This is the data and scripts for figure 4. Sample trajectory files are included which contain particle positions and box sizes.  To visualise the trajectories it is necessary (assuming unix/linux/mac environment) to compile rod_drawer as
  g++ rod_drawer.cpp -o rod_drawer
and then run rod_draw.sh using arguments (for example)
  ./roddraw.sh V 60 400 0.00 40000 0.88 0
which will take input from the file 
  trajectorys0.000TPS40000JID309112R0 
and produce a postscript file
  trajectorys0.000TPS40000JID309112R0.ps
This file was then converted to .pdf and resized to make the figure.

The arguments to roddraw.sh are 
  Regime - V or P for constant volume or pressure.
  Particles - The number of rods in the system.
  Slices - The number of slices in the trajectory.
  s - The value of s for the trajectory
  TPSmoves - The position of the trajectory in the sequence of transition path sampling (TPS) moves in which it was generated (included in trajectory filename)
  statepoint - The value for the density or the pressure of the trajectory.
  rank - The rank of the trajectory you want to visualise (included at end of trajectory filename)


The script pic.sh in this directory takes an intermediate file that is output from rod_drawer and converts it to PS format.
