Doug Franz

Also need to apply NPT Parinello (flexible box) dynamics. Probably requires addition of ij Force matrix (this is needed to calculate pressure in NVT anyways)

e.g. HA -> H HeC1 -> He etc.

MSD/diffusion calc

2

test case 100 Ar

i.e not just real but reciprocal space

mods to restart mode

1

detect if input_atoms_xyz was used, otherwise restart.pdb will overwrite the .xyz i.e. if xyz input is used, also print restart.xyz (and use that for restart.) Also update SA temperature in...

add RK4 integration for MD

1

error is order dt^4, slower calc but less deviation from real solution over time.

only relevant for rigid-body rotation