PHYSICAL INTERPRETATION OF ATOMISTIC

SIMULATIONS
Interpretation of the results of an atomistic simulation depends on the physical
problem studied. However, methods of interpretation fall broadly into two
categories:
(i)
Analyses of the structures.
(ii) Evaluation of physical quantities of the system studied. In the case of MD and
MC the temperature and pressure dependence of such quantities is analyzed
using statistical mechanics.

ATOMIC STRUCTURE
Structures obtained as the result of calculations may be interpreted in many different
visual ways, most commonly by a display of atomic positions and/or local quantities
such as local atomic volume, stress, coordination etc.
A quantity which describes the average structural features of any system whether
crystalline or amorphous is the radial distribution function, also called pair correlation
function.

Radial distribution function (RDF)

Let n i (r) be the number of particles found at distances between r and r+r from a
particle i. We define the average number of particles found between r and r+r from
any particle of the system as
1 N
(G26a)
n(r) = ! n i (r) ,
N i=1
where N is the total number of particles in the system.

!r

r
i

The average number of particles per unit volume found between r and r+r from any
particle of the system is

n(r)
n(r)
in
three
dimensions
and
in two dimensions.
2!r"r
4!r 2 "r

The RDF, marked g(r), is then defined as

g(r) =

g(r) =

1 n(r)
in three dimensions
! 4"r 2 #r
1 n(r)
in two dimensions
! 2"r#r

(G26b.1)

(G26b.2)

where = N/V is the average density of the material, defined as the average number
of particles per unit volume (or surface in two dimensions). In this definition the
RDF is normalized such that when r ! " g(r) ! 1 since for large r,
n(r) ! 4"r 2 #r $ % for every particle in three dimensions; in two dimensions
n(r) ! 2"r#r $ % .
If we know the RDF we can, of course, calculate the average number of particles at a
distance interval R, R+R from any particle of the system. It is simply equal to n(R)
and thus in three dimensions it is 4!R 2 "R # g(r) # $ and in two dimensions
2!R"R # g(r) # $ .

Crystalline material

g(r)

1st neighbors 2nd neighbors 3rd neighbors

g(r)

Liquid

r
Examples of radial distribution functions

Practical evaluation of RDF

In practice the RDF is calculated by first counting the numbers of particles at various
distances between r and r+r from each particle in the block and then taking the
average over all the particles. In MD and MC calculations the RDF must be taken as
a time average or ensemble average, respectively.
If a physical quantity, A, depends only on the separation of the particles, then its
average value in the three dimensional system is

4! "
A =
A(r)g(r)r 2 dr ,
#
V 0

(G27)

Local atomic volume-Voronoi polyhedra

Volume associated with a given atom is never determined uniquely but it is often
defined as the volume of the corresponding Voronoi polyhedron associated with this
atom. It is constructed as follows:

4
(i)
(ii)
(iii)

Connect the given atom by straight lines with its neighbors.

Draw planes bisecting these connecting lines.
Construct the polyhedron formed by these planes.

This construction is not completely unique but depends on how the neighbors are
defined. Use of more distant neighbors may lead to many small areas on the
polyhedron. Thus a cut-off of these areas is always introduced.
Atomic level stresses
The stress in the studied block is given by equations (G15 a,b) which can be re-written
as
1
total
i
(G28)
! "#
= % $i! "#
V i
where ! i is the volume associated with the atom i so that V = " ! i , and
i

%E
1
1
i
! "#
= ++ ( "p rik# & m iv"i v#i .. = & ++ ( Fik" rik# + m iv"i v#i ..
$i + k %rik
$i + k
.
.
* k'i

* k'i

(G29)

is defined as the atomic level stress evaluated at the position of the atom i.
The atomic level hydrostatic pressure is then

'
*
'
*
#E p $
1 ) 3
1 ) 3
2,
$ $
2,
p =!
& & r ! m iv i , = 3" ) & & Fik rik + m iv i ,
3" i )) $ =1 k #rik$ ik
,
i ) $ =1 k
,
( k %i
+
( k %i
+
i

(G30)

i
The time averages of atomic level stresses, ! "#
, give the average stress evaluated at

the position of the atom i. The average hydrostatic pressure p relates to the local
volume. When it is large positive the local volume is smaller than average and the
region is locally compressed; if it is large negative then the local volume is larger than
average and the region is locally expanded.
In the case of pair potentials, taking U = 0, the atomic level stress is

! i"#

)
,
1 + d%(rik ) rik" rik#
" #.
=
( ' mi v i v i
'
..
$ i ++ k drik
rik
i
* k &i
-

(G31)

5
and the atomic level hydrostatic pressure is

' 3
*
$ 2
1
d#(r
)
(r
)
ik
ik
)&&
pi = !
! m i v 2i ,
)
,,
3" i ) $ =1 k drik
rik
( k %i
+

(G32a)

or
&

1 ( d#(rik ) +
pi = !
rik + .
3"i (( %
dr
k
ik
+
' k$i

(G32b)

In molecular statics calculations, when particles have no velocities, the terms containing
velocities are simply zero. However, in molecular dynamics calculations the terms with
velocities need to be included.