There are five subdirectories in data/ named ti00[1-5], each containing ti00[1-5].out (which are copies of the ti001.out, with clambda edited) and ti00[1-5].en (copies of ti001.en).

The output files were obtained by executing the script with the following options:

python alchemical_analysis.py -a AMBER -d data/ -p ti*/ti -q out -u kcal -r 8 -v -o .

The argument that follows the -a flag should not necessarily be in all capitals; any combination of lower- and upper-case letters is OK. data is the path to the directory with the data files.

The -p flag seeks for the prefix of the data file. If the data files are in multiple subdirectories, the name of those subdirectories (in a form of the glob pattern) should preface the file prefix (like ti*/ti above).

Whenever the -v flag (verbose option) is used, the averages and RMS fluctuations of each quantity present in the MDEN file (ti00X.en in our example; no requirement for it to bear the same prefix as the MDOUT file) will be computed and displayed.

The dataset contained in the data/ directory was generated from the files obtained from a 21-window simulation of the vdw gas-phase methanol-to-ethane transformation run by Hannes Loeffler at STFC, UK.