Input and Keywords

The main input is a json file (e.g. called input.json) in the directory where the calculations will be run. The json dictionary lists the options and parameters of the KinBot run. When a default parameter value is defined, the keywords are optional. All keywords are case-sensitive. The username parameter needs to be specifically set for each user's .json file.

json files can be validated e.g. with this online tool: https://jsonlint.com/.

This is an example input:

{
"title":"pentyl_pes",
"queuing" : "slurm",
"queue_name" : "normal",
"charge" : 0,
"mult" : 2,
"method" : "b3lyp",
"basis" : "6-31+g*",
"qc" : "gauss",
"conformer_search" : 0,
"reaction_search" : 1,
"rotor_scan" : 0,
"high_level" : 0,
"pes" : 1,
"barrier_threshold" : 50.0,
"ppn" : 4,
"username" : "user",
"single_point_command" : "molpro -d /scratch/ --mpp -n 4",
"single_point_ppn" : 4,
"smiles" : "[CH2]CCCC"
}

Restart

While KinBot is fully restartable, some parameters cannot be changed upon restart without compromising the calculations. These are marked with an asterisk (*).

General

Reactant

Request Actions

Conformational Search

Variable reaction coordinate transition state theory (VRC-TST) calculations.

Quantum Chemistry

Computational Environment

Master Equation Calculations

Uncertainty Quantification