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PHYS 8602, set4
Molecular Dynamics Simulation of Argon
Using LinkedList Algorithm
Requirement
To implement linkedlist algorithm for the MD
simulation of Argon atoms, using LennardJones
interaction potential.
Introduction
The Lennard Jones potential is characterized by two
independent parameters, σ and ε . The potential is
written as:

.

\

− 
.

\

⋅ =
6 12
4 ) (
r r
r V
σ σ
ε [1]
The attractive term is the Van der Walls interaction
and its functional form
6

.

\

r
σ
comes from the quantum
mechanical calculations. The term
12

.

\

r
σ
is the
repulsion term.
Reduced Units
To minimize the effects of round off errors and for
computational advantages, reduced units are used in
computations. They are derived from the Lennard
Jones potential parameters:σ , ε , the mass M of a
single atom and the Boltzmann’s constant. The
reduced parameters are related to the real parameters
using:
Reduced Density
3 *
ρσ ρ =
Reduced Temperature
ε
T k
T
B
=
*
Reduced Energy
ε
E
E =
*
Reduced Time t
m
t ⋅ =
2
*
σ
ε
[2]
Reduced Length
σ
L
L =
*
In my simulation the reduced quantities were:
*
ρ = 0.636
E
*
= 101.79
σ
*
= 1.0 [3]
ε
*
= 1.0
M
*
= 1.0
System Initialization
When an MD simulation is started for the very first
time, one needs to specify the initial arrangement of
the atoms in space, as well as their initial velocities.
Below I mention the initial conditions that were used
in my simulation.
• Atoms were arranged on a 7x7x7 lattice using slab
like arrangement of particles. Only 256 lattice sites
were used to place atoms and rest were left
unoccupied.
• The potential and the kinetic energy is distributed
among the particles such that the conservation of
energy is satisfied.
• The system satisfies periodic boundary conditions
Using Verlet Algorithm
Verlet integration is used for calculating the
trajectories of particles in molecular dynamics
simulations. It offers more accurate solutions than the
Euler’s integration method, besides having time
reversibility. This algorithm calculates the positions
and velocities using iterative method as shown below:
( ) ∆ + t r = 2 ( ) t r + ( ) ∆ − t r + ( ) t a
2
∆
( ) t v =
( ) ( )
∆
∆ − − ∆ +
2
t r t r
[4]
It is seen that for calculating ( ) ∆ + t r we need ( ) t r
and ( ) ∆ − t r . So we need a different method to get
( ) t r using ( ) ∆ − t r , for this I chose the Taylor’s
method for calculating the positions at the first time
step using the formula:
( ) t r = ( ) ∆ − t r +∆ ( ) ∆ − t v [5]
( ) ∆ − t r is calculated using initialization of Argon
atoms on 7x7x7 lattice.
Calculating ( ) ∆ − t v
Using initial positions ( ) ∆ − t r , calculate the Potential
Energy (P.E) of the system using LennardJones
interaction.
Kinetic energy of the system can be calculated using
conservation of energy.
K.E ( ) ∆ − t =
¯
=
N
i
i
mv
1
2
2
1
= E
*
 P.E( ) ∆ − t
[6]
Using K.E, I determined the total velocity
¯
=
N
i
i
v
1
of
all the atoms. This total velocity was distributed
among N atoms equally in magnitude. The directions
of velocities for N atoms are chosen randomly.
Then the timeprogression of positions and velocities
is implemented using Verlet algorithm as described in
above section.
The simulation is started after choosing a timestep∆.
Data are calculated and stored in files for analysis.
LinkedList Approach
For calculating the potential energy and the
acceleration of a particular particle, we need the
relative distances between that particle and all its
neighbors that lie inside the sphere of cutoff radius.
Instead of using bruteforce method of
evaluating all the neighboring particles, we can check
only a fraction of the total particles using the linked
list approach. In linkedlist method the entire cubical
system is divided into smaller cubical cells. The edge
of these cells is greater than the cutoff radius.
At each iteration, linkedlist arrays namely
‘head[]’ and ‘list[]’ are created that store the label of
the particles in each of the cells. These arrays are
helpful in determining the particles in all the cells.
Using the fact that the length of each cell is greater
than the cutoff radius, we are sure of locating all the
neighbors of a particular particle, if we check all the
particles lying inside:
a) 1) the cell containing this particular particle and
2) the cells that are its nearest neighbors
This method of linkedlist arrays and the cellstructure
was implemented in this project for the calculations of
potential energy and accelerations of all the particles.
Below I present the results obtained in the
calculations.
Results
Knowledge from assignment #2
In assignment (2) I studied the time propagation of
error in the total energy for varying timesteps ( ∆).
The optimum value of timestep used in my
simulations is: ∆=1.0 x 10
4
.
The plot (1) and (2) show the time dependence
of kinetic energy and potential energy respectively.
Plot(1): Timeevolution of kinetic energy
Both kinetic and potential energy evolve with time in
a complementary way such that the total energy
remains a constant.
Plot(2): Time evolution of potential energy
Plot(3): Time evolution of T
*
Summary Table
Quantity Mean Error
KE
985.712 4.32
PE
856.831 4.32
T
*
2.56 0.01
References
[1]. “Computer Simulation of Liquids”
by Allen and Tildesley
[2]. Centre for Molecular Simulation
http://www.swinburne.edu.au
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