README file for the Materials Cloud Repository concerning the article 
"Topological Data Analysis of Ion Migration Mechanism" 
by Ryuhei Sato et al. Advanced Institute for Materials Research, Tohoku University (2022).

The zipped folders: 

444_NH, 444_NPT, and fixedMD
contain inputs and some results of the LAMMPS simulations of the AgI systems.

444_NH: input files for NVT-MD simulation with various temperature. You can find 5-ns MD simulation at 1000K 
(i.e. output files, lammps trajectory, products of charge and velocity during the simulation etc.) in "1000K.tar.gz".

444_NPT: input files for NPT-MD simualtion with various temperature.

fixedMD: input files and input structure with four-membered ring with different birth and death values.
         In output directory, you can find the potential energy durin these MD simulations at 1000K.


In analysis directory, you can find some calcualtion code(fortran and python) used in the subsequent analysis.

integrated_correlation_func_of_current.f90: used for the conductvity calculation with Green-Kubo formula
dump_to_pointcloud.f90 : used to obtain the txt file for Homcloud.
script_for_persistence_diagram.sh: the script file used to calculate the persistence diagram using Homcloud package.
inverse_analysis.py: to conduct the inverse analysis using Homcloud (Optimal volume method in Homcloud package)

The version of package used in these calculation are follows, 
LAMMPS (29 Octobar 2020)
Homcloud (3.5.1)