Setting Up KinBot on Your System

Setting Up KinBot on Your System

Prerequisites

KinBot is designed to run on high-performance computing resources.

The following software should be installed to run KinBot:

• Python >=3.8
• A PBS or SLURM workload manager.
• Gaussian. We have tested KinBot with G09 revision D01 (note that besides Gaussian on the compute nodes its formchk utility needs to be available on the head node where KinBot is running). We are currently working on NWChem and QChem to be available with KinBot.

Additionally, KinBot depends on the following libraries. However, all of them are downloaded automatically when KinBot is installed via pip or conda, so there's no need for you to install them manually.

• numpy>=1.17.0
• ase>=3.19
• networkx
• rmsd

Optionally:

• One of these master equation solvers to calculate rate coefficients
  • MESS
  • MESMER
• PESViewer to visualize the PES
• Pybel, a Python wrapper of OpenBabel
• RDKit including Python bindings

Installation

KinBot can be installed either via pip.

PIP

pip install kinbot

Note KinBot only works with Python >= 3.8.

In order to run KinBot, please provide the path of a valid batch file for your SLURM/PBS scheduler via the queue_template keyword. The details of this and other keywoords can be consulted here.