PHY480 - Computational Physics
Michigan State University, Spring Semester 2006
Due: Thursday, March 16

Assignment #5: Classical molecular dynamics

The purpose of this lab is to become familiar with the classical dynamics of a system of point-like particles interacting via two-body forces.

Consider a system of N particles of a given mass (the same for all particles). The spherically-symmetrical two-body potential is of Lennard-Jones type:

V1 2(r) = 4 e é
ê
ë
æ
ç
è
s
r
ö
÷
ø
12
 
 
- æ
ç
è
s
r
ö
÷
ø
6
 
 
ù
ú
û

Write a program ljmd.f that integrates the Hamilton equations of motion for a number N (input parameter; consider up to 4 atoms) with a method which has an error of O(h5) per step.

Calculate and print at t=0 and after every 200 steps:
  i. the total energy of the system;
  ii. all components of the total linear momentum;
  iii. all components of the center-of-mass (CM) of the system;
  iv. all the components of the total angular momentum.

Calculate the following quantity at each time step:

r.m.s. =   æ
 ú
Ö

1
N
N
å
i = 1
[  (xi - xCM)2 +  (yi - yCM)2 +  (zi - zCM)2 ]

Write the results in a file an make a plot of it using gnuplot. You should use your own input file to test the program. I will use mine for grading. Your report should contain a short description of the problem (including equation of motion, numerical techniques, etc.) and a plot of the r.m.s. for your test input data.

You can use the FORTRAN program ~tomanek/PHY480/HW5/xrgkt4.f for the damped linear harmonic oscillator or an incomplete mock-up code ~tomanek/PHY480/HW5/ljmdmu.f as a template for your code ljmd.f. Your code should run with the input file ~tomanek/PHY480/HW5/Na3.xyz (or its obvious modifications for up to 4 particles) for a hypothetical Na3 atomic cluster. Use double precision in your calculations.