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This directory contains all the scripts necessary to run the **FlashMD** NVT simulations for Al(110) slab at varying temperatures.

Running this example requires i-PI installation.

`run_skipmd.py` is the main Python script that handles the execution of the MD simulation, for the ``SkipMD'' version that was used in producing the paper results.

`run_flashmd.py` is the main Python script that handles the execution of the MD simulation, compatible with the latest FlashMD repo.

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

`Al110.xyz` is the xyz file of the starting configuration generated with ASE.

`flashmd_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 and stride sizes, saved under separate sub-directories.

`msd.py` is a support script that takes the trajectory xyz file as the first command line input, and the stride size as the second command line input.



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 `msd.py` to obtain the MSDs for the simulations of interest.

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