Granules

Granules is a DataFrame-based Python package to manage and analyze Molecular Dynamics simulations. Granules is still under development and support both CPU and GPU backends.

Objectives

Library to manage and analyze molecular dynamics simulations.
Supports noth NAMD2 and LAMMPS as simulation backend.
Provides both CPU and GPU backends for additional acceleration.

Installation

Build Conda Environment - Single Step (GPU support)

git clone https://github.com/jordancaraballo/xrasterlib.git
cd xrasterlib; conda env create -f requirements/environment.yml;
conda activate xrasterlib
python setup.py install

Build Conda Environment - Multi Step

git clone https://github.com/jordancaraballo/xrasterlib.git
cd xrasterlib; conda create --name xrasterlib;
conda activate xrasterlib
conda install -c anaconda pip 
conda install -c anaconda cudatoolkit=10.1 cudnn # if GPU available
pip install --upgrade -r requirements/requirements.txt
python setup.py install

Pip only

git clone https://github.com/jordancaraballo/xrasterlib.git
pip install -r requirements/requirements.txt
python setup.py install

Note: PIP installations do not include CUDA libraries for GPU support. Make sure NVIDIA libraries are installed locally in the system if not using conda.

Getting Started

├── archives              <- Legacy code stored to historical reference
├── docs                  <- Default documentation for working with this project
├── images                <- Store project images
├── notebooks             <- Jupyter notebooks
├── examples              <- Examples for utilizing the library
├── requirements          <- Requirements for installing the dependencies
├── scripts               <- Utility scripts for analysis
├── granules              <- Library source code
├── README.md             <- The top-level README for developers using this project
├── CHANGELOG.md          <- Releases documentation
├── LICENSE               <- License documentation
└── setup.py              <- Script to install library

jordancaraballo / granules