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https://github.com/shihchengli/ape
APE - Automated Property Estimator
https://github.com/shihchengli/ape
anharmonicity computational-chemistry python qchem quantum-chemistry
Last synced: 9 days ago
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APE - Automated Property Estimator
- Host: GitHub
- URL: https://github.com/shihchengli/ape
- Owner: shihchengli
- License: mit
- Created: 2020-04-12T08:08:46.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-01-11T07:24:33.000Z (almost 2 years ago)
- Last Synced: 2024-10-08T21:21:25.277Z (about 1 month ago)
- Topics: anharmonicity, computational-chemistry, python, qchem, quantum-chemistry
- Language: Python
- Size: 8.55 MB
- Stars: 1
- Watchers: 1
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Automated Property Estimator | APE
[](http://opensource.org/licenses/MIT)
**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](http://www.q-chem.com/) 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](https://doi.org/10.1021/acs.jctc.2c00664) in the Journal of Chemical Theory and Computation.
## Clone and setup path
Befor installing APE, download [Anacinda](anaconda.com/download/) and [Git](https://git-scm.com/downloads).
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=$PYTHONPATH:~/Path/to/APE/`
## Install dependencies
- Install the v3.1.0 version of RMG (which has Arkane). It is recommended to follow RMG’s [Developer installation by source using Anaconda](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html#for-developers-installation-by-source-using-anaconda-environment) instructions. Make sure to add RMG-Py to your PATH and PYTHONPATH variables as explained in RMG’s documentation.
- Clone the forked repo of [ARC](https://reactionmechanismgenerator.github.io/ARC/installation.html) from my github page in a separate folder and add it to your PYTHONPATH just as well.
`git clone https://github.com/shihchengli/ARC.git`
`export PYTHONPATH=$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)
```markdown
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 /APE.py -n input.py`
- Using the API
```markdown
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](https://doi.org/10.1021/acs.jctc.2c00664))
## Credits
- [Professor Yi-Pei Li's research group](https://webpageprodvm.ntu.edu.tw/Li-group/Default.aspx) at [National Taiwan University](https://www.ntu.edu.tw/english/spotlight/2020/1820_20200327.html)