README.md

tofhed

WARNING: This code is in active developement!

'tofhed' is a tool for handling heterogeneous atom trajectories. Its functionalities include:

• Importing atom trajectories (from xyz, extxyz, cif, etc.)
• Building a SQL database for data collection and subsequent analysis (only SQLite and Postgres have been tested)
• Analysing frames using the Hinuma algorithm
• Identifying surface atoms and their connectivities
• Finding connected atoms based on their Pyykko-Distance
• Detecting events such as pinging, adsorption, and desorption

Installation

Prerequisites

Python (Version 3.8 - 3.11)

Ensure Python (within version 3.8 to 3.11) is installed on your system. For an isolated and conflict-free setup, we advocate using a virtual environment.

Link: Setting up a Virtual Python Environment

Git

Since 'tofhed' is currently in its developmental alpha stage, it isn't available on PyPI. Thus, Git is essential for the installation process.

Link: Git Installation Guide

Installation Steps

Installing 'tofhed' is a straightforward process, be it through the terminal or Jupyter Lab. The tool takes care of all required dependencies during installation.

Option 1: Terminal Installation

It's prudent (though not mandatory) to activate a virtual environment prior to the installation. If you're unfamiliar with setting up a virtual environment, please revisit the Python prerequisites above. With your virtual environment active, enter the following command:

pip install git+https://git.rwth-aachen.de/modes/tofhed.git

While a virtual environment prevents potential package conflicts, choosing not to use one will install 'tofhed' and its dependencies system-wide.

Option 2: Jupyter Lab Installation

Ensure your desired virtual environment is selected within Jupyter Lab. Then, proceed with the installation command highlighted in the terminal section.

Link: Guide on Using Jupyter Notebook in a Virtual Environment

%pip install git+https://git.rwth-aachen.de/modes/tofhed.git

Quickstart

• Quickstart Guide