Vacancy Mediated and Interstitial Solute Transport in Zr from Density Functional Theory Calculations

The Interstitial folder contains the DFT dataset for the interstitial site and migration energies of all solutes, scripts required to extract the data and compute diffusivity. The Vacancy_Mediated folder contains the DFT dataset for the solute-vacancy binding and vacancy migration energies, scripts required to extract the data and compute diffusivity. The scripts/ directory in site Interstitial and Vacancy_Mediated folders contains the python and bash scripts, which extracts the input data for diffusion model from DFT dataset. The extraction of data can be done by running ExtractDFT.sh scripts for Interstitial or Vacancy_Mediated data for each solute located inside the /scripts directory of either data set. The vacancy mediated extracted data for each solute contains solute-vacancy binding energies and migration barriers in one file called solute_elist.yaml, and frequencies for sites and transitions in another file called solute_flist.yaml. Similarly, the interstitial data is separated into two yaml files for each solute. For the convenience, these files are already generated. The Diffusion folders inside Vacancy_Mediated and Interstitial directories each have subdirectories for the solutes. These solute sub-directories have scripts that read the extracted data and compute diffusivity. The scripts/ directories of each data set also consist of a master script "TransportCalculation.sh" which computes the diffusion coefficients of each solute instead of executing them manually. The results of diffusion calculations and arrhenius fits are saved under corresponding solute folders within the Diffusion directory. The "POTCARS.txt" file details the POTCAR used for Zr and solutes. Note: Before running "ExtractDFT.sh", make sure the pythonpath is correctly set in FrequencyCalculation.sh and AttemptFrequency.sh which are present in scripts/ directory. The python 3.4 and above with modules yaml, numpy, argparse, os, scipy, h5py and Onsager is required. The Onsager module can be obtained from [ONSAGER,http://dallastrinkle.github.io/Onsager].