CONTENTS.txt

Report folder contains my full report (including all auxillary files) as well as files for my intermediary report and project plan. 
  It is particularly worth noting that the report .tex file has the path for all figures used in the report as well.
  It also has my project presentation (and script), as well as misc graphs and my labbook files.

Test_cases folder contains basic code to run simulations on 2D and 3D ideal gases, as well as simple rigid rods. 
  It also contains test code from Jiaming Yu (Eiser Group, Cambridge) and LAMMPS used for benchmarking, and familiarisation with the LAMMPS software.


Phase_Structure contains all the code I wrote during this project. It is split into simulations for rigid rods, and simulations for nunchucks. 
  Two folders of rigid rod simulations are included for completeness, however the relevant code is all inside Rigid_Rods2.
    Rigid_Rods contains an earlier, loop free implementation of the code, described in more detail in the labbook.

Many analysis and running scripts are common between different directories, with only the running/system parameters varying. 
  I will provide a separate zip file of all the relevant scripts (commented etc) for prosperity at the end of the project. 
    
All directories contain in.run_setup and in.run_loop which run the simulation in LAMMPS, an input.file which contains the initial positions of the particles,
  an output file log.lammps with all thermodynamic data from the simulations, and possible output.dump files with particle positions at regular timesteps. 
     All python analysis files have self explanatory titles and docstrings to describe their function.