This package @2018 contains two programs.

---
Mail luke.davis.16@ucl.ac.uk for info.
---

## IMPORTANT #

!) Store these files in a directory called "src"
!) You must mkdir nodenetworkout/ in the same level as src/
!) The number of beads making up the rod is controlled in nodenetwork.h (Top)
!) Your xyz file has to have > 2 snapshots in. I recommend storing a whole trajectory and changing the interval value.

!) Most of the parameters can be changed by editing main_structure.cpp (wrapped) or unwrapped_structure.cpp (unwrapped). These include:

o) Bead diameter: dia
o) How many rods can make a strand: rodthresh
o) length of box: length (doesn't matter for unwrapped)
o) closeness percentage i.e. the distance which defines whether two beads touch: touchperc
 
~~~~~~~~~~~~~~~~~~~~~~
UNWRAPPED xyz files
~~~~~~~~~~~~~~~~~~~~~~

So you have unwrapped the xyz in lammps. The beginning looks like this:
1)

ITEM: TIMESTEP
3290000
ITEM: NUMBER OF ATOMS
36000
ITEM: BOX BOUNDS pp pp pp
-5.3000000000000000e+01 5.3000000000000000e+01
-5.3000000000000000e+01 5.3000000000000000e+01
-5.3000000000000000e+01 5.3000000000000000e+01
ITEM: ATOMS type xu yu zu

But we want:

2)

36000
Atoms. Timestep: 3290000

@)  If you place the file from (1) in the convert_unwrap like so: 

[perform on command line] convert_unwrap <filename.xyz>

@) You will get a file <filenameconverted.xyz> . So it looks like all the others. My program 
(compile_unwrap) requires this... but you also get the benefit of using VMD with it now :).

@) To compile the program simply do: 

[perform on command line] compile_unwrap

@) Instructions on output of the previous command will then direct you to run in the correct manner.


~~~~~~~~~~~~~
WRAPPED xyz files
~~~~~~~~~~~~~

@) No need to convert xyz file (assuming in format (2) above).

@) Compile: 

[perform on command line] compile_wrap

@) Instructions will then direct you to run in the correct manner.