The plan was to reproduce the following in order of importance:
Electronic Band Structures Phonon Dispersions Electron-Phonon Coupling Constants 3rd Derivatives of Force Constants The original work was done using quantum espresso, a code of which I have no experience with, instead I opted to get the same results using alternative DFT code I did have experience with, CASTEP.
I am familiar with DFT and generating phonon band structures for a material, but I normally work on bulk materials not specific geometries.
I already had a compiled version of CASTEP, all plotting and analysis was done using Python (matplotlib).
CASTEP, Python libraries: Matplotlib, Atomic Simulation Environment, numpy
Some of the main issues surrounded understanding the exact workflow the original authors used to generate their structures. For example, it wasn't too clear from the electronic band structure plots in the supp. material if they were individual geometry optimised structures, and also what the parameters for convergence were (I.e. how tight were they converging their forces etc).
Phonon calculations in CASTEP proved difficult to obtain. The main issues involved the simulation crashing halfway through without useful error messages to inform what the appropriate next step would be. (It was most likely being caused by out of memory events).
Using CASTEP and python to do analysis are quite easy tools to use on the surface (It's very quick to get started).
CASTEP reproduced the electronic bands mostly, however, there appeared to be a band missing from the paper results (we saw a band in CASTEP and FHI-AIMs that wasn't apparent in the paper for the BeC system)
For the most part. if one wanted to use quantum espresso to reproduce the work all elements were available. I think it would be beneficial to provide all three structures in the form of .xyz files (we had to manually extract the Be nanowire and C nanotube from the full BeC system). Another thing which could be provided is the direct data used in all the plots so one can plot their own data side by side (or at least data that is formatted in a accessible way).
All the relevant input files were provided for a quantum espresso calculation with clear instruction for the workflow to generate the data.
inclusion of the plotting scripts/analysis scripts would have been helpful.
I think the input files provided should be double checked against the supp. material. We caught a discrepancy surrounding the initial geometry of the box in the input files for quantum espresso and the reported values in the supp. material.
redoing the calculations in quantum espresso is trivial with the input files provided (however, one of our colleagues needed to change the plane wave cut off energy for stability).
I think it would of been useful to provide the plotting scripts (if possible) also.