The no kinbot mode

The no-kinbot mode

The pes script can be run without calling KinBot. This feature allows to quickly read everything that has been done so far and postprocess all the calculations. For this the 'no-kinbot' option needs to be added to the command line:

pes input.json no-kinbot

In this mode, it is also possible to highlight all pathways between two species:

pes input.json no-kinbot allpaths [chemid1] [chemid2]

The chemid1 and chemid2 are the ids of the two structures (wells or products). These can be found in the summary files and in the pesviewer.inp file. For bimolecular products, the chemids are sorted from lowest to highest and concatenated with underscores. The output of this is the pesviewer.inp file, which can be visualized with the PESViewer code.

Similarly, it is possible to select only the lowest energy pathway between two species:

pes input.json no-kinbot lowestpath [chemid1] [chemid2]

Or to visualize all reactions from one species:

pes input.json no-kinbot well [chemid1]

Finally, a functionality allows to only select pathways which have a branching fraction of 1% or more for a particular well at a given temperature (in K). This is done by starting from the initial well, and iteratively expanding the network of reactions by considering the products of the reactions with a sufficiently large branching fraction from the previous iteration. It is important to note that the results depend on the well the search is started from.

pes input.json no-kinbot temperature [temperature]