MOLECULAR SIMULATION COURSE: EXERCISES

This distribution contains the course exercise programs. The document
that describes all the exercises can be found in the directory
DOC. For each computer exercise, a separate directory is set up in
which the source and run-scripts are located:


NAME           NUMBER    DESCRIPTION

barrier1     : 5.1     : MD of a single particle in various ensembles
barrier2     : 7.1     : Barrier crossing of a single particle 
                         using rare events
boltzmann    : 2.2     : Boltzmann distribution
cbmc         : 8.2     : CBMC program for a simple system 
distribution : 2.1     : Calculate the distribution of particles 
                         among compartments
ewald        : 3.6     : The Ewald summation
gibbs        : 6.1     : Gibbs ensemble of LJ particles
harddisks    : 3.3     : Simulation of hard disks in a square
                         1) dynamic  : MC scheme
                         2) static   : brute force MC (random-insertion)
ising        : 5.3     : 2D Ising Model using multi-canonical simulations
lib          : -       : Source code of RNG and initial seed generator
                         Also a FORTRAN77 version of the RNG is available here
mc-lj        : 3.4/6.1 : MC simulation of LJ particles in the NVT ensemble
mc-npt       : 5.2     : MC simulation of hard spheres in the NPT ensemble
md-lj        : 4.1     : MD program of LJ particles
md-mpi       : 4.2     : Parallel MD program of LJ particles
oscillators  : 2.3     : System of coupled harmonic oscillators
overlap      : 8.3     : Overlapping distribution for polymers
photon       : 3.2     : MC simulation of a photon gas
pi           : 3.1     : Calculation of PI using brute force MC
pt           : 3.7     : Parallel Tempering
polymer      : 8.1     : CBMC of a single chain molecule
random1d     : 2.4     : 1D random walk of a single particle
random2d     : 2.5     : 2D random walk of multiple particles
scaling      : 3.5     : MC algorithm in which coordinates are scaled
tps          : 7.2     : Transition Path Sampling
umbrella     : 6.2     : Umbrella sampling for a particle over an 
                         energy surface

To compile the source, simply type

make

in the directory containing the source code. All makefiles have been
prepared for RedHat Linux 6.2 (Zoot) on an i386 using the GNU
compilers. For other Unix systems, the Makefile may have to be
modified and you may have to type "make clean" first. The random
number generator provided in this distribution was written in C
(lib/ran_uniform.c). Some care have to be taken, because some
compilers put underscores after FORTRAN77 subroutines. For example,
for SGI machines ran_uniform__ has to be changed into ran_uniform_
(see lib/ran_uniform_SGI.c). A FORTRAN77 version is also available in
the directory lib.

The program md-mpi is a simple parallel md program written in
FORTRAN77/MPI. To compile this program, one has to have an MPI
implementation. We recommend the use of LAM, which is available on the
web (http://www.mpi.nd.edu/lam/).

To run the programs, go to the Run directory and type

./run

In many of the exercises, a program has to be modified or
completed. Usually, the location of where the program has to be
modified is indicated with

C   Start Modification
C   End   Modification

The solutions of most of the programming exercises are available on
request: send an email to Berend Smit. Also, if you have any
suggestions the authors would like to hear them.

We have done our best to remove all errors from this document and the
programs. However, we have to make the following statement:

``We make no warranties that this document or the programs accompanied
by this document are free of error, or that they will meet your
requirements for any particular application. The authors disclaim all
liability for direct and consequential damages resulting from the use
of this document or the programs accompanied by this document. It is
not allowed to distribute this document and the accompanying
programs.''

Berend Smit
Department of Chemical Engineering
University of Amsterdam
Nieuwe Achtergracht 166
1018 WV Amsterdam
The Netherlands

tel   : +31 20 525 6917
fax   : +31 20 525 5604
email : smit@its.chem.uva.nl
web   : http://molsim.chem.uva.nl
