Automated Property Estimator | APE

Automated Property Estimator (APE) software is a tool to automatically calculate the thermodynamic properties with considering anharmonic effect. All calculations were done using a development version of the QChem software package.

Currently, APE can estimate the thermodynamic property of a given molecule and the kinetics properties of a given elementary reaction in gas-phase.

Please check out our published paper of Comparative Analysis of Uncoupled Mode Approximations for Molecular Thermochemistry and Kinetics in the Journal of Chemical Theory and Computation.

Clone and setup path

Befor installing APE, download Anacinda and Git.

Install the latest version of APE by cloning the source code via Git.

• git clone https://github.com/shihchengli/APE.git

Add APE to your local path in .bashrc (make sure to change ~/Path/to/APE/ accordingly):

• export PYTHONPATH=$PYTHONPATH:~/Path/to/APE/

Install dependencies

• Install the v3.1.0 version of RMG (which has Arkane). It is recommended to follow RMG’s Developer installation by source using Anaconda instructions. Make sure to add RMG-Py to your PATH and PYTHONPATH variables as explained in RMG’s documentation.

• Clone the forked repo of ARC from my github page in a separate folder and add it to your PYTHONPATH just as well.

  git clone https://github.com/shihchengli/ARC.git

  export PYTHONPATH=$PYTHONPATH:~/Path/to/ARC/

• Create an Anaconda environment for APE:

  conda env create -f environment.yml

• Finally either close and reopen your terminal to refresh your environment variables, or type the following command.

  source ~/.bashrc

• Activate the APE environment every time before you run APE:

  source activate ape_env

Add APE aliases to your .bashrc (for convenience)

export ape_path=$HOME'/Path/to/APE/'
alias ape_env='source activate ape_env'
alias ape_dir='cd $ape_path'

How to run a job

To run APE, make sure to first activate the APE environment.

• Basic run

  python <path_to_the_APE_folder>/APE.py -n <ncpus> input.py

• Using the API

  from ape.main import APE
  
  ape = APE(input_file, project_directory=None)
  
  ape.execute()

How to give feedback

If you are having issues, please post to our Issues page. We will do our best to assist.

Licence notifications

This project contains source material from the geomeTRIC package.

Copyright 2016-2020 Regents of the University of California and the Authors

Authors: Lee-Ping Wang, Chenchen Song\ https://github.com/leeping/geomeTRIC/blob/master/LICENSE

How to cite

Please include the following citation if APE was used for an academic study:

• Shih-Cheng Li, Yen-Chun Lin, Yi-Pei Li, Comparative Analysis of Uncoupled Mode Approximations for Molecular Thermochemistry and Kinetics, J. Chem. Theory Comput. 2022, 18, 11, 6866–6877 (DOI: 10.1021/acs.jctc.2c00664)

Credits

• Professor Yi-Pei Li's research group at National Taiwan University