Add main script to run material simulations & modified input file

[pauka833]

• main.py now parses arguments for which simulation method is to be used (EMT or LennardJones) and it also properly creates and reads the input TOME file. These are used in md.py which is called by this script.
• md.py now uses the arguments from argparse and it also uses the data in the input file for all the simulation parameters.
• formatted all the relevant files with isort and black
• updated requirements.txt