This package:
- reads in lammps trj, gro and pdb (unwrapped gro and pbc) into pandas dataframe and generate ions by centers of mass.
- calculates association of the counterions (AN) and categorizes hopping types of the counterions (AN).
- calcualtes non gaussian parameter and mean square displacement for AN.
- calculates van hove function and distribution of string like motions for AN.
- calculates continous time autocorrelation function, intermittent time autocorrelation function, tau_c and tau_s.
- Fs(q,t) and tau_q
- saves trj in lammps format
Tested on python 3.6.4, NumPy 1.14.2, SciPy 1.0.0, pandas 0.22.0 and matplotlib 2.0.2.
Not complete yet but already useful.
Howto:
pdb.main_.py is the 'template'. gro.main_.py is the 'template'.
Please cite:
Luo, X.; Liu, H.; Paddison, S.J.; Molecular Dynamics Simulations of Polymerized Ionic Liquids: Mechanism of Ion Transport with Different Anions, ACS Appl. Polym. Mater. 2021, 3, 1, 141–152