Bilayers of graphenylenes and octafunctionalized-biphenylenes
Using Greenwood (a Clojure library), DFTB+, and R these files can completely reproduce input files, gather the results, and perform our analysis on bilayers of graphene, graphenylene, net-C, Type-2, and net-W. The DFTB+ input files are easily recreated, but running the calculations take considerable time to run. Thus, the intermediate results and post-processing results of the calculations are also provided.
Steps to reproduce
Clojure scripts for reproducing the DFTB+ calculation input files is contained within files called notes.sh contained in each of the folders: bilayer_graphene, graphenylene, TYPE1, TYPE2, and TYPE3. The same folders contain the raw results of the calculations along with post analysis (also performed in Clojure as found in notes.sh) files that are then used to as input data for interpretation in R-markdown. The analysis folder has an R-markdown file that performs much of the data interpretation that our paper used. The data is included in the other folders as indicated in the bilayer_bpc_graphs.Rmd file. The html file by the same name shows the results of the analysis. The folder also contains some jpg files needed to successfully compile bilayer_bpc_graphs.Rmd. Within the sub-folders of BandStructure_DOS_output/BILAYER_band_new folder are zip files containing all of the band structure results produced by DFTB+. The contents of each zip file should be placed within the subfolder in which the zip file was found. If the reader wishes to redo all of the calculations performed in bilayer_bpc_graphs.Rmd themselves. Otherwise, they will find that the *.rds files will suffice. We did not use the results of running the WAVEPLOT program of the DFTB+ package in writing our paper. But the results are included in BandStructure_DOS_output/BILAYER_WAVEPLOT. BandStructure_DOS_output/BILAYER_SINGLE_LAYER contains the band structure results for single layers of the carbon allotropes studied.