This package @2018 contains two programs.

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

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## 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

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UNWRAPPED xyz files

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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.

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WRAPPED xyz files

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@) 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.