qcflow

This script has been developed by the Persson Group members including Sudarshan Vijay, Evan Walter Clark Spotte-Smith, Peichen Zhong, and others.

A customized package for Q-chem calculations & reaction network construction

• Use pip install -e . to install a cutomized custodian from the forked repo https://github.com/zhongpc/custodian.git
• Use pip install . to install a cutomized mrnet from the forked repo https://github.com/zhongpc/mrnet
• Set up your own config.yaml

The general approach using the qcflow

• Create a directory containing the initial molecules in init_mols
• Run python 1-FFopt-SP.py
• Create a scratch dir, go to the dir and use qlaunch to submit jobs
• Use qlaunch [OPTION], e.g. qlaunch rapidfire --nlaunches <N> to submit the job in one scratch directory, is the total number of jobs to be submitted
• Run python 2-create-mol-json.py to get the json files of optimized molecules
• Run python 3-fragment-recombine.py to get the fragmentation/recombination and store those in the MongoDB
• Run python 4-compute-recombine.py to add the recombination mols to the workflow
• Use qlaunch [OPTION] to submit the job in one scratch directory
• Run python 5-create-json.py to get the results from Q-Chem calculations
• Apply HiPGen [nix-shell] to analyze the results based on the json file