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ik
k=1
(KM1)
pij = 1 .
j=1
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.
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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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
(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 )
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expressed as
D v = lim ( K )
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.
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.
Activated state
Energy
Final state
E
Ground state
Reaction Coordinate
5
(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)
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
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
(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)
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
(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
Zosc
ground
exp p2 / 2m 2 / 2 / k T dp d
exp p2 / 2m / k T dp
(KM15)
exp 2 / 2 / k T d
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
+
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)
osc
k B T) exp(Fground
/ k B T)
(KM20)
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
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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
= 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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