Sairam Tangirala

PHYS 8602, set-1

Simple Harmonic Oscillator:

Molecular Dynamics Simulation

Requirement dx p
= (5)
dt m
Study the simple harmonic oscillator problem
using molecular dynamics. dp
= −K ⋅ x (6)
dt
Introduction

The Hamiltonian for the 1-D simple harmonic

Methodology
oscillator can be written as:
A standard method for solving such ordinary
p 2 Kx 2
H= + (1) differential equations is using finite difference
2m 2 methods. Numerical solutions for the equations of
here, motion can be obtained using Euler’s method. The
p = momentum solution is given as:
x = position
K = spring constant ⎛ p (t ) ⎞
m = mass x(t + ∆ ) = x(t ) + ∆ ⋅ ⎜ ⎟ (7)
⎝ m ⎠
For simplicity I chose following initial conditions: p(t + ∆ ) = p(t ) − ∆ ⋅ K ⋅ x(t ) (8)

At ‘t’ = 0.0 (2) The general idea is as follows: given the

molecular positions, velocities, and other dynamic
x(t = 0 ) = 0.0 information at time (t), we attempt to obtain the
position, velocities etc. at a later time (t+ ∆ ), to a
p (t = 0 ) = 4.0
sufficient degree of accuracy. The equations are
solved on a step-by-step basis: generally the time
System parameters: (3) interval ( ∆ ) is significantly smaller than the typical
time taken for the molecule to travel its own length.
K = 1.0
m = 1.0
Results
The system is constrained by the conservation of
energy principle. This can be written in the equation Error in ‘E’ Vs time
as:
p 2 Kx 2 Fig.(1) shows the plot of error in the computed
H= + = E = 8.0 units (4)
2m 2 energy as a function of time for varying time-intervals
( ∆ ). The error in the computed energy increases
monotonically with time for all values of ∆ . For
This system can be solved using Hamiltonian ∆ =0.1 the error increases more prominently as
formalism. The equation of motion can be obtained as compared to smaller time-intervals ( ∆ ’s).
two 1st Order differential equations:
 Fig.(1): Error in computed Energy Vs time
The error plot can be verified by having a look
at the Fig.(2) showing a comparison of the computed
energies with the analytic value. The analytic energy
is a constant that was calculated earlier using the
system parameters see eqn.(4). Both the Figs.(1),(2)
show the same behavior.
Fig.(2): Comparison of computed ‘E’ with the
analytic ‘E’
Error in ‘x’ Vs time
Fig.(3) shows the error in computed ‘x’ as a function
of time for varying ∆ ’s.
Fig. (3): Error in computed position Vs time
The Fig.(3) shows a periodic behavior with
time. The error in position increases with time to a
local maximum and then drops down to near zero, and
then increases again. This behavior is observed to
have a periodicity with time. Also the integrated error
shows a gradual increase with time.
Here I investigate the reason for this apparent
periodic nature of the error by comparing the
computed positions with the analytic value.
Analytic position can be derived to be:
x = 2 E ⋅ Sin (ω ⋅ t ) (8)
here,
K
ω= = 1.0 and (9)
m
E = 8.0 units
The below Fig.(4) shows the comparison of
analytic positions with the computed positions for
various ∆ . The computed positions show periodic
deviations with the analytic value. The deviations
become more prominent with the increase of the time-
interval ∆ . These deviations have a periodic nature
which explains the periodic nature of Fig.(3).
 Fig.(4): Comparison of computed ‘x’ with the
analytic’x’
Plot of ‘p’ Vs ‘x’
From the equation of the Hamiltonian eqn.(1)
and the system parameters eqn.(3), the plot of ‘p’
versus ‘x’ is expected to be a circle of radius = 4 units.
The Fig.(5) shows the plot of ‘p’ versus ‘x’ for
various values of ∆ . For ∆ =0.001, the plot is a
approximately a circle with radius = 4.0 units, as
expected. But as we go onto the larger ∆ , the nature of
the plot changes for being a circle to an ellipse. This
change of the behavior can be explained by the
violation of the energy conservation constraint,
introduced as an artifact of the algorithm used in the
calculations.
Fig.(5): Plot of ‘p’ versus ‘x’
Conclusions
It is seen that for any given time-interval ( ∆ ),
error in the calculated quantities increases as the time
progresses. The rate at which the error increases with
time depends on the value of ‘ ∆ ’. For lower values of
‘ ∆ ’, the rate at which the error increases is smaller
than that with a higher ‘ ∆ ’.
Error arises due to the truncation of Taylor
series expansion used in calculating ‘x’ and ‘p’ and
the discretization of time in the calculations. These are
inherent disadvantages of the algorithm.
References
[1]. “Computer Simulation of Liquids”, Allen and
Tildesley
 //SOURCE CODE

//HEADER FILES USED IN THE PROGRAM

#include<math.h>
#include<stdlib.h>
#include<stdio.h>
#include<limits.h>
#include<time.h>

//USER DEFINED SYSTEM PARAMETERS

#define M 1.0
#define K 1.0
#define INITIAL_T 0.0
#define FINAL_T 10.0
#define ENERGY 8.0
#define INITIAL_X 0.0
#define DELTA 0.01

//INLINE FUNCITONS TO SPEED UP CALCULATIONS

#define INITIAL_P() (double)sqrt( 2*M*(ENERGY-0.5*K*INITIAL_X*INITIAL_X) )

#define OMEGA() (double)sqrt(K/M)

FILE *fp,*error_fp;

//USER DEFINED FUNCTIONS

void file_operation(int mode); //mode=0:open file //mode=1:close file
void do_calculation(void);

//PROGRAM BEGINS HERE

main()
{
fprintf(stderr,"Simulation Started\n");

file_operation(0); // OPEN DATA FILES

do_calculation(); //DO CALCULATIONS
file_operation(1); //SAVE DATA FILES

fprintf(stderr,"Simulation Completed\n");
}
// END OF MAIN PROGRAM
//FUNCTION DEFINITIONS
//THIS FUNCTION PERFORMS THE OPENING AND CLOSING OF DATA FILES

void file_operation(int mode)

{
//mode = 0:open file
//mode = 1:close file
if(mode == 0)
{
fp = fopen("p_vs_x.dat","w");
error_fp = fopen("error.dat","w");

//CHECK IF FILES WERE OPENED CORRECTLY

if( (fp == NULL)||(error_fp == NULL) )
{
fprintf(stderr,"Couldnt open data file\n");
exit(1);
}
}
else if(mode == 1)
{
fclose(fp);
fclose(error_fp);
}
}

//THIS FUNCTION IMPLEMENTS EULER’S ALGORITHM AND

// CALCULATES POSITION AND MOMENTUM AT VARIOUS TIME-STEPS

void do_calculation()
{
double x,p,t,e,analytic_x;
double new_x,new_p,error_e,error_x;

//GET INITIAL CONDITIONS

x = INITIAL_X;
p = INITIAL_P();
t = INITIAL_T;

while(t < FINAL_T) //DO CALCULATION FOR USER-DEFINED TIME INTERVAL

{
new_x=x+DELTA*p/M; //EULERS ALGORITHM IMPLEMENTATION
new_p=p-DELTA*K*x;

e=(0.5/M)*p*p+ (0.5*K*x*x); //ENERGY CALCULATION

error_e=100.0*fabs(ENERGY-e)/ENERGY; //ERROR CALCULATION

analytic_x=sqrt(2.0*ENERGY)*sin(OMEGA()*t); //ANALYTIC POSITION ‘X’

 if(analytic_x!=0.0) //AVOID DIVIDE BY ZERO
error_x=100.0*fabs( (analytic_x-x)/analytic_x );
else
error_x=0.0;

fprintf(fp,"%lf\t%lf\t%lf\t%lf\t%lf\n",t,x,p,e,analytic_x); //WRITE DATA FILES

fprintf(error_fp,"%lf\t%lf\t%lf\n",t,error_x,error_e);

t=t+DELTA; //INCREMENT TIME-STEP

x=new_x;
p=new_p;
}
}