„ http://www.ch.embnet.org/MD_tutorial/pages/MD.Part1.html
„ Alder, B. J. and Wainwright, T. E. J. Chem. Phys. 27, 1208 (1957)
„ Alder, B. J. and Wainwright, T. E. J. Chem. Phys. 31, 459 (1959)
„ Rahman, A. Phys. Rev. A136, 405 (1964)
„ Stillinger, F. H. and Rahman, A. J. Chem. Phys. 60, 1545 (1974)
„ McCammon, J. A., Gelin, B. R., and Karplus, M. Nature (Lond.) 267, 585 (1977)
„ D. Frenkel and B. Smit Understanding Molecular Simulations: from Algorithms to
Applications, Academic Press, San Diego, 2nd edition (2002).
„ M.J. Buehler, A. Hartmaier, M. Duchaineau, F.F. Abraham and H. Gao, “The dynamical
complexity of work-hardening: A large-scale molecular dynamics simulation”, under
submission to Nature.
„ M.J. Buehler, A. Hartmaier, M. Duchaineau, F.F. Abraham and H. Gao, “The dynamical
complexity of work-hardening: A large-scale molecular dynamics simulation”, MRS
Proceedings, Spring meeting 2004, San Francisco.
„ M.J. Buehler, A. Hartmaier, H. Gao, M. Duchaineau, and F.F. Abraham, “Atomic
Plasticity: Description and Analysis of a One-Billion Atom Simulation of Ductile Materials
Failure.” In the press: Computer Methods in Applied Mechanics and Engineering (to
appear 2004).
„ B. deCelis, A.S. Argon, and S. Yip. Molecular-dynamics simulation of crack tip processes
in alpha-iron and copper. J. Appl. Phys., 54(9):4864–4878, 1983.

„ See additional references & material on the website:

http://web.mit.edu/mbuehler/www/Teaching/LS/lecture-1-supp.htm

© 2005 Markus J. Buehler, CEE/MIT