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Open Source Science

pylj

Teaching Utility for Classical Atomistic Simulation.

https://github.com/arm61/pylj

Science Score: 64.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    7 of 12 committers (58.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.6%) to scientific vocabulary

Keywords

chemistry computational-chemistry computational-physics education jupyter-notebook molecular-dynamics monte-carlo physics

Keywords from Contributors

bayesian-inference bayesian-statistics fitting markov-chain-monte-carlo nested-sampling
Last synced: 6 months ago · JSON representation ·

Repository

Teaching Utility for Classical Atomistic Simulation.

Basic Info
Statistics
  • Stars: 30
  • Watchers: 4
  • Forks: 21
  • Open Issues: 10
  • Releases: 26
Topics
chemistry computational-chemistry computational-physics education jupyter-notebook molecular-dynamics monte-carlo physics
Created about 8 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Code of conduct Citation Zenodo

README.md

Visit the pylj webpage for more information about pylj.

To build from source:

```python

pip install -r requirements.txt

python setup.py build

python setup.py install

python setup.py test

``` Check out our publication in the Journal of Open Source Education to find out more about pylj.

Be aware! pylj runs within a Jupyter notebook, and therefore requires this to run. We advise installing anaconda python as this includes many required libraries as well as the Jupyter notebooks framework.

If you need any help using pylj contact arm61 in the pylj/HELP gitter chatroom.

Check out some examples of how pylj can be used in undergraduate teaching exercises.

Badges

JOSE DOI status
Latest Release PyPi version
DOI
Documentation Documentation Status
License License MIT
Build Status Build Status
Coverage Status
Gitter Gitter chat

Owner

  • Name: Andrew McCluskey
  • Login: arm61
  • Kind: user
  • Location: Copenhagen
  • Company: European Spallation Source

instrument data scientist @essneutron (he/him)

Citation (CITATION.cff) 

cff-version: 1.0.3
message: If you use this software, please cite it as below.
authors:
  - family-names: McCluskey
    given-names: Andrew R.
    orcid: 0000-0003-3381-5911
  - family-names: Symington
    given-names: Adam R.
    orcid: 0000-0001-6059-497X
  - family-names: Morgan
    given-names: Benjamin J.
    orcid: 0000-0002-3056-8233
  - family-names: Edler
    given-names: Karen J.
    orcid: 0000-0001-5822-0127
  - family-names: Parker
    given-names: Stephen C.
    orcid: 0000-0003-3804-0975
title: pylj
version: 1.2.0
doi: 10.5281/zenodo.2170746
date-released: 2018-12-10
references:
  - type: article
    journal: "Journal of Open Source Education"
    doi: 10.21105/jose.00019
    authors:
      - family-names: McCluskey
        given-names: Andrew R.
        orcid: 0000-0003-3381-5911
      - family-names: Morgan
        given-names: Benjamin J.
        orcid: 0000-0002-3056-8233
      - family-names: Edler
        given-names: Karen J.
        orcid: 0000-0001-5822-0127
      - family-names: Parker
        given-names: Stephen C.
        orcid: 0000-0003-3804-0975
    title: "pylj: A teaching tool for classical atomistic simulation"

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 496
  • Total Committers: 12
  • Avg Commits per committer: 41.333
  • Development Distribution Score (DDS): 0.26
Past Year
  • Commits: 76
  • Committers: 5
  • Avg Commits per committer: 15.2
  • Development Distribution Score (DDS): 0.579
Top Committers
Name Email Commits
arm61 a****1@b****k 367
maxdolan m****n@M****l 32
Max Dolan 1****n 31
symmy596 a****4@b****k 20
sansona j****n@g****m 11
Andrew McCluskey a****y@d****k 10
Andrew McCluskey a****w@m****t 8
maxdolan m****n@e****k 8
Andrew McCluskey a****y@b****k 4
andrew a****w@a****e 2
Fabian Wermelinger f****w@m****h 2
maxdolan m****n@e****k 1
Committer Domains (Top 20 + Academic)
bath.ac.uk: 3 eduroam-141-105.nomadic.bris.ac.uk: 1 mavt.ethz.ch: 1 andrews-air.home: 1 eduroam-145-236.nomadic.bris.ac.uk: 1 mccluskey.scot: 1 diamond.ac.uk: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 30
  • Total pull requests: 43
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 1 day
  • Total issue authors: 7
  • Total pull request authors: 6
  • Average comments per issue: 1.6
  • Average comments per pull request: 1.49
  • Merged pull requests: 40
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 13
  • Average time to close issues: about 7 hours
  • Average time to close pull requests: 2 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.31
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • arm61 (17)
  • shivupa (7)
  • Mi-chael (2)
  • markperri (1)
  • markgalassi (1)
  • TJFord (1)
  • sansona (1)
Pull Request Authors
  • arm61 (24)
  • maximillian-dolan (21)
  • sansona (3)
  • ctudpython (2)
  • symmy596 (1)
  • fab4100 (1)
Top Labels
Issue Labels
good first issue (4) help wanted (3) enhancement (1) documentation (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 266 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 62
  • Total maintainers: 1
pypi.org: pylj

Simple teaching tool for classical MD simulation

  • Versions: 62
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 266 Last month
  • Docker Downloads: 0
Rankings
Docker downloads count: 2.4%
Dependent packages count: 10.0%
Average: 12.3%
Downloads: 15.0%
Dependent repos count: 21.7%
Maintainers (1)
arm61
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • coverage *
  • coveralls *
  • cython *
  • ipympl *
  • jupyter *
  • matplotlib *
  • numba *
  • numpy >=1.16
docker/Dockerfile docker
  • ubuntu 20.04 build
setup.py pypi
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • paambaati/codeclimate-action v2.7.5 composite
.github/workflows/release.yml actions
  • actions/checkout master composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish release/v1 composite