mdapy 0.7.9

A simple and fast python library to handle the data generated from molecular dynamics simulations

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

• python (3.7-3.10)

• taichi>=1.4.0

• numpy

• scipy

• pandas

• tqdm

• matplotlib

Optional Dependencies

• SciencePlots (Optional, for plotting results)

• pyfftw (Optional, for fast FFT)

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

Release Notes

V0.7.9

• Fix bug of create_polycrystalline module in Linux.

V0.7.8

• Update TaiChi version to 1.4.0.

• Set SciencePlots as a optional package.

• Fix bug in create_polycrystalline.