GENERAL ASPECTS OF ATOMISTIC

COMPUTER MODELING
OBJECTIVES OF ATOMISTIC SIMULATIONS
(1) Determination of the equilibrium configuration of a system of interacting
particles and analysis of the structure and its relation to physical properties.
At finite temperatures this corresponds to the minimization of the free or Gibb's
free energy. If temperature effects are not included the potential energy is
minimized.
Methods: Molecular statics, Molecular dynamics, Monte Carlo.
(2) Study of the dynamical development of a system of interacting particles at finite
temperatures.
Methods: Molecular dynamics, Kinetic Monte Carlo.

INITIAL CONFIGURATION
The first step in any simulation is the geometrical construction of the block of
particles in the computer. This block usually represents a first approximation to the
structure of the system studied. Each particle is assigned three coordinates, i. e. a
position vector ri and, if there are more than one type of species (e.g. alloys), an
indicator of the species.

Examples
Complex crystal structure
Crystallographic construction of the unit cell of a complex structure with basis
atoms placed to estimated positions.

Manganese

DNA

Point defects in a crystal lattice

Crystallographically constructed block containing e.g. vacancies, interstitials,
impurities, etc.

Example: Tetragonal C11b crystal structure of MoSi2 with the vacancy on one of the majority
sites (Si in MoSi2)

Structure and properties of crystalline surfaces

Crystallographically constructed block terminated by the surface parallel to a
chosen crystal plane.

Structure and properties of interfaces and grain boundaries

Crystallographically constructed block containing a chosen interface and/or grain
boundary in the center. In the latter case the block is a bi-crystal and in the former
case the block may consist of two parts with different crystal structures and,
possibly, composition.

Example: Asymmetrical tilt boundary in an fcc crystal. Rotation axis is <110>

Structure and behavior of nanocrystals

Example: Computer-simulated sample of nanocrystalline Ni with a mean grain diameter of 10

nm. Each side of the box is 37 nm long, and the sample contains 4.6 million atoms. Gray atoms
sit in perfect crystalline positions; colored atoms are grain boundary atoms.

Structure and properties of dislocations

Crystallographically constructed block containing a chosen geometrically defined
dislocation line. The introduction is usually done by imposing linear elastic
displacement field, known from the continuum theory of dislocations for given
elastic properties of the material, which is evaluated at corresponding atomic
positions and the atoms displaced accordingly. The same approach is used in the
case of cracks

Edge dislocation

Screw dislocation

Structure and properties of liquids and glasses

Starting block of atoms is usually constructed by using a random number generator
to determine the position vectors and type of the particles for a chosen material.
This block needs to be large, often well over one million atoms, and commonly
periodic boundary conditions (see bellow) are employed.

BOUNDARY CONDITIONS
FINITE BLOCKS
The relaxed block of atoms always contains a finite number of particles this
corresponds to investigation of a finite cluster of particles, for example a nano-scale
structure such as quantum well.
If this cluster is isolated and possesses, therefore, free surface, the relaxation near the
surface may be very significant. Thus simulation of the free surface is in this case
carried out as a part of any study. This may be desirable if surface effects of small
clusters are investigated. On the other hand, it can be a serious drawback when bulk
properties are of interest. In this case very large blocks need to be used so that the
studied region of the bulk and surfaces are well separated. An alternative approach is
to consider blocks that are effectively infinite as described below.

EFFECTIVELY INFINITE OR SEMI-INFINITE BLOCKS

Periodic boundary conditions (PBC)
Simulations are always made for a finite number of particles and periodic boundary
conditions mimic an infinite system. The principle is the same as the Born-Von
Karman boundary conditions commonly used in studies of periodic systems.
The simulated block is represented by a 'repeat cell' which is then assumed to be
periodically repeated in space as shown schematically in the Fig. 1. Particles in the
simulated block generally interact with their images in other boxes and the
displacement of a given particle in the simulated block applies to all its images.
Importantly, if during the relaxation process a particle leaves the box on one
side, its image from a neighboring box re-enters on the opposite side.

Fig. 1. Periodically repeated simulated block that is denoted by bold lines

The chosen periodicity may reflect physical reality. An example is periodicity
imposed by the crystal structure. However, in many cases this is just a computational
trick to avoid free surfaces and mimic infinite systems. In this case the simulated box
must be large enough so that the PBC do not affect the physical behavior
investigated. This has to be tested by performing the calculations for various box
sizes.
This type of boundary conditions is often called the supercell method.

Usage of PBC
Employed practically always in ab initio quantum mechanical calculations based on
the density functional theory (DFT).
Usually used in studies of phonons, though frozen phonons do not require PBC.
Studies of liquids and glasses where the 'repeat cell' may contain 103 - 107 particles.
The size must be large enough so that the results are independent of the block size.
Often used in studies of point defects, interfaces and line defects but see semiperiodic boundary conditions below.

Boundary conditions not periodic in three dimensions

The block is divided into two regions as shown in Figure 2.
(i) Relaxed region containing the studied structure (e.g. a crystal defect).
(ii) Border region which may be treated in several different ways:
(a) No atoms are present in this region: The relaxed block is then finite with free
surfaces. However, in this case relaxation near the surface may be very
significant and calculation of the free surface is in fact carried out
simultaneously with the study of a defect in the interior.
(b) Atoms in this region are at fixed positions, for example, ideal lattice positions
(e. g. in the case of interfaces) or positions of atoms are determined by longrange elastic fields associated with the defect studied (e. g. dislocations, cracks).
(c) Positions of atoms in the border region may be adjusted during the relaxation
process but not using the atomistic relaxation algorithm.
For example,
continuum mechanics calculation are employed to assure the continuity of the
displacement fields in the relaxed and the border region. Such methods provide
a link between the atomic structure in the center of the block, where a defect is
positioned, and long-range displacements fields associated with the defect.

Usage
Generally employed when studying localized crystalline defects such as point defects,
impurities interfaces, surfaces, cavities, inclusions, dislocations.

BORDER REGION

RELAXED
REGION

STUDIED
STRUCTURE

Fig. 2. Non-periodic boundary conditions

Semi-periodic boundary conditions

Periodicity is imposed in one or two directions only. In the periodic directions the
repeat cell may be the primitive cell determined by the corresponding crystal
periodicity or a chosen multiple of the primitive cell.
Examples
Atomic structure of straight dislocations (see Fig. 3).
Periodicity is imposed in the direction of the dislocation line; this is usually the
corresponding periodicity of the underlying crystal structure in this direction.

ELASTIC FIELD OF THE

DISLOCATION

RELAXED
REGION

Fig. 3. The configuration employed

in studies of dislocations. Atoms in
the border region are displaced in
accordance with the displacement
field associated with the dislocation
studied, determined by anisotropic
linear elasticity. This field may be
modified during the relaxation to
assure the self-consistency of the
elastic field and the dislocation
configuration in the relaxed region.
The same approach may be used in
studies of cracks, cavities, inclusions
etc.

Atomic structure of interfaces and surfaces.

Periodicity is imposed in two directions parallel to the interface (surface). The repeat
cell may be the primitive cell of the corresponding crystal plane but it may also be
larger. This allows investigation of possible reconstructions of the interface (surface),
local interfacial defects such as vacancies, segregated impurities, dislocations that
entered the interface (extrinsic dislocations).
The relaxed block containing an interface is depicted schematically in Fig. 4. In the
border regions atoms are in the positions of the corresponding ideal lattices joined
along the interface. However, these regions may be rigidly displaced relative to each
other invoking a relative displacement of the adjoining crystallites. The energy is,
therefore, minimized with respect to:

8
(a)
(b)

Positions of individual atoms in the relaxed region.

Relative displacements of the two crystallites, both perpendicular and
parallel to the interface. This leads to expansion and/or contraction at the
interface and to relative rigid body displacements of the adjoining crystallites
parallel to the interface.

BORDER
REGION
RELAXED
REGION

INTERFACE

BORDER
REGION

Fig. 4. The configuration employed in studies of interfaces. Atoms in the border

region are in the positions of the ideal lattice of the upper and lower crystallite,
respectively. In the case of a grain boundary the upper and lower crystallites
represent the same material but are misoriented with respect to each other. In the case
of an interface between two different materials the upper and lower crystallites
represent the corresponding distinct materials joined at the interface.