Phase Transformations in Computer

Simulated Icosahedrally Ordered Phases

Fredrik Zetterling

Stockholm 2003

Doctoral Dissertation
Royal Institute of Technology

Department of Numerical Analysis and Computer Science

Akademisk avhandling som med tillstnd av Kungl Tekniska Hgskolan framlgges
till offentlig granskning fr avlggande av teknologie doktorsexamen 13 juni 2003 i
Kollegiesalen, Valhallavgen 79.

ISBN 91-7283-547-8
TRITA-NA-0313
ISSN 0348-2952
ISRN KTH/NA/R--03/13--SE

Fredrik Zetterling, Maj 2003

Universitetsservice US AB, Stockholm 2003

 Abstract
Computer simulations play a profound and fundamental role in modern
theoretical physics, chemistry and materials science. To understand the complex
physics of metally liquids, metals, quasicrystals and metally glasses a working
model imposing the local and global order is needed. Experiments and theory have
predicted the local order in liquid metals to be icosahedral.

The current work has been done using molecular dynamics computer simulations
of a monatomic system using a simple pair-potential for the interactions. Two
new pair-potentials has been developed, the Zetterling-1(Z1) and Zetterling-2(Z2)
potentials. They are specically modeled to impose icosahedral order. The basis for
the development of the potentials was the old Dzugutov potential which is known to
freeze into a dodecagonal quasicrystal. The new Zetterling potentials have a longer
interaction range and a narrower rst minimum. The more narrow rst minimum
will enhance the local icosahedral ordering and the longer interaction range was
introduced to incorporate a second maximum in the potential mimicing the Friedel
oscillations found in metallic systems. These Friedel oscillations are due to the
singularity which arises at the Fermi surface due to the screening of the positive
charge by the electron gas.
Five papers are included in the study. The rst two papers are studies of
icosahedral clustering in the liquid and supercooled liquid. The simulations in
Paper I was done using the old Dzugutov potential while the new potentials were
used in Paper II using both molecular dynamics and the Basin Hopping algorithm
presented in Chapter 5. Paper III considers the concept of dynamical ergodicity in
the context of the super-cooled liquid behaviour. The simulations were made using
the old Dzugutov potential. Paper IV reports a molecular dynamics simulation
using the Dzugutov potential under super-cooling. A formation of icosahedrally
structured domains with distinctly slow diusion which grows with cooling in a
low-dimensional manner and percolate around Tc , the critical temperature of the
mode-coupling theory. A sharp slowing down of the structural relaxation relative to
diusion is observed. It is concluded that this eect cannot be accounted for by the
spatial variation in atomic mobility. The low-dimensional clustering is discussed as a
possible mechanism of fragility. Paper V investigates the crystallization of a simple
monatomic liquid model which utilizes the Zetterling-1 potential. The system forms
a thermodynamically stable solid phase exhibiting cubic symmetry. Its diraction
pattern is identied as that of -brass, a tetrahedrally packed crystalline structure
with 52 atoms in the unit cell.
Keywords: simple liquids, molecular dynamics, pair potential, icosahedral cluster.

An electronic version of the thesis can be found at:

http://www.nada.kth.se/~fzet/thesis.pdf
ISBN 91-7283-547-8 TRITA-NA-0313 ISSN 0348-2952 ISRN KTH/NA/R--03/13--SE

iii
iv
Contents

1 Introduction 1
1.1 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Icosahedral Ordering . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Essential New Results . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.4 Presentation of papers . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.4.1 Paper I . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.4.2 Paper II . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.4.3 Paper III . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.4.4 Paper IV . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4.5 Paper V . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2 Tetrahedrally Close-Packed Phases in Intermetallic Systems 5

3 Computer Simulations 9
3.1 Why Do We Need Simulations in Condensed Matter Physics? . . . 9
3.2 Statistical Mechanics . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.2.1 Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3.3 Periodic Boundary Conditions . . . . . . . . . . . . . . . . . . . . . 11
3.4 Time Stepping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.5 The Verlet Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.6 Implementation and Parallellization . . . . . . . . . . . . . . . . . 14
3.7 Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.7.1 Main steps of an MD algorithm . . . . . . . . . . . . . . . . 15
3.7.2 Force calculation . . . . . . . . . . . . . . . . . . . . . . . . 16
3.7.3 Preparation of the Data Structure . . . . . . . . . . . . . . 16
3.7.4 Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.8 Parallelization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

4 Pair Potential 19
4.1 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
4.2 The Pair Potentials Used in this Study . . . . . . . . . . . . . . . . 20
4.2.1 The Zetterling Potential . . . . . . . . . . . . . . . . . . . . 20

v
vi Contents

5 Energy Landscapes 23
5.0.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 23
5.1 The Method of Basin Hopping . . . . . . . . . . . . . . . . . . . . 25
5.1.1 Metropolis Monte Carlo . . . . . . . . . . . . . . . . . . . . 26
5.2 Analysis of Potential Energy Minima Clusters . . . . . . . . . . . . 27
5.2.1 Results for the Lennard-Jones Potential . . . . . . . . . . . 28
5.2.2 Results for the modied Dzugutov (m-Dz) Potential . . . . 28
5.2.3 Results for the Dzugutov Potential . . . . . . . . . . . . . . 28
5.2.4 Results for the Z1 and Z2 potential . . . . . . . . . . . . . . 29

6 Icosahedrally Ordered Solid Phases 33

6.1 Spatial Correlations . . . . . . . . . . . . . . . . . . . . . . . . . . 33
6.2 Diraction Patterns . . . . . . . . . . . . . . . . . . . . . . . . . . 34
6.3 Dynamical properties . . . . . . . . . . . . . . . . . . . . . . . . . . 34
6.4 Identication of Icosahedral Clusters . . . . . . . . . . . . . . . . . 35
6.5 Crystallization Patterns for the Zetterling-1 Potential . . . . . . . 36

References 39

Papers 42
I Formation of large-scale icosahedral clusters in a simple liquid
approaching glass transition 43

II The favoured cluster structures of model glass formers 59

III Non-ergodic dynamics in supercooled liquids 71

IV Decoupling of diusion from structural relaxation and spatial het-

erogeneity in a supercooled simple liquid 85

V -Brass Crystallization In a Simple Monatomic Liquid 99

Acknowledgments

I would like to thank a bunch of people for making this work possible. But I will
do it in swedish. Frst vill jag tacka min handledare, Mikhail Dzugutov, fr all
hjlp, alla samtal om allt man kan tnka sig och lite till, och fr att du r en
lysande vetenskapsman. Jag vill ocks tacka kollegor i branschen, framfrallt Sergei
Simdyankin fr hjlp och rumssllskap. Tack alla andra som har sttt mig nr
det har gtt dligt, hjlpt mig nr jag har behvt hjlp(Erik, tack fr hjlpen
med bilden som jag aldrig anvnde), spelat ipper med mig(Maria, Magnus, Mns,
Olle E), kt och badat med mig(Anna, Dennis, Olle B, Olof), sett till att jag
inte haft trkigt(Erik, Matti, Anders), lackat onmnbara frsiga metallsaker svarta
i Lill-Jans skogen med mig(Calle) eller lagat min rygg(Klas). Just det, delar av
min doktorandtjnst var sponsrad av NTM, ntverk inom tillmpad matematik,
tacktack.

vii
viii
Chapter 1

Introduction

The history of numerical simulations of atomic systems started fty years ago. The
rst atomistic computer simulation of a liquid was carried out in 1953[29] using a
method called Monte Carlo (MC). It is so called because it explicitly uses a random
number generator.
A dierent simulation method called Molecular Dynamics (MD) was rst im-
plemented in 1959[1][2]. In this method, the dynamical evolution of a system of
interacting particles is followed by solving Newtonian equations of motion. Since
then, both of these methods have been elaborated and widely used for simulation
of various kinds of systems.
The rst MD simulation was carried out with a system of hard spheres. In
this idealized model, particles interact only at the contact distance. Several years
later, Rahman[34] performed a successful MD simulation in which the equations
of motion were solved for a system of particles interacting via a continuous
nite-range Lennard-Jones pair-potential, see equation 3.9.

Intermetallic alloys have scientically interesting and technologically import-

ant structures and properties. Their special mechanical, thermal, and chemical
properties are practically very useful. Their complicated crystal and quasicrystal-
line structures are of fundamental scientic interest. Atomic interactions govern
the crystal structure and mechanical properties, and understanding the atomic in-
teractions in metallic compounds will deepen the general understanding of their
structures and properties.

1.1 Methods
Investigating the inter-atomic interactions in metals can be undertaken by
electronic-structure calculations but are very hard computationally. Quantum-
mechanically based computations are well suited to the problem but becomes very

1
2 Chapter 1. Introduction

vast and complicated quickly. A third approach is the use of a simple pair-potential
reproducing the interactions within the metals on a pair-wise level. This will reduce
the calculations enormously and it will be even better if using a monatomic system.
Monatomic simulations using a simple pair-potential has been very successfully his-
torically with the famous Lennard-Jones potential reproducing the properties of the
noble gases accurately. Later, many dierent potentials have been proposed and
used for a large number of dierent materials.

1.2 Icosahedral Ordering

Experiments show that a large number of metals show icosahedral local order in the
liquid state. There are theories concerning the structure and formation of metal
glasses, eg Landau theory, which reproduce metallic glasses good with local ico-
sahedral order. Recently there have been computer simulations performed which
crystallize into a icosahedral quasicrystal, and the icosahedral ordering was imposed
with a simple pair-potential interacting in a monatomic system. Further develop-
ment of that potential have been successful in enhancing the icosahedral ordering
for further studies of the subject.

1.3 Essential New Results

I have developed and introduced two new pair-potentials, the Zetterling-1 and
Zetterling-2 potentials, specically modeled to impose icosahedral order. The basis
for the development of the potentials was the old Dzugutov potential which is
known to crystallize into a dodecagonal quasicrystal. The Zetterling potentials
have a longer interaction range and a narrower rst minimum. The more narrow
rst minimum will enhance the local icosahedral ordering and the longer interaction
range was introduced to incorporate a second maximum in the potential mimicing
the Friedel oscillations found in metallic systems. These Friedel oscillations are
due to the singularity which arises at the Fermi surface due to the screening of the
positive charge by the electron gas. The period of these oscillations is a function of
the electron density of the material.

1.4 Presentation of papers

The studies have been divided into three parts. Paper one and two discuss the
dynamics and ergodicity aspects of icosahedrally ordered materials using the old
Dzugutov potential. Paper three and four concern the diusive aspects and spatial
heterogeneity in icosahedrally ordered phases, and paper ve and deal with spe-
cic material crystallizations found in the icosahedrally ordered metallic systems
imposed by the newly developed potentials.
1.4. Presentation of papers 3

1.4.1 Paper I
The paper presents formation of extended icosahedral congurations in a molecu-
lar dynamics simulation of the IC[13] liquid under super-cooling. Geometrical
frustration limit bulk growth of connected icosahedral congurations - for most
one-component systems icosahedral clusters contain very few particles. Due to the
shape of the IC potential, the inter-penetrating and face-sharing 13-atom icosa-
hedra in our simulations have been found to form clusters with signicant tendency
for low-dimensional growth, thus circumventing the constraints imposed by frus-
tration. It has been observed that the size of the largest icosahedral cluster grows
under cooling and eventually forms a percolating network. These results directly
demonstrate that the super-Arrhenius slowing down of the liquid dynamics under
super-cooling and the eventual glass transition are accompanied by an appreciable
structural transformation.

1.4.2 Paper II
The paper examines the favoured cluster structures for the two Zetterling poten-
tials discussed in chapter 5. Both potentials behave as monatomic glass-formers
in bulk. The oscillations in the potential are found to lead to global minima that
are non-compact arrangements of linked icosahedra. The structural properties of
the clusters correlate with the glass-forming propensities of the potentials. The
fragilities of the corresponding super-cooled liquids are also found to correlate.

1.4.3 Paper III

The paper considers the concept of dynamical ergodicity in the context of the
super-cooled liquid behaviour. A major problem involved in the statistical mech-
anical denition of ergodicity, stating that the ensemble and time averages of a
dynamical variable are equivalent, is that it refers to an ensemble of identical sys-
tems and innite observation time. In practice, however, we need to assess the
ergodicity of a single system within a nite time interval[24]. We discuss possible
ways to resolve this problem. Among them is a conjecture[15] that the ergodicity
of a dynamical system should be understood as a global chaotic connectivity of its
regions of motions in phase space. We present arguments, supported by evidence
from simulation, indicating that the discrepancy between the volume of a single
stochasticity region and the total volume of the region of motion can be assessed
by exploiting the universal relation between the diusion coecient and the en-
tropy. A central postulate in the model of liquid diusive dynamics in ergodic
domain presented in the paper is that the probability of transition from a current
energy-minimum conguration to an adjacent one is entirely determined by the
total number of these congurations. This postulate implicitly assumes that all
adjacent congurations are accessible within a single time scale which characterizes
the local relaxation dynamics.
4 Chapter 1. Introduction

The existing theoretical model are only successful in describing the early, relat-
ively high-temperature stages of super-cooled dynamics. Further cooling results in
a fundamental transformation of the liquid state.

1.4.4 Paper IV
The paper reports a molecular dynamics simulation of a simple monatomic glass-
forming liquid. The transition to deeper minima in the energy landscape under
super-cooling are shown to result in the formation of icosahedrally structured do-
mains with distinctly slow diusion. The domains grow with cooling in a low-
dimensional manner and percolate around Tc , the critical temperature of the mode-
coupling theory. Simultaneously, a sharp slowing down of the structural relaxation
relative to diusion is observed. It is concluded that this eect cannot be accounted
for by the spatial variation in atomic mobility. the low-dimensional clustering is
discussed as a possible mechanism of fragility.

1.4.5 Paper V
The paper present a molecular dynamics simulation investigating the crystallization
of a simple monatomic liquid model which utilizes an inter-atomic interaction poten-
tial. The shape of the potential imitates eective inter-ionic interaction in metallic
systems. The potential is constructed to favour icosahedral arrangement in the
rst coordination shell. We observe that, having been cooled from the equilibrium
liquid state to below its apparent freezing point, the system forms a thermodynam-
ically stable solid phase exhibiting cubic symmetry. Its diraction pattern can be
identied as that of -brass phase[5], a tetrahedrally packed crystalline structure
with 52 atoms in the unit cell. We conclude that the monatomic version of -brass
structure generated in this simulation can be regarded as a new archetype for the
-brass structures observed in many inter-metallic compounds.
Chapter 2

Tetrahedrally Close-Packed Phases

in Intermetallic Systems

Analysis of liquid metals, metallic clusters and metallic glasses will show the local
order to be predominately tetrahedral[39][16][7].

Tetrahedral packing is the densest known packing of spheres in Euclidian space

and it is the most favorable in minimizing the Gibbs free energy
G = U TS + PV (2.1)
where G is the Gibbs free energy, U is the energy of the system, T is the temper-
ature, S is the entropy, P is the pressure and V is the volume of the system.
Five tetrahedra will t almost perfectly around a common edge to form a
pentagonal bipyramid and 20 tetrahedra can be put together sharing a common
central vertex, with slight distortions, to form a regular icosahedron. The icosahed-
ron has 6 vefold symmetry axes and cannot be periodically packed to ll space.
This inability to ll space is already clear in the geometry of the pentagonal bipyr-
amid and the icosahedron with the gaps in the outer atoms. This incompatibility
is known in condensed matter physics as frustration.

tetrahedra

5-fold bipyramid

5
6 Chapter 2. Tetrahedrally Close-Packed Phases in Intermetallic Systems

icosahedron

There are three known ways of close-packing atoms in 3-D, FCC face centered
cubic, HCP hexagonally close packed, and icosahedrally packed. But only the
former two will pack periodically containing a mixture of tetrahedra and octahedra.

By combining particles of dierent sizes the frustration inherent in the tetra-

hedral packing can be relaxed and Frank-Kasper[17][18] phases composed entirely
of distorted icosahedra become stable.
Metallic glasses and under-cooled liquids can be seen as being composed of dis-
torted icosahedra. The discovery of quasicrystals[35][23], which have a macroscopic
icosahedral symmetry and are related to the Frank-Kasper phases help further in
the understanding of local icosahedral ordering.
It can be shown that the energy of an 13-atom icosahedral cluster relaxed
in a Lennard-Jones4.2 potential is 8.4% lower than that of the 13-atom clusters
corresponding to FCC and HCP packed crystals[21], the other two known ways of
close packing.

Molecular dynamics simulations of slowly cooled Lennard-Jones clusters

show a predomination for pentagonal and especially icosahedral symmetry in
clusters up to approximately 40 atoms. The transition to FCC structures does
not occur until the number of atoms exceed a couple of thousand[22][4]. Other
polytetrahedral structures have been found by more sophisticated methods, for
instance the General Valence Bond method[25][26][27], and are similar to the
nearest-neighbour environments found in the -brass structure containing several
pentagonal bipyramids.

The icosahedra can also be distorted by inserting more atoms surrounding the
central atom. This is useful if the tetrahedra are only slightly distorted as in some
complex alloys of atoms similar in size. This will allow the formation of bulk phases
with polytetrahedral order. Frank and Kasper[17][18] analyzed the structure of
such alloys and found 3 other coordination polyhedra beside the Z12 which closely
 7

resembles an icosahedron, called Z14, Z15 and Z16, with approximately equilateral
triangles as faces, see gure 2.1.

Figure 2.1. Frank-Kasper polyhedra. Courtesy S. Simdyankin

They all have 12 vertices with a coordination of 5, and two, three and four
vertices with a coordination of 6. The vertices with a coordination of 6 are never
adjacent.
Under cooling, these non-icosahedral defects can be linearly connected forming
four-fold and six-fold disclination lines. Under further cooling, the four-fold and
six-fold defects cancel each other, but there will always be remaining six-fold defects
in the form of disclination lines in the system left.
The disclination lines can further be connected forming a network throughout
the bulk of the system and thus connecting all of the coordination polyhedra besides
the Z12.
Under suciently slow cooling, the disclination lines can align and order them-
selves in space, forming a regular periodic pattern thus leading to the crystal form-
ation. Alternatively, if the cooling rate is suciently fast, the disclination lines
will not be able to form a globally ordered periodic pattern; instead, they can be
entangled in an aperiodic network, which leads to the formation of a glass.
Frank and Kasper dened a class of crystals with a skeleton of disclination lines
connecting the atoms with 6 common neighbours. The Z14, Z15 and Z16 are two-,
three- and fourfold nodes in this structure. The periodic crystalline structures
8 Chapter 2. Tetrahedrally Close-Packed Phases in Intermetallic Systems

which are formed in the described way constitute the family of Frank-Kasper
phases. Several such Frank-Kasper phases have been identied. See [32][33][36] for
further references.

The Zetterling-1 potential was shown in Paper V to crystallize into the -brass
structure containing several pentagonal bipyramids in the nearest-neighbour en-
vironment. Paper II discuss the similarities and the dierence between the two
Zetterling potentials in their icosahedral local order.
The identication of icosahedra and icosahedral clusters are further discussed
in Chapter 6.
Chapter 3

Computer Simulations

3.1 Why Do We Need Simulations in Condensed

Matter Physics?
Many problems which can be rigorously formulated are not exactly analytically solv-
able. Most of the problems in statistical mechanics belong to this class. Therefore,
computer simulations are needed for testing theories and models. The results from
a computer simulation may then be compared with experimental results. Computer
simulation is a bridge between theories and theoretical models on the one hand, and
real liquids and solids on the other. By comparing the experimental results and
the model results, theories and theoretical predictions can be either accepted or
rejected. Computer simulations also provide insight in both the microscopic and
macroscopic properties of interest, some of which may not even be accessible via real
experiments. It is for instance quite possible to simulate radiation-induced damage,
rapid super-cooling of liquids and to explore a system at extreme thermodynamical
conditions.
The main requirements on the numerical solution of the equations of motion in
an MD simulation of a dynamical system are that the phase-space volume and the
total energy of the system is conserved. Also the total momentum should be held
constant at zero.
The Verlet algorithm[3], used in this study, satises these requirements.

3.2 Statistical Mechanics

A system is usually dened by the number of particles N , the volume V , and the
temperature T . Other properties such as density , chemical potential , pressure
P and the heat capacity Cv etc may be derived therefrom. Even the diusion

9
10 Chapter 3. Computer Simulations

coecient D, shear viscosity and the structure factor S(k) may be derived al-
though they describe macroscopic properties. The structure factor describes the
Fourier components of the density uctuations in a liquid, k is the magnitude of
the wave-vector.
An isolated macroscopic system of N identical particles each of which has three
translational degrees of freedom is completely specied by 3N coordinates:
q = (q1 , q2 , . . . , qN ) (3.1)
and 3N momenta:
p = (p1 , p2 , . . . , pN ) (3.2)
of the particles. These values dene a phase-point in the 6N -dimensional phase-
space of the system. The motion of the phase-point in phase-space along its phase-
trajectory is determined by Hamiltons equations
HN
q i = ;i = 1...N (3.3)
pi
HN
p i = ;i = 1...N (3.4)
qi
Also 6N initial values of the coordinates and momenta are required for a simulation.

The phase-space of N spherical particles is spanned by the 6N coordinates and

momenta of the N particles which form the whole system. Hamiltons canonical
equations dene the dynamical evolution in phase-space of the system, a phase-
space trajectory.

3.2.1 Model
The Hamiltonian H of a system of N molecules can be written as a sum of kinetic
and potential energy functions of the set of coordinates qi and momenta pi of each
molecule. With equation 3.1, and equation 3.2, we have
H(q, p) = K(p) + V(q). (3.5)
The kinetic energy K is of the form
N



K= p2i /2mi (3.6)
i=1
where mi is the molecular mass and the index runs over the dierent momentum
coordinates.
The potential energy may be divided into terms depending on the coordinates
of individual atoms, pairs, triplets etc, accounting for pair, triplet etc interactions.







V= v1 (qi ) + v2 (qi , qj ) + v3 (qi , qj , qk ) + . . . (3.7)
i i j>i i j>i k>j>i

Usually, only an eective pair-potential is used for simple systems.

3.3. Periodic Boundary Conditions 11

The potential energy function of spherical particles then takes the form



ef f
V= v1 (qi ) + v2 (rij ). (3.8)
i i j>i

where rij is the distance between atom i and atom j. The rst term represents the
eect of the container walls and an external eld. The second term represents the
eects of the interactions between every pair of molecules in the system. All higher
terms such as three-body contributions are neglected.
The rst MD simulation was carried out with a system of hard spheres. In
this idealized model, particles interact only at the contact distance. Several years
later, Rahman[34] performed a successful MD simulation in which the equations of
motion were solved for a system of particles interacting via a continuous nite-range
Lennard-Jones pair-potential, equation 3.9.
In order to solve the equations of motion for a system with continuously changing
interaction potential, a step-wise algorithm had to be employed. After these early
studies, the eld of computer simulation of liquids and solids has grown rapidly.
The eective pair potential is usually the Lennard-Jones[46] 12-6 potential, g-
ure 4.2, of the form
v LJ (r) = 4((/r)12 (/r)6 ). (3.9)
The parameters and  should be chosen appropriately. It has a negative well of
depth  and a steeply rising repulsive wall at distances less than . The parameter
 is usually expressed in units of temperature and divided with kB , where kB is
Boltzmanns constant. The Lennard-Jones potential is valid for e.g. liquid noble
gases.
Other highly idealized pair-potentials are sometimes used in testing the prop-
erties of a liquid. These are unrealistic but very simple in their form and to use in
computer simulations. The hard-spheres potential is of the form
 , r <
v HS (r) = . (3.10)
0, r
Other examples of pair-potentials can be seen in 5.3 and [3].
The simple pair-potential is usually used in simulations of noble gases, but can
also be used in simulations of liquid metals. Liquid metals are two component
systems but can within the Born-Oppenheimer approximation be treated as a one
component system of ions, where the movements of the electrons and ions are
separated in time-scale. The average distribution of electrons is included in the
eective inter-ionic pair-potential.

3.3 Periodic Boundary Conditions

When simulating a liquid the number of particles is usually chosen between 10 and
100.000. For such small specimens a large number of the particles lie on the surface.
12 Chapter 3. Computer Simulations

If, for instance a liquid drop is subject to simulation, that is not a problem since the
suface tension will keep the liquid together, otherwise one has to implement some
kind of container wall to hold the atoms together. This is not always satisfactory
since it will inuence a major part of the particles, therefore periodic boundary
conditions are usually introduced.
Periodic boundary conditions mean that when an atom leaves the central cube
subject to simulation, its periodic image enters at the opposite face of the cube.
That is, the cube is repeated in all directions so that no boundary conditions apply.
In gure 3.1 the atom 1 leaves the central box and enters box B, at the same time
its copy from box F enters at the bottom of the box.

A B C

1
2

H D

G F E

Figure 3.1. A two-dimensional periodic system. Atoms can enter and leave each
box across each of the four edges.

Of course, only one set of atoms is needed during the simulation. The particles
should not be able to sense the symmetry of the cube, and therefore the potential
has to be cut o at a certain distance, and the cube must be at least 2rcutof f wide,
gure 3.2.
The introduction of a cut o potential leads to the introduction of neighbour
lists of the atoms. A neighbour list is a list containing the neighbours of each atom
of the system within the cuto distance, it is continuously updated. Since every
atom only interacts with the atoms within a certain distance, the calculation of the
force acting on the atom is reduced. Otherwise, every atom must be checked with
every other atom in every timestep of the simulation.

3.4 Time Stepping

The standard solution to the dierential equations is the nite dierence approach.
Given the particle position r(t), velocity v(t) and other dynamic properties at a
time t, one tries to calculate the same dynamic properties at the time t + t. The
3.5. The Verlet Algorithm 13

A B C

1
2

H 3 D

G F E

Figure 3.2. The cut-o distance in a two-dimensional periodic system represented

as a dotted circle around atom one.

acceleration a(t) for each particle will be the vector sum of the force acting on each
particle imposed by the pair-potential used in the simulation. The equations are
solved in a step-by-step basis and the time t is chosen appropriate to the system.
It is usually much smaller than the time it takes for a particle or molecule to travel
its own length.

3.5 The Verlet Algorithm

The Verlet algorithm[3] is one of the most widely used examples of a nite dierence
method. It uses the positions and accelerations, and the positions in the previous
step of the calculation. The equation for advancing the positions is:

r(t + t) = 2r(t) r(t t) + t2 a(t) + O(t4 ) (3.11)

By a Taylor expansion about r(t)

t2 a(t)
r(t + t) = r(t) + tv(t) + + ... (3.12)
2

t2 a(t)
r(t t) = r(t) tv(t) + ... (3.13)
2

and addition of the two equations 3.12 and 3.13 the equation for advancing the
positions is

r(t + t) = 2r(t) r(t t) + t2 a(t). (3.14)

14 Chapter 3. Computer Simulations

The velocities do not enter the equation at all, although they are useful in cal-
culating the kinetic energy. The velocities are obtained by subtraction of equation
3.12 with 3.13 to get

r(t + t) r(t t)
v(t) = + O(t2 ) (3.15)
2t
The Verlet algorithm advances all of the particle positions in one step instead
of two as in other algorithms which rst predict the positions and velocities of the
particles in one step, and then add a correction to the positions and the velocities
in another following step.

The Verlet algorithm is also symplectic. This means that the algorithm correctly
holds the phase-space volume constant during the simulation. This implies time
reversibility. It is also possible to prove that an algorithm with the property of
phase-space conservation can be rewritten as an exact solution for a Hamiltonian
H which diers from the Hamiltonian of the simulated system H by terms of
order of the time-step .
Predictor-corrector schemes are non-symplectic. This can lead to unphysical
results[30] and care has to be taken when using such algorithms.
A modication to the Verlet algorithm with better round-o properties is the
half-step leap-frog scheme. The algorithm is
1
r(t + t) = r(t) + tv(t + t) (3.16)
2
1 1
v(t + t) = v(t t) + ta(t). (3.17)
2 2
The equation 3.17 is evaluated rst to get the mid velocities and then the new
positions are calculated via equation 3.16. The current velocities may be evaluated
between the two steps by
1 1 1
v(t) = (v(t + t) + v(t t)). (3.18)
2 2 2
This is necessary in order to calculate the total energy (H = K + V) of the system
in each step of the simulation. It is nescessary to monitor the total energy during
the simulation since a deviation from an expected constant value may be a sign of
the timestep being to long.

3.6 Implementation and Parallellization

Molecular dynamics is limited as method because of the nite size of the simulated
system and the nite time-length of the simulation. Even the largest ever simulated
systems, of the order of 109 particles, are minute compared to real systems. A
3.7. Implementation 15

simulation carried out for several millions of timesteps is still only of the order of
nanoseconds in real time. This is in practice not really a problem since we only
need to consider systems with a size suciently large compared to the correlation
length observed for a time suciently large compared to the correlation time .
These can be estimated from space- and time-correlation functions [24, 20].
The nite-dierence integration method used in the simulation is not critical in
speeding up the calculations. The time-consuming part of molecular dynamics is
the calculation of the force acting on every particle for each step. Using a pair-
potential, the force can be calculated as:
N 


dv(rij ) rij
Fi = (3.19)
drij rij
j
=i

where ri is the position vector of particle i and v(r) is the pair potential. The
identication of all of the interacting pairs of particles is of major importance in
the design of an ecient algorithm.
The size of the time-step used should be as large as possible enabling the sim-
ulation to cover the desired observation time in as few as possible time-steps. The
Verlet algorithm is of second order and the error will of course be larger for a large
time-step which may interfere with energy conservation of the system. This is true
for all simulations and you need to chose a time-step giving an acceptable accuracy
running as fast as possible.

3.7 Implementation
Considering only simple monatomic systems interacting via a pair-potential min-
imizes the load of the computer in the simulation and maximizes the observation
time. This is often necessary to study the extreme conditions in condensed phases
at very low temperatures and studying phase transitions. This also simplies the
analysis of the output.

3.7.1 Main steps of an MD algorithm

The following steps make up a model molecular dynamics program:

Input. Read the initial velocities and coordinates from le.

Data structure initialization.

Time-stepping. For each value of t = n t, n = 1, 2, . . . , Nsteps

calculate the forces;

calculate new coordinates rj (t + t) and new velocities vj (t + t), j =
1, 2, . . . , N ;
16 Chapter 3. Computer Simulations

apply boundary conditions;

(optionally) calculate the dynamical variables;

Output. Write the resulting conguration to le.

3.7.2 Force calculation

For a straight-forward force calculation for all particles interacting via a pair-
potential the number of oating point operations(ops) will scale as N 2 . If the
potential has a cut-o distance much smaller than the dimensions of the simulation
box, most of the calculations will be unnecessary. It is then possible to reduce the
time to scale as Nn N , where Nn is the number of particles within a sphere of
the interacting radius of the potential.
By dividing the box into sub-cells and constructing a neighbor-list with the
particles sorted this can be achieved[3]. Any particle can only interact with the
particles within its own cell and the surrounding cells.

3.7.3 Preparation of the Data Structure

The above approach can be extended by sorting the coordinates of the interacting
particles in auxiliary arrays next to each other. This will minimize the memory
paging in common pipe-line computers. Data locality improves the cache coherency
[8] and reduces the execution time. See gure 3.3,
The box shape is usually chosen as a rectangular parallelepiped although any-
thing on which periodic boundary conditions can be applied will do, for instance a
hexagonal cylinder.
The simulation box is divided into Nc = Nx Ny Nz identical small cells.
Every cell will hold an average of less than one particle, this improves the sorting
of all the particle cells.
A vertical array of cells with dimensions 1 1 Nz will be referred to as a
column. A vertical array of cells with dimensions 1 Ny Nz or Nx 1 Nz will
be referred to as a slab.
A horizontal array of cells with dimensions Nx Ny 1 will be referred to as a
layer.
Only half of the surrounding cells are included in the computation so that every
interaction is counted only once [3].
The periodic boundary conditions are implemented by surrounding the simula-
tion box with images of the central box.
An index array is used to keep track of the columns of the simulation box and
their corresponding images. This is a map between the simulation box and the
extended box used in the simulation. At each time-step the map is used in lling
the data-structure arrays with the coordinates of the particles after all interactions.
The index arrays will have twice as many elements than the average number of
particles per column, these elements are referred to as particle sites.
3.7. Implementation 17

y
x

Figure 3.3. Data structure, the shaded cells belong to the simulation box. The
curved arrows indicate the translations of the periodic images which are represented
by transparent cells. Figure courtesy of S. Simdyankin.

The particle sites are lled by using the map between the simulation box and
the extended box.

3.7.4 Usage
For the force calculation it now suces to loop over the columns from the simulation
box. The contributing forces from all pairs of particles from the same column and
from the neighboring columns are accumulated.
The particle sites will introduce a very high locality in the data so that particles
that are close in space will be close to each other in memory.

The potential and its derivative, the force, is usually precalculated using a table
in which they are tabulated for specic distances between particles to save time in
the computation. For intermediate separations of particles interpolation is used.
18 Chapter 3. Computer Simulations

3.8 Parallelization
The described algorithm and data-structure can very easily be parallelized by the
use of a divide-and-conquer strategy. The approach is very similar whether it is a
shared-memory or a distributed memory computer. The cells are divided equally
among the processors and to prevent accidental overlap which may lead to incorrect
results, there is a need for synchronization at a barrier. Parallelization will only give
a speed-up if the system simulated is large enough. For shared-memory computers
the speed-up can be somewhat hindered by heavy memory-bus trac.
Chapter 4

Pair Potential

4.1 History

It is not possible at present to perfectly calculate the behaviour of metallic alloys

according to the present models, although it is easily described mathematically,
because of the very large number of interacting particles to take into account,
including the nuclei of the atoms and all of the valence electrons. An approximation
is needed, and one commonly used is to reduce the problem of interaction between
all atoms in the system in only taking in pair interactions between nuclei using a
simple spherically symmetric pair potential which includes the behaviour of the
electron cloud surrounding the nuclei. One pair potential is needed for each pair
of dierent type of species of atoms, and the calculations can be further simplied
by using a simple monatomic system.

Historically, the eective pair inter-ionic potentials(pair potentials) used have

been of the simple Lennard-Jones[46] type, with a short range repulsive core, and
a long range attractive tail.
Investigating the inter-atomic interactions in inter-metallic compounds is a con-
siderable theoretical challenge. Ab initio electronic-structure methods applied to
low-symmetry inter-metallic structures[45], can become computationally very de-
manding, due to large unit cells with many unequivalent atomic sites and the like-
lihood of structural and chemical disorder. Quantum-mechanically -based inter-
atomic potentials[31], on the other hand, are well suited to complex or disordered
structures. At the same time, the multiplicity of chemical species requires the cal-
culation of numerous interacting potentials, which may be composition dependent.
The potential(s) introduced in the next section is based on the rst principle
calculations of the generalized pseudo-potential for metallic alloys. See [44].

19
20 Chapter 4. Pair Potential

1.2
u/

1.2
1 3
r/

Figure 4.1. A generic metallic pair potential, featuring Friedel oscillations, courtesy
of Sergei Simdyankin.

4.2 The Pair Potentials Used in this Study

The spherically symmetric pair potentials developed for the present studies are
based on an earlier potential developed by Dzugutov[13], imposing local icosahedral
order. The ordering is implicitly imposed by prohibiting the formation of octahedra
in thesystem by the placement of the rst maximum in the potential at approxim-
ately 2 times the equilibrium pair-distance. This is the distance between opposite
vertices in octahedra, see g4.2.
This forces the order to be polytetrahedral, and icosahedral, since the
intrinsic close-packing of spheres, face-centered cubic(FCC) and hexagonally
close-packed(HCP) consist of tetrahedra and octahedra as opposed to the pure
tetrahedral packing in an icosahedrally ordered structure.

4.2.1 The Zetterling Potential

The new potential based on the success of the Dzugutov potential that I have intro-
duced have two variants, varying in the amplitude of the maxima in the potential
4.2. The Pair Potentials Used in this Study 21

1.5

0.5
U

0.5

1
0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 2.6
r

Figure 4.2. Comparison of the Lennard-Jones(solid line), Dzugutov(dash-dotted),

and Zetterling-1(dotted) potentials.

and a slightly dierent cuto distance. The functional form of this potential is
expressed by 4.1:
A exp(r) cos(2KF r) P
V (r) = + B (r) + V0 (4.1)
r3
It utilizes a repulsive core followed by the periodic decaying tail imitating the
Friedel oscillations. The parameter V0 is chosen so that the potential and its deriv-
ative, the force, vanish at rcut , the cuto distance, which is chosen to be the point
at the third minimum of the potential.
The potential consists of a short-range repulsive core and a longer-range oscil-
latory part. The latter is assumed to represent the Friedel oscillations which are
characteristic of the eective inter-ionic potentials in simple metals. The period of
these oscillations is determined by the Fermi wave-vector KF which is the function
of the density of valent electrons n.

n = KF 3 /3 2 (4.2)
22 Chapter 4. Pair Potential

It is thus possible to calculate the theoretical valency of the model metal from
the KF used in the simulation. For the current potentials it is between two and
three, consistent with the materials it is supposed to crystallize into.
Using a proper choice of parameters the potential was constructed to encour-
age icosahedral arrangement in the rst coordination shell, consisting of all of the
nearest-neighbour atoms. The values of parameters dening the Zetterling-1 pair-
potential are presented in Table 4.2.1, and the Zetterling-2 potential is tabulated
in Table 4.2.1.

A B KF P
1.58 0.95533 4.12 -0.22 -18

Table 4.1. The values of parameters used in the present study for dening the
Zetterling-1 pair potential described by Eq. 1.

A B KF P
1.04 0.94656 4.139 0.33 -14.5

Table 4.2. The values of parameters used in the present study for dening the
Zetterling-2 pair potential described by Eq. 1.

The Zetterling-1 potential is known to promote crystallization into the -

brass structure, see Paper V, and the -manganese structure(unpublished). The
Zetterling-2 potential will promote crystallization into the esoteric A2 B13 structure,
these results are also still unpublished.
The crystallization structure of the Zetterling-1 potential is density dependent
and the formation into the dierent, but related, structure can possibly be attrib-
uted to the double well in the potential, forcing more atoms into the second minima
for higher densities.
Chapter 5

Energy Landscapes

5.0.2 Introduction

For a system containing N atoms, the potential energy is a function of the 3N

coordinates. The multidimensional surface spanned by the potential energy and
the coordinates is thus 3N -dimensional, the potential energy hyper-surface.
This surface determines the structure, dynamics and thermodynamics of the
system. The local minima on the surface corresponds to the stable congurations
with zero gradient in the potential energy and where no forces are acting on the
particles. The thermodynamics of the system is given by ensemble averages on the
potential energy hyper-surface, and the dynamics of the particles is determined by
the forces, the gradients of the surface. This applies to all systems, regardless of
the potential energy function.

At a minimum a small displacement in any direction will increase the potential

energy of the system. The potential energy surface usually has a large number of
local minima. The lowest is the global potential energy minimum of the system.
Dierent systems may have very varying energy landscapes, a reason why natural
proteins and crystals tend to nd one specic structure out of many possible ones,
which glasses with a much more complex potential energy surface will fail to do.
For an overview, see [42][10]

The topography of the potential energy hyper-surface, the potential energy land-
scape, see g 5.1, provides useful information about materials. This schematic
picture makes clear why it is sometimes referred to as an energy landscape.
The set of points following a steepest descent potential energy minimization
that would end up in a specic minimum are referred to as a basin of attrac-
tion for the minimum. These basins are connected by the saddle-points of the
hyper-surface. The more complex the potential is, the more complex is the energy
landscape, with more saddle points and a more complex connectivity.

23
24 Chapter 5. Energy Landscapes

Figure 5.1. Schematic diagram illustrating the energy landscape, open circles are
maxima, lled circles are minima, crosses are saddle points. The solid curves are
equipotential curves. Dierent basins are indicated by dashed curves. Picture from
[37].

Protein folding, the complex physics of glasses, and the structure and dynamics
of molecular and atomic clusters used to be studied separately. Energy landscape
theory unies the experimentalists and theorists in the apparently dierent dis-
ciplines as a way to describe the structural formations and the dynamics in these
diverse systems.
These three systems, proteins, glasses and clusters, can all be seen as having a
energy landscape with a low-dimensional free energy surface.

In order to study the behaviour of varying materials and the correlation between
the potential, or pseudo-potential, and the structure in computer simulated systems,
a method called the basin-hopping [43] global optimization algorithm has been
developed. It explores the energy landscape of a potential in a system, revealing
clues to the clustering tendencies and the underlying structure.
The method can generate clusters of increasing sizes for a given potential.
These can be directly compared to clusters in a molecular dynamics simulation.
The local order of the clusters should be very well comparable to the smaller
clusters of the liquid and the larger cluster sizes should resemble the network of
clusters found in the super-cooled liquid of the molecular dynamics simulation.
5.1. The Method of Basin Hopping 25

The idea of the potential energy surface as a key to determining the prop-
erties of glasses was recognized by Goldstein [19]. There was much progress
in the 1980s in calculating the thermodynamical properties directly from the
knowledge of local minima. An approach that has been extended to dynam-
ical properties and used on a large variety of atomic and molecular clusters.
Also, global features of the energy landscape can explain dierent properties of
a variety of glasses. It has recently been suggested [47] that glassy liquids are
composed of large numbers of dierent clusters, each with its own energy landscape.

Following Goldstein, Stillinger and Frank [37] introduced the inherent structure
for liquids, a multidimensional potential-energy minima that can be reached by
steepest-descent minimization of the liquid structure. The inherent structure gives
insight to the complexity of the liquid-solid transition and the solid structure of
the system, and stays remarkably constant at varying temperatures in the liquid
domain, undergoing a distinct change as the system crystallizes and leaving the
area sampled at the liquid state for a minimum at a lower potential energy.
The theory of the inherent structure is a help in the understanding of the
thermodynamics and dynamics by the energy landscape for any system of particles.

5.1 The Method of Basin Hopping

The potential energy surface of even a simple system will contain a very large
number of local minima, of the order of eN . The thermodynamical properties
of the system will depend on the relative potential energies of these minima
and the conguration space volume associated with them. The dynamical
properties are dependent on the connectivity of the minima. To understand
the variations in behaviour in dierent systems, some easily crystallizing while
other glass-forming, a full view of the potential energy landscape is needed. The
pathways between the basins of the energy landscape will determine the con-
nectivity in the system which is important in the studies of the relaxation dynamics.

Previous work [6] on energy landscapes has identied features enabling the sys-
tem to nd its global minimum eciently. The analysis of model energy landscapes
has been particularly helpful with the use of a master equation approach for the
dynamics, providing evidence of a large potential energy gradient and the lowest
possible transition state energies or rearrangement barriers for such a surface. A
simple way of transforming the potential energy surface which does not change the
global minimum nor the relative energies of the local minima was introduced by
Wales and Doye [43].
To every point X they assign the transformed energy E dened by

E(X) = min{E(X)} (5.1)
26 Chapter 5. Energy Landscapes

where X represents the 3N -dimensional vector of nuclear coordinates and min

signies that a steepest descent energy minimization is performed starting from X.
The potential energy surface is then mapped to inter-penetrating staircases
with plateaus, see gure 5.2, these corresponding to the congurations leading to
a given minimum after optimization. These basins of attractions have been used
in previous work [40] [41] in comparing the eciency of dierent transition state
searching techniques.

Figure 5.2. Schematic diagram illustrating the energy transformation, The solid
line is the energy of the original surface, the dashed line is the transformed energy.

5.1.1 Metropolis Monte Carlo

The method of Monte Carlo was developed during the second world war [28] in
the making of the rst nuclear bomb for simulating the behaviour of a plasma.
The calculations involve explicit use of random numbers(hence the name).

The Metropolis Monte Carlo method aims to generate a phase-space trajectory

by statistical sampling of an ensemble for a system, in our case a system of particles.
The sampling is performed in a manner to generate a canonical ensemble. This will
generate statistics for static properties of the system, otherwise only available by
Molecular Dynamics. In the Monte Carlo method, a large number of congurations
for a system of atoms is generated by random displacements of the particles.
Congurations are chosen from the generated set of congurations by statistical
sampling, and the equilibrium properties are determined by averaging over the
chosen set. The dynamics is not simulated for the system and time-dependent
properties can not be measured by the Monte Carlo method.

In the basin hopping algorithm, a canonical Metropolis Monte Carlo simulation

is used to explore the energy landscape for the function E(X) at a constant tem-
perature. The coordinates are displaced randomly at each step and a variant of the
conjugate gradient algorithm is used in the minimization.
5.2. Analysis of Potential Energy Minima Clusters 27

The convergence criterion for the conjugate gradient method used in the Monte
Carlo simulation does not need to be very tight for the method to function properly
[43].

5.2 Analysis of Potential Energy Minima Clusters

Basin hopping can be used for nding the vacuum potential energy minima clusters.
They can be compared to real clusters available from molecular dynamics simula-
tions of a system with the potential.
This method has successfully been applied to such diverse material models as
C60 , quasicrystalls, metallic glass formers and protein folding[9].

Using the basin-hopping algorithm, a xed number of atoms interacting via the
chosen potential are placed in a container. The combination of the Monte Carlo
simulation and the minimization at each step will eventually produce the potential
energy minimum cluster for that number of atoms. The algorithm is applied to an
increasing number of atoms in the system to study the behaviour and structural
growth of clusters at increasing sizes. The method is not guaranteed to produce
the global minimum cluster for every chosen size, but the main interest is in the
growth pattern and the local structure of the atoms in the cluster produced.

Pair Potential
2
Zetterling1 Potential
Dzugutov Potential
1.5 Zetterling2 Potential
Modified Dzugutov Potential
1

0.5
U

0.5

1
1 1.5 2 2.5
r

Figure 5.3. Dierent pair-potentials used for the basin-hopping algorithm.

Some of the potentials to which the basin-hopping algorithm has been success-
fully applied are displayed in gure 5.3. These are further discussed in the following
sections.
28 Chapter 5. Energy Landscapes

5.2.1 Results for the Lennard-Jones Potential

The Lennard-Jones potential was developed for simulating the noble gases. It is
quite easy to apply the basin-hopping algorithm to the Lennard-Jones potential [43]
and calculate global minimum clusters. This has been done in previous work [38]
using other methods. Not only did the basin hopping algorithm replicate earlier
results, it also superseded it by nding lower energy minima for some of the cluster
sizes, see g 5.4.

Figure 5.4. Previously unreported global minima for the Lennard-Jones potential.
Figure from [43]

The Lennard-Jones potential is included here for comparison as showing a 3-

dimensional bulk growth of the clusters contrary to the Dzugutov potential and
the Zetterling potentials discussed below which prohibit bulk growth. All three
potentials show an decreasing tendency for bulk growth with more and more strain
involved in the forming of the clusters.

5.2.2 Results for the modified Dzugutov (m-Dz) Potential

By narrowing the rst minimum in the potential energy function, the bulk growth
of the system is hindered by reducing the number of nearest neighbours. This is
clearly visible for the Dzugutov[13][14] and the modied Dzugutov[12] potentials.
The modied Dzugutov potential was introduced to bridge the gap between the
original Dzugutov potential and the Lennard-Jones potential in having a wider rst
minimum than the original Dgugutov potential. This has the eect of increasing the
number of nearest neighbours and allowing growth of Frank-Kasper phases. These
structures are polytetrahedral phases consisting of icosahedra and Z14 clusters. See
gure 5.5.
The modied Dzugutov potential also show a remarkable feature in that a series
of the lowest energy minimal clusters have disclination networks similar to those of
hydrocarbons. See gure 5.5.

5.2.3 Results for the Dzugutov Potential

The tendency for low dimensional growth seen in the liquid and super-cooled
Dzugutov system [11] is clearly visible when looking at the lowest energy congur-
5.2. Analysis of Potential Energy Minima Clusters 29

17 57

26 76

55 129

78 166

Figure 5.5. Representative structures of the global minima for the modied
Dzugutov potential. On the right is the complete structure, in the middle the dis-
clination network and to the left the center of the cluster. Figure from [12]

ations for increasing sizes. One consequence of the maximum in the potential is the
favouring of polytetrahedral structures, and the expected structures are found for
the smallest sizes of the clusters. The 13-atom global minimum is the icosahedron
and the smaller sizes is the growth sequence for an icosahedron. The further growth
exhibit a linear character, as shown in gure 5.6.
At larger sizes the global minima become more two-dimensional because of the
strain associated with polytetrahedral growth. The conclusion is that Dzugutov
clusters tend to form non-compact polytetrahedral structures based on a local ico-
sahedral structure.

5.2.4 Results for the Z1 and Z2 potential

The basin hopping algorithm has been used to explore two variant of the Zetter-
ling(Z1, Z2) potential, see Paper II. The tendencies for low-dimensional growth is
even more amplied in these two systems.
30 Chapter 5. Energy Landscapes

13 19 23 25 29

31 33 35 37 38

42 46 52 58

60 66 67 86

Figure 5.6. Representative structures of the global minima for the Dzugutov po-
tential. Figure from [11]

For both potentials the structures exhibited are non-compact arrangements of

connected 13-atom icosahedra. There are three ways in which the icosahedra are
linked: (i) two icosahedra can inter-penetrate sharing a common vefold axis, as in
the 19-atom double icosahedron; (ii) two icosahedra can share a face as in the 23-
atom structure that is the global minimum for both potentials; (iii) two separated
icosahedra can be joined by a tetrahedron whose opposite edges are shared with
the two icosahedra, as in the 26-atom structure that is the Z2 global minimum. All
these ways of linking icosahedra are common in metallic alloys.
These three dierent modes of linkage leads to a large number of possible ico-
sahedral aggregates, especially at larger sizes. For example, the 55-atom Z1 global
minimum involves all three possibilities: there is one pair of inter-penetrating ico-
sahedra, one pair of face-sharing icosahedra and three pairs of icosahedra that are
bridged by tetrahedra, see gures 3 and 4 in Paper II.
Both potentials have global minima developing into chains of linked icosahedra
for smaller cluster sizes. At larger sizes, the Z1 potential will start to form
5.2. Analysis of Potential Energy Minima Clusters 31

ring-like structures of connected icosahedra, while the Z2 potential will form

one-dimensional chains of icosahedra even at the larger cluster sizes explored.
These two systems are even more frustrated than the Dzugutov system. It is
harder to keep the preferred polytetrahedral order in 3D-space. The Z2 potential
with the most narrow potential well have the most frustrated clusters.
32
Chapter 6

Icosahedrally Ordered Solid Phases

During the molecular dynamics simulation thermodynamical properties of the sys-

tem are computed to closely monitor the system looking for phase transitions and
other anomalies. Both spatial and dynamical properties are calculated and used
to predict the behaviour of the system and to determine whether the system is in
equilibrium or not. Phase transitions will be revealed by singularities in the po-
tential energy of the system, a crystallization will be noticed by sharp peaks in the
static structure factor.

6.1 Spatial Correlations

The normal way of getting the static structure factor for comparison with the ex-
perimentally available structure factor for real materials, is by Fourier transforming
the radial distribution function. This is dened by
 N

1 1


g(r) = (r + rj ri ) (6.1)
N
i
=j

This is usually computed as a statistical average of the distribution of atoms in

r-space. See Figure 6.1.
The static structure factor is then dened as

sin Qr
S(Q) = 1 + 4 r2 (g(r) 1) dr (6.2)
0 Qr

See gure 6.2

The discrete sine transform can be used in approximating the integral in the
denition of S(Q).

33
34 Chapter 6. Icosahedrally Ordered Solid Phases

Radial distribution function

7

4
g(r)

0
0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5
r

Figure 6.1. A sample radial distribution function.

6.2 Diraction Patterns

In order to analyze the pattern of the long-range order arising in the process of
the described liquid-solid transition we calculated the distribution of the diraction
intensity in the wave-vector space. This quantity, S(Q), was calculated as:
N 2


1  iQrk 
S(Q) = N  e  (6.3)
 
k=1

where vectors rk denote the particle positions. First we consider the spatial de-
composition of the main maximum of S(Q). For this purpose, S(Q) is calculated
on the sphere the radius of which corresponds to the position of the maximum, Qo .
In this way, the symmetry of the structure can be established. After detecting the
symmetry axis, the diraction pattern can be calculated for comparison with the
diraction patterns for known structures. See gure 6.3.

6.3 Dynamical properties

Throughout the simulation the mean square displacement of the particles are con-
tinuously monitored for evidence of phase transitions, crystallizations and for de-
termination of whether the system is in a equilibrium state. The diusion coecient
can be calculated from the mean square displacement by the Einstein relation. Due
to the extremely slow dynamics in super-cooled systems, an equilibration can take
6.4. Identification of Icosahedral Clusters 35

0
0 5 10 15 20 25 30

Figure 6.2. The static structure factor computed from the radial distribution
function in gure 6.1.

several millions of time-steps and the simulation will be stopped when it is determ-
ined by dynamical properties that the system is statistically in an equilibrium state.
This must be determined by investigating the course-grained potential energy and
pressure of the system which must be stable. The mean square displacement is
empirically known to be at a value of at least 1 for a normal liquid, before it is
in equilibrium, and for super-cooled liquids the mean square displacement must be
even higher before it can be considered to be in an equilibrium state. Any phase
transition will show itself as discontinuities in the potential energy and as a change
in the slope of the mean square displacement, and the system must be equilibrated
at the new phase.

6.4 Identication of Icosahedral Clusters

Both in the liquid and in the solid there will be local icosahedral ordering imposed
by the potentials used. In the liquid, the number of icosahedra is counted by identi-
fying twelve vefold bipyramids sharing a common central atom. This is of interest
as the number of icosahedra will increase as the system is cooled. The number of
icosahedra will stagnate at the onset of a percolating icosahedral cluster. Two icosa-
hedra are dened as being bound to each other if they share three or more atoms(a
face), in the computer program written by me for the purpose. The program iden-
ties and counts all separate icosahedral clusters in the system. These clustering
properties can be seen plotted in Paper I for the original Dzugutov potential.
36 Chapter 6. Icosahedrally Ordered Solid Phases

Figure 6.3. Isointensity plots of S(Q) in a plane perpendicular to the [100]-axis

and passing through the origin for the system in Figure 6.1 and Figure 6.2.

After identifying the clusters, the stability of the clusters can be monitored by
looking at the trajectories of the individual atoms in the cluster, and the diusion
rate can be computed for atoms within and outside clusters.

6.5 Crystallization Patterns for the Zetterling-1

Potential
Molecular dynamics simulations using the Zetterling-1 potential has revealed two
distinct crystallization patterns at two dierent number densities of the system.

At the higher density, having been cooled from the equilibrium liquid state to
below its apparent freezing point, the system forms a thermodynamically stable
solid phase exhibiting cubic symmetry. This was identied as that of the -brass
phase, a tetrahedrally packed crystalline structure with 52 atoms in its unit cell.
This is reported in Paper V.

At the lower reduced density = 0.84, the system forms another thermody-
namically stable solid phase with cubic symmetry after a stepwise cooling from the
liquid state. The system was thoroughly equilibrated at each step in the cooling
6.5. Crystallization Patterns for the Zetterling-1 Potential 37

procedure. A liquid-solid phase transition occured as the system was cooled below
the reduced temperature T = 0.50. This was observed as a discontinuous drop
in the systems potential energy. The onset of an anisotropic long-range order is
signaled by the appearance of the sets of sharp peaks in S(Q) gure 6.2.

The structure was identied by rst looking at the spatial decomposition of

the main maximum of S(Q). For this purpose, S(Q) was calculated on the sphere
the radius of which corresponds to the position of the maximum of S(Q). In this
way, the structure was established to have cubic symmetry. Having detected the
symmetry axes, we could calculate the diraction patterns in a plane perpendicular
to the [100]-axis as seen in gure 6.3. This has been identied as that of the -
manganese structure, with 20 atoms in the unit cell. The diraction pattern for a
perfect model -manganese structure is shown i gure 6.4 for comparison with the
diraction pattern in gure 6.3 from the simulation. The agreement of the two sets
of diraction patterns is apparent.

Figure 6.4. The diraction pattern for a perfect model -manganese structure.

The perfect -manganese structure was also relaxed at a nite temperature and
was stabilized by the potential used thus conrming that it is at least in a metastable
equilibrium. The nature of the apparent 8-fold symmetry of the diraction pattern
in 6.3 is revealed by a closer inspection of the structure. A case of twinning is
present and in gure 6.5 three separate domains are tiled and outlined, showing the
angle between domains to be 45 degrees and 90 degrees.
38 Chapter 6. Icosahedrally Ordered Solid Phases

Figure 6.5. A layer of the -manganese structure cut perpendicular to the axis
corresponding to the diraction pattern in gure 6.3, showing the twinning of the
crystal.

The tiling is performed by identifying rings of atoms with one or two atoms in
between the rings enclosed in a rhombus. The chosen layer is quite thin to ease the
guiding of the eye in the tiling process. This result is still to be further analyzed
and published.
The apparent dierence between the structures formed from the same pair po-
tential at dierent densities opens up for studies of possible liquid-liquid and solid-
solid phase transitions in the simulated metallic-like model system.
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Paper I

Formation of large-scale icosahedral

clusters in a simple liquid
approaching glass transition

F. H. M. Zetterling, M. Dzugutov, and S. I. Simdyankin, Formation of large-scale

icosahedral clusters in a simple liquid approaching glass transition J. Non-cryst.
Solids 293-295, 39(2001).
Paper II

The favoured cluster structures of

model glass formers

J. P. K. Doye, D. J. Wales, F. H. M. Zetterling and M. Dzugutov The favoured

cluster structures of model glass formers, J. Chem. Phys. 118, 2792-2799 (2003).
Paper III

Non-ergodic dynamics in
supercooled liquids

M. Dzugutov, S. I. Simdyankin, F. H. M. Zetterling, Non-ergodic dynamics in

supercooled liquids, a chapter in book Phase Transitions and Self-Organization
in Electronic and Molecular Networks edited by Phillips and Thorp (Kluwer Aca-
demic, 2001) pp. 111-122.
Paper IV

Decoupling of diusion from

structural relaxation and spatial
heterogeneity in a supercooled
simple liquid

M. Dzugutov, S. I. Simdyankin, and F. H. M. Zetterling, Decoupling of diusion

from structural relaxation and spatial heterogeneity in a supercooled simple liquid,
Phys. Rev. Lett. 89, (2002).
Paper V

-Brass Crystallization In a Simple

Monatomic Liquid

F. H. M. Zetterling, M. Dzugutov and S. Lidin -Brass Crystallization In a Simple

Monatomic Liquid, MRS Symposium Proc., 643 K9.5.1(2001).