Dear Sourav,
To calculate the TOF manually, you need the number of molecules produced over the time interval of interest (obtained from specnum_output.txt) and the elapsed simulation time.
The TOF can be reported either per lattice site or per unit surface area. In both cases, the required information (total number of lattice sites and total lattice area) can be found in general_output.txt.
Alternatively, you can use Zacros-post to read the output files and plot the TOF directly.
Another option is ZacrosTools. Instructions on how to do this with ZacrosTools can be found here:
zacrostools.readthedocs.io/en/latest/reading_output_files.html
Note that ZacrosTools reports TOFs normalized by surface area (molecules/s/Å2). To convert these values into TOFs per lattice site, simply multiply by the total lattice area and divide by the total number of lattice sites, e.g.:
tof_per_site = kmc_output.tof * kmc_output.area / kmc_output.n_sites
Make sure to use the same TOF normalization as in the paper to reproduce the reported values.
