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analysis of MD results
A(t)
Time, t
The level of correlation plotted against time would start at some value
and then decay to a low value.
A(t)
Time, t
and multiply the values in new data set to the values of the original data set.
Now let us average over the whole time range and get a single number
G(tcorr). If the the two data sets are lined up, the peaks and troughs are
aligned and we will obtain a big value from this multiply-and-integrate
operation. As we increase tcorr the G(tcorr) declines to a constant value.
The operation of multiplying two curves together and integrating them over
the x-axis is called an overlap integral, since it gives a big value if the curves
both have high and low values in the same places.
0 25 50 75 100
T im e fs
Time,
0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000
Timefs
Time,
600
400
Velocity, m/s
200
-200
-400
-600
0 5000 10000
Time, fs
350
300
Intensity, arb. units
250
200
150
100
50
0
0 25 50 75 100
Frequency, cm-1
Lets define g(r), density density correlation function that gives us the
probability to find a particle in the volume element dr located at r if at r
= 0 there is another particle.
(ri r j ) = 1
N
r r r r r r r
C( r ) = ( ri ) ( ri + r ) i
where ( ri ) =
j
(ri + r r j ) = (r rij )
N N
r r r r r r r
and ( ri + r ) =
j j
Therefore
(r rij ) (r rij )
N N N
r r r r r r 1 r r
C( r ) = ( ri ) ( ri + r ) i = =
j i
N i j
r
(r rij )
N N
r C( r ) V r r
c( r ) =
0
=
N2
i j
(r rij ) = (r rij )
N N N N
r 1 r r V r r
c( r ) =
N0
i j N2
i j
For isotropic system g(r) can be averaged over angles and calculated
from MD data by calculating an average number of particles at distances
r r+r from any given particle: r
N (r) = c( r ) r angle
i j
g(r) can be calculated up to the distance rg that should not be longer than
the half of the size of the computational cell.
Although g(r) has the same double sum as in the force subroutine, the
range rg is commonly greater than the potential cutoff rc and g(r) is
usually calculated separately from forces.
g(r) for pure Ni in a liquid state at 1773 K (46 K above Tm). Experimental
data points are obtained by Fourier transform of the experimental structure
factor.
i j
G(r) = 4r0 ~
g (r) or H(r) = 4r 2 0 ~
g (r)
Reduced Pair Distribution Function
15 G(r) for FCC Au at 300 K
10
G(r) (Atoms/ )
2
-5
-10
0 4 8 12 16 20
Distance r ()
r2
N
n =
V
r1
g ( r ) 4 r 2 dr
Source
Sample
4 sin
Q =| k f ki |=
ki
kf S (Q) I (Q)
Detector
1
g (r ) = 1 + 2
2 r 0 0
Q[ S (Q) 1] sin(Qr )dQ
j =1 i =1
f
2
By dividing this equation by i we obtain the structure function
i =1
I (Q) 2 N N sin(Qrij )
S (Q) = N
=1+ N fi f j Qrij
f
i =1
i
2
f
i =1
i
2 j =1 i < j
The expression for the structure function can be now reduced to the
integration over r (equivalent to Fourier of g(r) ):
sin(Qr )
S (Q) = 1 + 4r 2 0 g (r ) dr
0
Qr
(3 1 1) 80.0
15 with W(r) 100.0
(2 0 0) 140.0
15
(2 2 0)
10 (3 3 1)
(4 2 0)
(4 2 2)
(2 2 2) 10 (3 3 1)
(4 2 0)
5
(4 0 0)
(2 2 2) (4 2 2)
5
0 (4 0 0)
0
-5
2 3 4 5 6 7 2 3 4 5 6 7
-1 -1
Q ( ) Q ( )
Competition between
heterogeneous and
homogeneous melting
Simulation:
Z. Lin and L. V. Zhigilei,
J. Phys.: Conf. Series 59,
11, 2007.
Shifts of diffraction
peaks reflect transient
uniaxial thermoelastic
deformations of the film
an opportunity for
experimentally
probing ultrafast
deformations.
1 (1 1 1)
uniaxial lattice (2 2 0)
deformation (3 1 1)
0.8
Normalized Peak Height
0.6 homogeneous
melting
0.2
0
0 2 4 6 8 10 12 14
Time (ps)
Evolution of diffraction
profiles can be related to
time-resolved pump-
probe experiments, with
connections made to the
microstructure of the
target.
For pairwise interaction, g(r) can be used to calculate the potential energy
per particle,
N N
1 r N 2
P.E. =
N U(| rij |) = 2
V
r U(r )g(r )dr
i =1 j>i 0
This calculation can be used to check the consistency of the calculation of
energy and g(r). Integration should be done from 0 to rc.
Integrating from rc to infinity gives the energy correction due to the
potential cutoff.
For pairwise interaction, g(r) can be used to calculate the pressure in the
system,
2
Nk B T 2 N dU ( r ) 3
P=
V
3V 2 dr
r g ( r ) dr
0