Kinetic Monte Carlo (KMC)

Let us consider phenomena such as diffusion, nucleation of a new phase,

transformation to a different structure, a chemical reaction etc., which all involve a
process that is much longer than what can be captured by the molecular dynamics. At
the same time these processes are kinetic and time dependent.
A general aspect of all these processes is that they occur via transitions between
various states or configurations that occur with various frequencies. It is these
frequencies that determine the time development of the whole process but they are
not results of the KMC procedure but must be known in advance. This means that
before performing a KMC calculation the transitions involved in a kinetic process
have to be known and corresponding frequencies of these transitions have to be
determined independently of the KMC calculation. The frequencies can be, of
course, calculated on the fly but these calculations are independent of the KMC
process. In the following the KMC calculation is explained on the example of
diffusion.
Diffusion studied by KMC
We consider diffusion via jumps of vacancies in a crystal structure. For example, in
the tetragonal C11b structure shown below (MoSi2 crystallizes in this structure), a
vacancy is shown on one of the sites of majority atoms (Si in MoSi2). This vacancy
can move to a number of sites, as shown by the arrows, and each such jump appears
with a different frequency. There are N possible positions of the vacancy and if the
vacancy is at a position i it can jump into M different positions with frequencies
i1 , i2 , i3 ,........, iM . When it is in a different position j it can again jump into M
positions with frequencies j1, j2 , j3 , ........, jM etc. Thus the diffusion process is
characterized by the NxM matrix of frequencies {ik } , where N is the maximum
number of possible positions of vacancies and M the maximum number of possible
jumps that can take place starting from a position of the vacancy. Some of these
frequencies may be equal to zero since the number of available jumps need not be the
same for different positions of vacancies.
The probability that a jump i j occurs is then
ij
pij =
M

ik
k=1

(KM1)

Obviously pij < 1 and

pij = 1 .
j=1

The probabilities pij are commonly called rate

constants. In this definition of jump frequencies it is assumed that when the vacancy
moves from i j it completely 'lost the memory' of how it got into the state i so that
the probability pij is completely independent on the previous jumps that lead into the
position i.

Ideal C11b crystal structure

C11b crystal structure with the vacancy on one of the majority sites (Si in MoSi2).
Arrows show possible jumps to other vacancy positions.
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Kinetic Monte Carlo procedure

We start with a vacancy at a position marked i and select randomly a possible jump
into a position j. This jump is then made with the probability pij . To do this we
generate a random number such that 0 1 and make the jump i j if pij .
However, if pij < we do not make any jump and repeat the process starting again
by selecting randomly another possible jump. After a jump occurred we start with a
new vacancy position that is associated with new jump frequencies (new rate
constants) and the process is repeated. In this way the vacancy travels and attains
various positions but to determine the rate at which it moves we have to associate a
time with each step of this random walk.
i

If the vacancy is at a site i then the frequency tot with which it will leave the site i is
equal to the sum of the frequencies of all possible jumps away from the site i:
i
tot

= ik .

(KM2a)

k=1

Hence the time the vacancy stays at the site i is

1
.
ti =
itot

(KM2b)

In this way we have associated with every vacancy position i the time ti during
which the vacancy waits at this position. This time is usually dominated by one of
the frequencies that is much higher than all the other frequencies. During the Kinetic
Monte Carlo process we associate with every state i into which the vacancy got
during the process, the time ti during which the vacancy remains at the position i,
determined by (KM2b). The time associated with the process consisting of K steps of
the Kinetic Monte Carlo is then

t (K) =

k corresponding
to all states attained

tk

(KM3)

The diffusion coefficient of the vacancy, Dv , can now be determined using the
Einstein formula (MD53)
1
2
(KM4a)
Dv = lim ( )
r( ) r(0 )
6
expressed as

D v = lim ( K )

r(t (K) ) r(0) 2

6t (K)

(KM4b)

where r(t (K) ) is the position of the vacancy after K steps and r(0 ) the starting
position. Averaging has to be taken over a large number of Kinetic Monte Carlo
paths that start with different original positions of the vacancy.
We could also use the autocorrelation function of the velocity with which the vacancy
travels. During the K steps the velocity is
r(t (K) )
(K)
(KM5)
v =
t (K)
The velocity can be calculated for various times t (K) and autocorrelation evaluated.

In order to obtain the self-diffusion coefficient, Dself

v , the vacancy diffusion
coefficient, D v has to be multiplied by the concentration of vacancies that is equal to

c v = exp(E f / kB T) , where E f is the vacancy formation energy. Thus, the vacancy

diffusion coefficient is Dself
v = c v D v and it is found to depend exponentially on
temperature so that it can be written as Dself
, where E mig is
v = exp(E mig / k BT)
identified as the migration energy of vacancies.
Application of the Kinetic Monte Carlo to other phenomena
The Kinetic Monte Carlo procedure can be employed to investigate various
processes, such as diffusion of impurities, chemical reactions, growth of nuclei of
new phases, thermally activated glide of dislocations etc. The meaning of the
reaction path is different in each case and has to be chosen and interpreted in line
with the problem studied. Hence, the fundamental physics of the problem studied
must be understood before embarking on KMC calculations.

Essential precursor of the Kinetic Monte Carlo modeling

Frequencies ik of the transition i k between states i and k have to be known prior
to performing the KMC modeling.
These frequencies may be determined
theoretically or by computer modeling using molecular dynamics or molecular
statics. In the case of MD the transition process is modeled dynamically and the
corresponding frequency is extracted from the rate with which the process occurs in
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the MD study. Whether this is possible or not depends on whether the jump can
occur in the time covered by the MD calculation. If the frequency is too low so that
the time needed is longer than the time of the calculation the frequency cannot be
determined within the MD calculation.
An alternative is to determine the energy barriers for transitions using molecular
statics and these may be used to evaluate corresponding jump frequencies, for
example employing the transition (reaction) rate theory, which is described below.
The most common approach for determining the barriers is so called nudged elastic
band method. If external forces are involved than the work done by these forces
during the processes studied has to be evaluated and enthalpies rather than energies
enter evaluation of the transition frequencies.

Transition (reaction) rate theory

We investigate a process in the course of which the potential energy varies in the way
shown in the figure below. The initial and final states are metastable and correspond
to minima of the energy (or enthalpy, if external forces do work). However, at some
intermediate stage the energy (enthalpy) raises to a maximum that corresponds to the
so-called activated state. The axis called 'reaction coordinate' represents a path along
which the reaction occurs and during this process the system acquires temporarily an
amount of energy equal to the height of the barrier, E.
We ask now the following question: Assuming that we know the reaction path
and associated barrier of the height E, what is the frequency with which
transition from one equilibrium state to the other occurs.

Activated state

Energy

Final state
E

Ground state

Reaction Coordinate
5

This question can be answered to a good approximation in the framework of the

classical transition state theory (reaction rate theory) first presented fully in:
Glasstone, S., Laidler, K. J. and Eyring, H., The theory of rate processes, McGraw
Hill, 1941. In the following we summarize the main aspects of this theory.
Basic assumption of the reaction rate theory
1. The reaction is characterized by some initial and final configurations that are stable
states and the transition between them occurs along a reaction coordinate or a
reaction path.
2. There is an energy barrier between the initial and final states when moving along
the reaction path and the most favored path is that for which this barrier is the lowest.
The state associated with this maximum is called activated state.
3. When following the reaction path it is assumed that the system remains in the
activated state long enough so that this state can be considered as being in the
thermodynamic equilibrium during the time the system is in the activated state.
This means in this state the movement in any other direction but along the reaction
path corresponds to vibration. However, along the reaction path it has only a
translational degree of freedom. In contrast, the stable states have vibrational degrees
of freedom along both the reaction path and along any other direction. Whether this
assumption is valid or not depends on the mechanism considered and the final arbiter
is experiment that decides whether the conclusions based on the theory are correct.
Frequency of activations
The frequency of jumps over the activated state is
v
= act x probability, pact , to attain the activated state ,
act

(KM6)

where v act is the average velocity along the activated path in the activated state and

act is the distance traveled in the activated state along the reaction coordinate .
Assuming the Boltzmann distribution of states the probability of being in the
activated state, pact, is:
exp(E j / k BT)
pact =

j summation over
allconfigurations
inactivated state

i summation over
all configurations

exp(E i / k BT)

(KM7)

Since the activated state is considered to be in the thermodynamic equilibrium we can

define the partition function of the activated state

Zact =

j summation over
allconfigurations
in ativated state

exp(E j / k BT)

(KM8)

The ground state is, of course, in the thermodynamic equilibrium and its partition
function is

Zground =

exp(E i / k B T)

(KM9)

i summation over
all configurations

Thus the probability of being in the activated state is

pact =

Zact

(KM10a)

Zground

The general relation known from statistical physics is that the free energy
F = k B T ln Z , where Z is the partition function. Therefore, the probability of being
in the activated state is
exp(Fact / k B T)
pact =
= exp(F / k B T)
(KM10b)
exp(Fground / k B T)
where F = Fact Fground is the difference between the free energy of the system in
the activated and ground state, respectively1.
Let us consider now the simple one-dimensional case depicted in the figure. In the
ground state the free energy is
config

osc

Fground = Fground + Fground

(KM11)

config
where Fground
is the free energy associated with the configuration of the ground state
osc
and Fground
is the free energy associated with the oscillatory modes of the motion in

the ground state. Similarly, in the activated state the free energy is

If the process is helped by an externally supplied work than F is replaced by G, where G is the
Gibbs' free energy.

config

Fact = Fact
config

where Fact

trans

+ Fact

(KM12)

is the free energy associated with the configuration of the activated

trans

state and Fact is the free energy associated with the translation mode of the motion
in the activated state; for the one-dimensional case we assume here that there are no
vibrational modes in the activated state. Therefore
config

F = (Fact

config

trans

osc

Fground ) + (Fact Fground )

(KM13)

The first term in (KM13) is the difference between the free energies of the
configurations in the activated and ground state, respectively. It can be written as
config
config
Fact
Fground
= Econfig TSconfig

(KM14)

where Econfig is the difference in the internal energy between the activated and
ground states and Sconfig is the corresponding change in the configurational
entropy.
osc
In order to determine the term exp(Fground
/ k B T) , we employ the partition function

associated with oscillations along the reaction path, which is

+ +

Zosc
ground

exp p2 / 2m 2 / 2 / k T dp d

exp p2 / 2m / k T dp

(KM15)

exp 2 / 2 / k T d

where m is a 'mass' associated with the oscillator, p = mv the momentum and

+

the 'force constant' of the oscillator. Since

2
exp(x )dx = we get

osc

Zground = 2k B T

m
1
= k BT

(KM16)

1
is the frequency of oscillations of the harmonic oscillator. Using
2 m
the general relation F = k B T ln Z
k T
osc
(KM17)
exp(Fground / k B T) = B
0
where 0 =

trans
/ k B T) , we employ the partition
In order to determine another term, exp(Fact
function associated with the translation along the reaction path, which is

act +
trans
Zact

0
+

exp p2 / 2m / k T dp d

act

(KM18)

exp p2 / 2m / k T dp
d

B

0

where p = mv is the momentum for the translation along the reaction path. Since
no oscillations take place in the activated state, the energy associated with the
translation is only the kinetic energy. is in the range <0, act > of positions in the
+

activated state. Again since

2
exp(x )dx = we get

trans
Zact =

act 2mk B T

(KM19a)

and therefore
trans

exp(Fact

/ k B T) = act 2mk B T

(KM19b)

Following (KM13) and (KM14)

config
config
exp(F / k B T) == exp[(Fground
Fact
) / k B T]
trans
exp(Fact

osc
k B T) exp(Fground

/ k B T)

(KM20)

It follows from (KM17) and (KM19b) that

trans
osc
exp(Fact
/ k B T) exp(Fground
/ k B T) = 0 act

2m
k BT

and therefore

exp(F / k B T) == 0 act

2m
exp(Sconfig / k B ) exp[(Econfig ) / k B T] (KM21)
k BT

In order to determine the frequency of activations we still need to evaluate v act that
enters (KM6). Since only the kinetic energy is associated with the velocity and in the
activated state and the velocity may vary from 0 to
9

v exp(mv
v act =

/ 2k B T)dv
=

exp(mv / 2k B T)dv

kB T
2m

(KM22)

when using integration by parts to evaluate the integral in the numerator. The
frequency of activations is then according to (KM6), (KM10b), (KM21) and (KM22)

v act
act

exp(F / k B T) = 0 exp(Sconfig / k B ) exp[(Econfig ) / k B T] (KM23)

To evaluate Sconfig is difficult and it is commonly assumed that it is small so that

exp(Sconfig / k B ) 1 . Since Econfig is the same as E in the figure depicting the

activation process, the frequency of activations is usually taken as

= 0 exp[(E) / k B T]

(KM24)

The frequency 0 is called the attack frequency and has to be determined judiciously
according to the problem studied. Because of the exponential dependence on E
<< 0 ; the difference between these two frequencies is usually several orders of
magnitude.
Test that a process is well described by the transition state theory
Plot the logarithm of the quantity proportional to the frequency of activations as a
function of 1/T. This is so called Arrhenius plot and it has to be a linear function if
the transition state theory applies.

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