TrajectoryTools

TrajectoryTools is a Python library designed for loading and processing trajectory data into pymatgen structures from molecular dynamics simulations. The package is structured into various sub-packages, each with a specific focus on different aspects of trajectory analysis and preparation.

Sub-packages Overview

loaders: Import trajectory lazily data from different formats and convert them into pymatgen-compatible structures.
- base_structure_loader: Basic loading capabilities for structural data.
- lammps_structure_loader: Specialized loader for LAMMPS simulation output.
- xyz_structure_loader: Loader for XYZ file format.
writers[WIP]: Export pymatgen structures into various file formats suitable for downstream analysis.
transforms[WIP]: Advanced sub-package for smoothing and averaging trajectory data. Also has tools to reshape trajectory.
parallel[WIP]: A collection of parallel computing utilities for efficient trajectory analysis and processing.
- task_runner: Execute parallel processing tasks on trajectory data for faster data manipulation and transformation
- task_que:

Installation

Prerequisites

Python 3.11 or higher.

Clone from Git Repository

git clone https://github.com/ChrisDavi3s/TrajectoryTools.git
cd TrajectoryTools

Install Package

pip install .

Or for a development environment:

pip install -e .

Dependencies

numpy==1.26.3
pandas==2.1.4
pymatgen==2023.12.18
scipy==1.11.4
ase==3.22.1

Note: The exact versions are specified in requirements.txt and will be installed automatically.

Usage

Import the desired sub-package module and utilize its classes and functions in your Python scripts:

from trajectory_tools.loaders import XYZStructureLoader

Contributing

Please refer to CONTRIBUTING.md for guidelines on contributing to this project.

License

The code is available under the terms of the license specified in LICENCE.md.