README

To get started you will need to run the following:

FIRST TIME SETUP:

	source ./build_lammps.sh

TO RUN THE NOTEBOOK:

	run: "jupyter notebook" in terminal

	go to: "http://localhost:8888/tree?" in a web browser

	open np-toolkit.ipynb

TO USE THE NOTEBOOK:

	run all cells in the notebook using "shift+return" or "execute all"

	use the slider to control the interaction strength of your nanoparticle

	switching off "log" will allow you to run multiple simulations at once (don't overdo it)

TO VISUALISE RESULTS:

	an .xyz file will be generated in the parent directory, which can be opened in ovito or vmd or any other visualiser

	the easiest way to view the data in a nice way is to open the base_state ovito program state, and use the "pick new file" button on the right side to choose a new file

	DO NOT USE OPEN FILE in the top left, it will clear the modifiers, if this happens, close ovito and open the base state again