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mdproptools

A Python package for LAMMPS analysis tools

https://github.com/molmd/mdproptools

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: nature.com
  • ✓
    Committers with academic emails
    3 of 4 committers (75.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.7%) to scientific vocabulary

Keywords

analysis dynamics ensemble lammps materials-science molecular-dynamics properties python structure
Last synced: 6 months ago · JSON representation

Repository

A Python package for LAMMPS analysis tools

Basic Info
  • Host: GitHub
  • Owner: molmd
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 68.2 MB
Statistics
  • Stars: 11
  • Watchers: 3
  • Forks: 2
  • Open Issues: 0
  • Releases: 3
Topics
analysis dynamics ensemble lammps materials-science molecular-dynamics properties python structure
Created over 6 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

MDPropTools: MD Property Tools

codecov PyPI - Python version PyPI version GitHub release GitHub commit activity

MDPropTools is a Python package for computing structural and dynamical properties from LAMMPS trajectory and output files.

The supported properties are:

| Category | Property | | ---------- | ---------------------------------------------- | | Structural | Radial distribution function (RDF) | | | Coordination number | | | Cluster analysis | | | Hydration number | | | Number density | | Dynamical | Mean square displacement (MSD) | | | Diffusion coefficient | | | Ionic conductivity (using Green-Kubo relation) | | | Viscosity (using Green-Kubo relation) | | | Residence time |

The release history and changelog can be found in the changelog.

Installation

MDPropTools can be installed using pip:

pip install mdproptools

Or by cloning the repository and running the setup script:

git clone https://github.com/molmd/mdproptools.git cd mdproptools pip install -r requirements.txt pip install .

If you are planning to contribute to the development of MDPropTools and need access to development tools and dependencies, you can install the package with the dev extra:

pip install ".[dev]"

[!IMPORTANT]
MDPropTools has been tested using Python 3.10. It is recommended to use this version.

Usage

For examples on how to use MDPropTools, please see the Jupyter notebooks in the examples directory.

Contributing

All bug reports, suggestions, feedback, and pull requests occurs in the MDPropTools GitHub repository. Some contribution guidelines can be found in the contributing notes.

Citation

If you use MDPropTools in your research, please consider citing the following paper:

License Information

MDPropTools is a free, open-source software package (distributed under the MIT license).

Owner

  • Name: MolMD Research Group @ SBU
  • Login: molmd
  • Kind: organization
  • Email: navnidhi.rajput@stonybrook.edu
  • Location: Stony Brook

GitHub Events

Total
  • Release event: 2
  • Push event: 18
  • Create event: 2
Last Year
  • Release event: 2
  • Push event: 18
  • Create event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 149
  • Total Committers: 4
  • Avg Commits per committer: 37.25
  • Development Distribution Score (DDS): 0.081
Past Year
  • Commits: 20
  • Committers: 2
  • Avg Commits per committer: 10.0
  • Development Distribution Score (DDS): 0.2
Top Committers
Name Email Commits
rashatwi a****r@h****u 137
mmbliss m****s@s****u 5
mmbliss m****1@t****u 5
Matt Bliss m****1@g****m 2
Committer Domains (Top 20 + Academic)
tufts.edu: 1 stonybrook.edu: 1 husky.neu.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • mmbliss (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 45 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
pypi.org: mdproptools

mdproptools contains MD analysis tools

  • Versions: 4
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 45 Last month
Rankings
Dependent packages count: 4.8%
Stargazers count: 18.5%
Average: 20.0%
Dependent repos count: 21.6%
Forks count: 22.7%
Downloads: 32.7%
Maintainers (1)
rashatwi
Last synced: 6 months ago

Dependencies

setup.py pypi
  • doepy *
  • llvmlite *
  • matplotlib *
  • numba *
  • numpy *
  • pandas *
  • scipy *
  • seaborn *
  • statsmodels *
pyproject.toml pypi