Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-1

Leonid V. Zhigilei

In this lecture we will talk about the computational materials science, a relatively new and one of the fastest
growing disciplines in materials science. We will start from a short discussion of the basic ideas behind
computer simulations and the increasingly important role the simulations play in scientific research in
general and in materials research in particular. Then we will have a short overview of contemporary
computational methods used in design and optimization of new and existing materials, consider a few recent
success stories, and discuss some of the current limitations and challenges faced by the computational
materials science.
From mathematical description to computer simulation

Galileo Galilei (1564-1642)

The idea of the necessity of mathematical/computational description of

physical phenomena is not a new one. Nearly 400 years ago Galileo Galilei
insisted that once a certain number of experiments (sensate esperienze)
have been performed, it is necessary to describe the results mathematically.
If we succeed in describing the phenomenon with mathematical equations,
then we can predict, by computing, the behavior of the system of interest for
a wide range of conditions, including the ones for which experiments are
difficult, too expensive, or not possible at all.

Over the centuries that followed the time of Galileo, the computational work was focused on finding
analytical solutions of the equations that describe the behavior and properties of a system of interest.
Finding analytical solution for complex systems is a very difficult task. In 1929 one of the fathers of
quantum mechanics, Dirac, wrote The underlying physical laws necessary for the mathematical theory of a
large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that
the exact application of these laws leads to equations much too complicated to be soluble.
Indeed, not only the solution of quantum mechanical equations is intractable, except for some special cases,
but the classical mechanics problem of many interacting bodies cannot be solved analytically for more than
3 bodies. Similarly, the equations for the gas/fluid flow, electrical/magnetic fields induced by static or
moving charges, etc. are well known but usually difficult to solve for any conditions of practical interest. In
the situation when analytical solution of the equations is difficult, the invention of computers has provided a
new exciting possibility to solve the complex equations numerically, in a computer simulation. During the
last half century computer modeling has developed into a very powerful method of scientific research used
in almost all areas of science, from biology and economy to nuclear physics and astronomy. The pace of the
development of computational methods and applications of computer simulations was different in different
areas of science, though. The majority of chemical and pharmaceutical companies these days are routinely
using computer simulations of molecular structures and interactions to accelerate the design of new drugs
and chemical compounds. The leading engineering companies, such as Airbus, Boeing, Ford, and GM, are
modeling aerodynamic and mechanical characteristics of aircrafts and automobiles before building physical
models and testing them in a wind tunnel or crashing them into a wall. At the same time, the development
and application of computer modeling in material science was rather slow over the years and only now we
are experiencing a very fast increase in the number and quality of computational studies in materials
research. In order to understand the reasons for the dramatic change in use of simulations in materials
science, we shall consider, first, the specifics of problems that traditional materials science is dealing with
and, second, the drastic increase in the available computational power, resulting from the design of new
computers with multiple processors and special parallel architecture tuned for computationally intensive
calculations. Below we will consider these two factors in more details.

Computer modeling of material behavior p. 36-2

Leonid V. Zhigilei

Department of Materials Science and Engineering

University of Virginia

Characteristic length- and time-scales in materials modeling

As you learned in the previous lectures, real materials have many defects, including vacancies, impurities,
dislocations, grain boundaries, domain walls (in magnetic and ferroelectric materials), etc. It is the structure
and properties of the defects, their interactions, and their thermodynamics that define the macroscopic
properties of real materials. The totality of all lattice defects is called microstructure of the specimen. You
have also learned that the microstructure can be changed/controlled by thermal or mechanical processing.
Therefore, investigation of the structure, properties and interactions of defects, their evolution during
processing and their response to the external conditions is in the core of materials research.
While some of the most fundamental questions concerning the behavior and interaction of defects still
remain unresolved, the application of computational methods to address this questions has been rather
limited. The lack of computational activities in this area can be attributed to the fact that lattice defects
belong to the intermediate (or mesoscopic) length-scale. They are too big to be simulated by atomiclevel computational models, commonly used in chemistry, and, at the same time, they are too small to for
macroscopic continuum modeling, used in engineering. While atomistic and continuum simulation
techniques are well established and extensively used, the mesoscopic modeling is still in its infancy. The
development of mesoscopic models is hampered by insufficient understanding of the microscopic properties
and behavior of defects. Only now a quickly growing computational power of modern computers is
reaching the level that allows one to perform realistic atomic-level analysis of lattice defects and their
interactions. The insights extracted from such simulations are used as input for the development and
parameterization of computational models for mesoscopic simulations. The range of time and length scales
relevant to different materials science problems is illustrated in a schematic drawing in the next page.
Growth of the computational power. Moores law.
As discussed above, it is the steep and steady increase in
the available computational power that is responsible for
the current fast development of the computational
materials science. Gordon Moore, co-founder of Intel,
noted in 1965 that that the number of transistors per square
inch on integrated circuits (and computational speed) had
doubled every year since the integrated circuit was
invented. Moore predicted that this trend would continue
for the foreseeable future. Currently it is expected that the
Moore's Law will hold for at least another two decades.

The figure to the left shows ASCI White, the RS/6000

SP supercomputer developed by IBM and installed at the
LLNL in 2001, is considered to be the world's fastest
supercomputer. It covers an area the size of two
basketball courts and is mostly used by the DOE for
computations related to the safety and reliability of the
US nuclear weapons stockpile. Some of the recordbreaking materials science related simulations
discussed below have been performed on this computer.

Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-3

Leonid V. Zhigilei

Time Scale, seconds

10-7

Vasily Bulatov et al., LLNL

Dislocation dynamics simulation

Mesoscopic

Continuum, macroscopic modeling

constitutive relations

Elizabeth Holm, Sandia

Simulation of intergranular fracture
Monte Carlo Potts model

Farid Abraham et al., IBM

Atomistic simulation of crack propagation

Leonid Zhigilei et al., UVa

Phase transformation on diamond surfaces

10-9

Mo Li, JHU, Atomistic

model of a nanocrystalline

10-12

Atomistic / Nanoscopic

1021
Length Scale, number of atoms
109
103

106

10-3
Length Scale, meters
10-9

10-8

10-7

Macroscopic

Length- and time-scales in materials modeling

Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-4

Leonid V. Zhigilei

Atomic-level simulations: Molecular Dynamics

Molecular dynamics is a computer simulation technique that allows one to predict the time evolution of a
system of interacting particles (atoms, molecules, granules, etc.). The basic idea is very simple:
! First, for a system of interest, one has to specify a set of initial conditions (e.g. initial positions and
velocities of all particles in the system) and interaction potential (energy of the system as a function of
atomic positions). The forces among all the atoms can be derived from the interaction potential.
! Second, the evolution of the system in time can be followed by solving a set of classical equations of
motion for all particles in the system. Within the framework of classical mechanics, the equations that
govern the motion of classical particles are the ones that correspond to the second law of classical
mechanics formulated by Sir Isaac Newton over 300 years ago:
r
2r

r r
m i a i = Fi

or

mi

dv i r
= Fi
dt

or

mi

d ri r
= Fi
dt 2

If the particles of interest are atoms, and if there are a total of Nat of them in the system, the force acting on
the ith atom at a given time can be obtained from the interatomic potential V(r1, r2, r3, , rNat) that, in
r
r
general, is a function of the positions of all the atoms, F = - V( rr , rr , rr ,..., rr )
i

N at

Energy, eV, Force, eV/

For example, if we only have 2 atoms in a system (e.g. a diatomic molecule),

the potential depends only on the distance between the two atoms V(r12):
0.005

r
F2

Force

r
F1

r r
r12 = r1 r2
Energy

r
r
V(r12 )
F1 = F2 = dr12

-0.005

repulsion

-0.01
2

attraction
4

Distance between atoms, rij,

Once the initial conditions and the interaction potential are defined, the equations of motion can be solved
numerically. The simplest but not very accurate method that can be used to solve the equations is so-called
Eulers method:
r
r
If we know the positions and velocities of all particles in a system at time t, ri (t ), v i (t ) , we can find the
positions and velocities at time t + t:

r(t + t) = r(t) + v(t) t

v(t + t) = v(t) + a(t) t = v(t) +

F(t)
t
m

The result of the solution are the positions and velocities of all the atoms as a function of time.

Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-5

Leonid V. Zhigilei

Schematic diagram of a basic molecular dynamics computer code

r

Define initial positions and velocities ri (t 0 ) and v i (t 0 )

Example: collision of a droplet with

a substrate (Yasushi Katsumi, UVa)

Calculate forces at current time tn:

500 m/s

r
r
r r r
r
Fi = - i V( r1 , r2 , r3 ,..., rN at )

Solve equations of motion for all particles in the system

r
r
over a short timestep t.

tn+1 = tn + t

ri (t n ) ri (t n +1 )
r
r
vi (t n ) vi (t n +1 )

initial conditions are specified

r
r
ri (t 0 ) and v i (t 0 )

MD simulation

Calculate desired physical quantities,

write data to trajectory file

is tn+1 > tmax ?

Snapshot from MD simulation

at time tn = 100 ps

Write to the disc final atomic configuration & finish

As we can see from the snapshots from the simulation of droplet collision above, a rather complex behavior
can result from the integration of a set of very simple equations of motion for a group of interacting atoms.
One of the main strengths of the molecular dynamics method is the ability to reproduce fast non-equilibrium
processes with atomic-level resolution (e.g. microscopic mechanisms of damage/plastic deformation due to a
shock wave propagation, dynamic fracture and crack growth, ion or cluster bombardment, etc.). The method
can be also used to study equilibrium thermodynamic properties of the materials under conditions that is
difficult to achieve experimentally. Below we will first discuss the limitations of the molecular dynamics
method and then consider a few examples of application of this technique to materials-related problems.

Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-6

Leonid V. Zhigilei

Limitations of the molecular dynamics method

As soon as you have a computer code that is working, there is a temptation to immediately apply it to a wide
range of problems. It is very important, however, to clearly understand the approximations that were used in
designing the mathematical model and the related limitations of the computational technique. It is not
unusual for mathematical modeling to be misused by being applied to the phenomena that lays outside the
domain for which the model was developed. Confusing or simply wrong results can be obtained (and
occasionally published) in these cases. It is, therefore, very important to understand the limitations of
computational models. In particular, the main limitations of the classical molecular dynamics simulation
technique are listed below.

1. Classical description of interatomic interaction. In a molecular dynamics simulation electrons are not
present explicitly, they are introduced through the potential energy that is a function of atomic positions only
(this is called Born-Oppenheimer approximation in quantum mechanics). The potential energy, in turn, is
approximated by an analytic function that gives the potential energy U as a function of atomic positions. As
you remember, we need the potential energy to calculate forces, that are obtained as a gradient of a potential
energy function. Design of the potential function and choice of the parameters is often based on fitting to
available experimental data (e.g. equilibrium geometry of stable phases, cohesive energy, elastic moduli,
vibrational frequencies, temperatures of the phase transitions, etc.). If the potential is designed based on one
set of properties, it may not work well in the description of other properties that were not included in the
parameterization
2. Classical description of atomic motion. In classical molecular dynamics we replace Schrdinger
equation for nuclei with classical Newton equation. Quantum mechanical analysis suggests that the wave
nature of electrons dominates over the particle behavior, and electrons can not be considered within classical
approximation. At the same time, all atoms, except for the lightest ones such as H, He, Ne, can be
considered as point particles at sufficiently high temperature and classical mechanics can be used to
describe their motion.
3. Time- and length-scale limitations. The fact that in a molecular dynamics simulation we have to
integrate the equations of motion for all atoms in a system puts severe limitations on the number of atoms
that can be included in the simulation and the time of the simulation. These limitations constrain the range
of problems that can be addressed by the method.
Time-scale: The maximum timestep of integration in a molecular dynamics simulation is defined by the
fastest motion in the system. The period of vibrational motion of atoms in a solid is typically on the order of
hundreds femtoseconds (1 fs = 10-15 s) to picoseconds (1 ps = 10-12 s). Therefore, a typical timestep in the
simulation cannot be longer than a femtosecond. Using modern computers it is possible to calculate 106
108 timesteps. Therefore we can only simulate processes that occur within 1 100 ns. This is a serious
limitation for many problems that involve diffusion, cluster/vapor film deposition, relaxation of irradiation
damage, and other processes that occur at a longer time-scale.
Length-scale: The size of the computational cell is limited by the number of atoms that can be included in
the simulation, typically 104 107. This corresponds to the size of the computational cell on the order of
tens of nm. Any structural features of interest and spatial correlation lengths in the simulation should be
smaller than the size of the computational cell. To make sure that the finite size of the computational cell
does not introduce any artifacts into the simulation results, one can perform simulations for systems of
different size and compare the measured properties.

Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-7

Leonid V. Zhigilei

Dealing with the time- and length-scale limitations of the molecular dynamics method

The record-breaking simulations are:

Record time scale protein folding simulation. Simulation of 1 microsecond of folding of a small, 36
amino-acid, protein with surrounding water molecules (12,000 atoms total) took ~3 months of dedicated
computing using all 256 processors of CRAY-T3E supercomputer at Pittsburgh Supercomputer Center.
Timestep of 2 fs was used 1s = 5108 steps of integration.
Record length scale multi-billion simulations of crystal fracture, discussed in the next page.
Due to the limitations on the size of the system that can be simulated, an important aspect of any molecular
dynamics simulation is an adequate description of the interaction of atoms in the system (sometimes called
computational cell) with surrounding infinite material. We have to define boundary conditions and
apply special methods for temperature and pressure control in the molecular dynamics computational
cell (heat and work exchange between the molecular dynamics computational cell and the surroundings).

Large external system

surface

MD
MD
Large external system

Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-8

Leonid V. Zhigilei

Current applications of the MD simulation technique in

materials science include investigations of point, linear, and
planar defects in crystals and their interactions, microscopic
mechanisms of fracture, surface reconstruction, melting and
faceting, film growth, friction, surface modification by ion or
cluster bombardment, etc.
Shockwave-induced plasticity
[B.L. Holian and P.S. Lomdahl,
Science 280, 2085 (1998)]

Nano-jet implantation of functional molecules into a polymer substrate [Masahiro Goto et al., J. Appl. Phys.
90, 4755-4760, 2001]

Current state of the art (length-scale): billions of atoms

Billion atoms simulation of work-hardening
and ductile failure of a FCC solid under
tension. The system is a FCC crystallite with
the total number of atoms of 1,023,103,872.
The total simulation time is 200,000 timesteps.
It takes 1.7 seconds per timestep for a 4096node simulation on ASCI White computer
(~four clock-days of total simulation time).
http://www.almaden.ibm.com/st/Simulate/df.html

Test run with 5,180,116,000 particles has been performed in 2000 by J. Roth, F. Ghler, and H.-R.. Trebin
[Int. J. Modern Phys. C 11, 317-322, 2000] in Jlich, Germany on 512 processors of Cray-T3E computer.
The test run took 40 minutes for 5 timesteps of integration.

Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-9

Leonid V. Zhigilei

Kinetic Monte Carlo method for simulation of slow thermally-activated processes, such as diffusion.
As you remember from previous lectures, the atomic diffusion
is a thermally-activated process. In the case of the vacancy
diffusion mechanism this means that in order for an atom to
jump into a vacancy site, it needs to overcome a high energy
state, when old bonds are already broken and new ones are not
formed yet. The probability for an atom to get enough energy
for a jump can be described by the Arrhenius equation:

Energy

Em
Atom

Vacancy

Distance

Schematic representation of the vacancy

diffusion mechanism

R j = R 0 exp E m

k
T
B

where R0 is an attempt frequency proportional to the frequency

of atomic vibrations and Em is the diffusion activation energy
height of the barrier.
If we try to study diffusion using molecular dynamics method,
the resulting picture will be rather boring most of the time
atoms will spend oscillating around their equilibrium
positions, as in the picture on the left side of the page.
The simulation can be significantly accelerated if instead of
solving equations of motion, me will directly use the jump
rates predicted by the Arrhenius equation. In other words, we
will just move atoms randomly from one equilibrium position
to another equilibrium position with frequencies that are
defined by the energy barriers that separate the equilibrium
positions. This idea to randomly move atoms with the rates
defined by the activation barriers is in the core of the kinetic
Monte Carlo method.

MD simulation by T. Kwok, P. S. Ho,

and S. Yip. Initial atomic positions are
shown by the circles, trajectories of
atoms are shown by lines. A region
around a grain boundary is shown.

The main limitation of the kinetic Monte

Carlo method is that we have to specify all
the barriers/rates in advance, before the
simulation. As the system becomes more
complex, the number of possible events
becomes larger and parameterization of
the model becomes more difficult

The pictures below show the result from kinetic Monte Carlo
simulation of island growth on a homogeneous substrate and a
substrate with nanoscale patterning.
http://www.lce.hut.fi/publications/annual2000/node22.html

Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-10

Leonid V. Zhigilei

Dislocation Dynamics
As you remember from the lecture on defects, dislocations are linear defects that are responsible for plastic
deformation in crystalline solids. If we understand the dynamics and interaction of dislocations in materials,
we will be able to understand and, ultimately, control the mechanical properties (strength and plasticity) of
materials. The complexity of a collective behavior of a large number of dislocations in crystals undergoing
plastic deformation makes it difficult to provide a complete and consistent theoretical description of plastic
deformation. Mesoscopic simulation method of dislocation dynamics provides additional means for
checking existing theoretical concepts and development of new ideas in this research area.
The dislocation dynamics model is based on the following ideas:

Spatial discretization: The simulated area is grided with grid size that is larger
than the distance of spontaneous annihilation of two dislocations (typically
several nanometers).
Dislocation lines are represented by chains of connected dislocation segments.
New segments are introduced if two adjacent segments become too long (if the
curvature is too crudely described).
Forces acting on dislocations are calculated based on the elasticity theory. These forces include forces due
to the interaction of the elastic fields of different dislocations, external forces of mechanical loading, etc.
Short-range interactions (reactions) of dislocation cores are described based on the results of molecular
dynamics simulations and experimental data.
Equations of motion of dislocations are solved (different methods has been proposed for description of
dislocation motion, including Monte Carlo-type and molecular dynamics type methods).
Below are a few examples of dislocation dynamics simulations:

A nice collection of animations from dislocation dynamics

simulations can be found at http://zig.onera.fr/lem/DisGallery/
Simulation of dislocation networks in
relaxed quantum-dot structures
http://www.research.ibm.com/dislocationdynamics/

Department of Materials Science and Engineering

University of Virginia

Computer modeling of material behavior p. 36-11

Leonid V. Zhigilei

Finite element method continuum description of materials

Finite element method (FEM) is a very popular computational method that is used in materials science. In
the FEM there are no restrictions on the scale of the object (can be large a wing of an aircraft or a bridge)
or small (stress distribution around a tip of a micro-crack or small island on a surface). The FEM method is
the most popular simulation method in engineering, it is used in mechanical and aerospace engineering,
structural analysis, bioengineering, analysis of fluid flow, etc.
A (very simplified) description of the FEM can be given as follows:

! An object is divided into small pieces (like in a Lego game) that are called elements. Each element is
defined by nodes.
! A proper behavior is assigned to the elements and physical quantities are defined on each element.
! A system of equations, that describes evolution of quantities in the system of connected elements is
solved.
! Quantities of interest (e.g. stress, strain, density, temperature, etc.) are calculated on each element.

Element

Nodes

As with any numerical tool, FEM can be easily misused and it is

important to understand the limitations of the method. In the
case of FEM, the limitations are defined by the physical models
that lead to the equations incorporated into the FEM.
http://www.physics.cornell.edu/sethna/
teaching/Simulations/FEM.html

To learn more about modeling in materials science, check the web page for MSE 524 course
http://www.people.virginia.edu/~lz2n/mse524/
and take this class.