Getting Started

Welcome to quantumAllostery!

1 Overview

The quantumAllostery package was designed to automate the identification of charge-transfer events in ab-initio molecular dynamics simulations. Routine tasks can be easily automated using the functionality contained in the library.

2 Installation

Install the package by running the follow commands inside the repository. This will perform a developmental version install. It is good practice to do this inside of a virtual environment. A yaml environmental file has been created to automate the installation of dependencies.

Creating a Conda environment

All the dependencies can be loaded together using the prebuilt environment.yml files. We provide two YAML files. The dev version contains additional packages for code maintenance.

conda env create -f environment.yml

If you are going to be developing the package run:

conda env create -f environment_dev.yml

Setup developing environment

Follow these steps to install quantumAllostery.

git clone git@github.com:davidkastner/quantumAllostery.git
cd quantumAllostery
pip install -e .

3 What is included?

.
├── docs
├── qa
│   ├── qa           # Top-level script that interacts with the rest of the package
│   ├── process      # Processes the raw AIMD data
│   ├── predict      # Machine learning analysis
│   └── plot         # Automated plotting and vizualization
└── ...

4 Expected file structure

quantumAllostery was originally build for ab-initio simulations with multiple replicates. The replicates were run in multiple pieces, as they were computational expensive and required restarts. To use the package without changing anything, consider setting up your work flow with this suggested file structure.

The functions will be expecting the following file structure:

. ├── variant │ ├── replicate │ │ ├── start │ │ ├── restart │ │ └── … │ ├── replicate │ │ ├── start │ │ ├── restart │ │ └── … │ └── … ├── variant │ ├── replicate │ │ ├── start │ │ ├── restart │ │ └── … │ ├── replicate │ │ ├── start │ │ ├── restart │ │ └── … │ └── … └── …

4 Documentation

Update ReadtheDocs.

cd docs
make clean
make html

5 Developer guide

GitHub Refresher

git status
git add .
git commit -m "Change a specific functionality"
git push -u origin main