Physics 171.635: Molecular Simulation

Spring Semester, 2007

Due Feb. 23

For the following you can use the code on the book’s website, which apparently has a couple of bugs you need to find. You can also download one of the other codes given below or use your own favorite MD code. If you don’t use the books code, then you should run your simulations with 1000 particles interacting with a Lennard-Jones potential. To speed things up you should truncate the potential at the minimum 2^1/6 s.

Start all particles on a three dimensional cubic lattice with separation 1.1s. You’ll want to use periodic boundary conditions so you’ll have to have the period in each direction be 10*1.1s =11.0s. Work at or near a temperature of unity in LJ units.

Contact me if you have any problems.

1) Question 10, p. 105, part 1.

2) Exercise 10, part 3. Try running your MD code with a time step of 0.0025, 0.0075, 0.010, 0.15, 0.2, to see what happens to the energy.

3) Exercise 10, part 6. You don’t need to use the fancy block algorithm to get this.

You may find it interesting to look at Exercise 4.

Possible programs:

LAMMPS

http://www.cs.sandia.gov/~sjplimp/lammps.html

This is a cool parallel MD code that our group uses. The one problem is that you’ll need mpi on your machine in order to compile it. It is in C++.

http://www.ccp5.ac.uk/librar.shtml has several codes including “moldy” and the programs from Allen and Tildesley.

Moldy has a variety of flavors for unix and windows. It seems to be a fairly complete code and is in C.

ftp://ftp.dl.ac.uk/ccp5/ALLEN_TILDESLEY/F.03 is a very simple and dumb code for Lennard-Jones that works well for this assignment. Note that you have to scale all the particles to a unit cube. It can go from 0 to 1 in each direction or from -0.5 to 0.5. You then give it the density and the code maps it back to real units. The code is in fortran or basic