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This directory contains all the scripts necessary to run the **PET-MAD reference** NpT simulations for LiPS at varying temperatures, then compute the Li MSDs that can later be used to compute the Nernst-Einstein Li conductivity.

Running this example requires i-PI installation, as well as a utility script called trajworks, which can be installed from here: https://github.com/lab-cosmo/toolbox (then found in the bin).

`run_ipi.py` is the main Python script that handles the execution of the MD simulation.

`input.xml` is the xml formatted i-PI input file containing all the specifications for the MD simulation.

`LiPS_gamma.xyz` is the xyz file of the starting configuration taken from Gigli et al. (DOI: 10.1021/acs.chemmater.3c02726)

`petmad_ipi.sh` is the slurm job file that can be queued for the MD simulations.

`create_jobs.sh` is a shell script that creates all jobs at different temperatures, saved under separate sub-directories.

`compute_msd.sh` and `gather_msds.sh` computes and gathers the Li MSDs from the simulations.




With the proper set up of the environment, one can do the following:

1. execute `create_jobs.sh` to create all the MD jobs targeting different temperatures.

2. queue all the jobs from the subdirectories.

3. execute `compute_msd.sh` to compute the Li MSDs, then execute `gather_msds.sh` to create the `msds` directory and gather all results there.

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