A simple and fast python library to handle the data generated from molecular dynamics simulations
Project description
mdapy : Molecular Dynamics Analysis with Python
Overview
The mdapy is a python library providing a set of simple, flexible and powerful tools to analyze the atomic trajectories generated from Molecular Dynamics (MD) simulations. Benefit by the TaiChi project, we can effectively accelerate the pure python code close to those written in C++. Moreover, mdapy is highly parallelized to make full use of resources of both multicore CPU and GPU. mdapy can directly handle the DUMP and DATA format in LAMMPS. All data in mdapy is stored in NDARRAY format in Numpy, enabling integration with the scientific ecosystem in python and corporation with other post-progressing codes, such as OVITO and freud.
Resources
Homepage: https://github.com/mushroomfire/mdapy
Documentation: https://mdapy.readthedocs.io/
Source Code: https://github.com/mushroomfire/mdapy
Issue Tracker: https://github.com/mushroomfire/mdapy/issues
Dependencies
Installation
Install from pip (recommended).
pip install mdapy
Install from source code.
You should install pybind11 and have a C++ compilation environment.
pip install pybind11
Download source code
git clone https://github.com/mushroomfire/mdapy.git cd mdapy python setup.py install
Usage
import mdapy as mp
mp.init('cpu') # use cpu, mp.init('gpu') will use gpu to compute.
system = mp.System('./example/CoCuFeNiPd-4M.dump') # read dump file to generate a system class
system.cal_centro_symmetry_parameter() # calculate the centrosymmetry parameters
system.cal_atomic_entropy() # calculate the atomic entropy
system.write_dump() # save results to a new dump file
Project details
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