• The Potential_Gen directory contains the bash scripts required for the first stage (generating the potentials).
• The Compute_Rates directory then uses these potentials to compute the transition rates and rate coefficients.

Potential_Gen: - This set of files is used to generate the potentials. - First run Lattice_Gen.sh: * Define the site type, potential, surface temperature and interaction model (1,2,3) in this script file. * The gen_lattice.py is then called from this script. Currently, the number of unit cells in x,y,z directions are specified in this py file. * Once the lattice coordinates and velocities are generated, the appropriate lammps input file is then used to generate the lattice snapshots. * Some of the important parameters required for furture computations are written in info.jobs and info.lattice - Then run Extract_Pot.sh: * This divides the large number of small interaction potential simulations (jobs) into a job array and each job array is run on a seperate node. * At the end of each sub-job, all the individual files generated by the sub-job are merged into a single file. * Since the total number of files that can be held on /nobackup is constrained to 500,000 I further split each sub-job into further chunks. * At the end of each chunk, all the individual files belonging to a particular chunk are merged. * Set the appropriate properties : total number of jobs, number of sub-jobs and number of chunks. - Finally run Merge_all.sh: * It reads the prior generated info.* files and reads the necessary parameters. * It merges all the merged files generated by each sub job. * Finally, it calles the Compute_pot.py which computes the overall average V(z) and the rms values.

Compute_Rates: - Set the necessary inputs in Input.cfg - Run the Main.py with the appropriate Input.cfg file. - The Post_Processing/Test_QCF.py can incorporate most of the QCF models. - Finally, the Post_Processing/Plot_trans_rate.py can be used to generate temperature dependent kinetics.