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AtomsBase

A Julian abstract interface for atomic structures.

https://github.com/juliamolsim/atomsbase.jl

Science Score: 54.0%

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
  • ✓
    Committers with academic emails
    1 of 8 committers (12.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A Julian abstract interface for atomic structures.

Basic Info
Statistics
  • Stars: 89
  • Watchers: 12
  • Forks: 21
  • Open Issues: 33
  • Releases: 15
Created over 4 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

AtomsBase

A Julian abstract interface for atomic structures.

Stable Dev Build Status Coverage

AtomsBase is an abstract interface for representation of atomic geometries in Julia. It aims to be a lightweight means of facilitating interoperability between various tools including, e.g.,

  • Simulation engines, e.g. molecular dynamics, geometry optimization, etc
  • Computing chemical or mechanical properties, e.g., via DFT, or interatomic potentials,
  • Integration with third party-libraries
  • I/O with standard file formats (.cif, .xyz, ...)
  • automatic differentiation and machine learning systems
  • numerical tools: sampling, integration schemes, etc.
  • visualization (e.g. plot recipes)

While AtomsBase focusses on representation of atomic systems, the sister package AtomsCalculators provides a general interface to compute properties of such systems.

Currently, the design philosophy is to be as lightweight as possible with a small set of required function dispatches to make adopting the interface easy. We also provide prototype implementations that we envision to be broadly applicable. If features beyond these are required we encourage developers to open PRs or provide their own implementations. For more on how to use the package, see the documentation.

Packages using AtomsBase

The following (not all yet-registered) packages currently make use of AtomsBase: * ACEpotentials * ASEPotential * ASEconvert : integration with the Atomistic Simulation Environment * AtomIO: I/O for atomic structures, also wraps some ASE functionality * Atomistic: integrated workflow for MD simulations, part of CESMIX * AutoBZCore.jl: Brillouin-zone integration * BFPIS * ChemistryFeaturization: Interface for featurization of atomic structures for input into machine learning models, part of Chemellia * DFTK: density functional theory simulations * EmpiricalPotentials * ExtXYZ: Parser for extended XYZ files * InteratomicPotentials: implementations of a variety of interatomic potentials, also part of CESMIX * Molly: molecular dynamics simulations * Xtals: I/O and structure representation for crystals

Owner

  • Name: Molecular Simulation in Julia
  • Login: JuliaMolSim
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Herbst"
  given-names: "Michael"
  orcid: "https://orcid.org/0000-0003-0378-7921"
- family-names: "Kurchin"
  given-names: "Rachel"
  orcid: "https://orcid.org/0000-0002-2147-4809"
title: "AtomsBase.jl"
version: 0.2.5
date-released: 2023-01-03
repository-code: "https://github.com/JuliaMolSim/AtomsBase.jl"
url: "https://juliamolsim.github.io/AtomsBase.jl/stable/"
license: MIT

GitHub Events

Total
  • Create event: 7
  • Commit comment event: 14
  • Release event: 2
  • Issues event: 9
  • Watch event: 5
  • Delete event: 10
  • Issue comment event: 64
  • Push event: 55
  • Pull request review event: 20
  • Pull request review comment event: 16
  • Pull request event: 21
  • Fork event: 3
Last Year
  • Create event: 7
  • Commit comment event: 14
  • Release event: 2
  • Issues event: 9
  • Watch event: 5
  • Delete event: 10
  • Issue comment event: 64
  • Push event: 55
  • Pull request review event: 20
  • Pull request review comment event: 16
  • Pull request event: 21
  • Fork event: 3

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 122
  • Total Committers: 8
  • Avg Commits per committer: 15.25
  • Development Distribution Score (DDS): 0.41
Top Committers
Name Email Commits
Rachel Kurchin r****n@c****u 72
Michael F. Herbst i****o@m****m 27
Rashid Rafeek r****k@g****m 11
Joe Greener j****r@h****k 5
Grigory Starkov 3****q@u****m 4
Jeff 1****n@u****m 1
Jan Habscheid 1****b@u****m 1
chemicalfiend t****1@g****m 1
Committer Domains (Top 20 + Academic)
hotmail.co.uk: 1 michael-herbst.com: 1 cmu.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 61
  • Total pull requests: 75
  • Average time to close issues: 4 months
  • Average time to close pull requests: 11 days
  • Total issue authors: 16
  • Total pull request authors: 18
  • Average comments per issue: 7.85
  • Average comments per pull request: 3.04
  • Merged pull requests: 58
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 12
  • Pull requests: 16
  • Average time to close issues: 15 days
  • Average time to close pull requests: 16 days
  • Issue authors: 6
  • Pull request authors: 6
  • Average comments per issue: 2.17
  • Average comments per pull request: 3.19
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • rkurchin (21)
  • cortner (14)
  • mfherbst (6)
  • Gregstrq (4)
  • ejmeitz (3)
  • rashidrafeek (3)
  • tjjarvinen (2)
  • jameskermode (1)
  • stefanbringuier (1)
  • singularitti (1)
  • lxvm (1)
  • Alexsp32 (1)
  • jgreener64 (1)
  • chemicalfiend (1)
  • JuliaTagBot (1)
Pull Request Authors
  • mfherbst (31)
  • cortner (14)
  • rkurchin (11)
  • dependabot[bot] (9)
  • rashidrafeek (5)
  • jgreener64 (4)
  • JanHab (3)
  • tjjarvinen (3)
  • ejmeitz (2)
  • joachimbrand (2)
  • jamesthesnake (2)
  • jty-computation (1)
  • DhairyaLGandhi (1)
  • Liozou (1)
  • Gregstrq (1)
Top Labels
Issue Labels
question (15) enhancement (3) documentation (2) bug (1)
Pull Request Labels
dependencies (9) bug (1) github_actions (1)

Packages

  • Total packages: 2
  • Total downloads:
    • julia 840 total
  • Total dependent packages: 24
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 26
juliahub.com: AtomsBase

A Julian abstract interface for atomic structures.

  • Versions: 18
  • Dependent Packages: 24
  • Dependent Repositories: 0
  • Downloads: 832 Total
Rankings
Dependent packages count: 6.4%
Average: 9.8%
Dependent repos count: 9.9%
Stargazers count: 11.0%
Forks count: 11.7%
Last synced: 7 months ago
juliahub.com: AtomsBaseTesting

A Julian abstract interface for atomic structures.

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 8 Total
Rankings
Dependent repos count: 9.9%
Stargazers count: 11.0%
Forks count: 11.3%
Average: 17.9%
Dependent packages count: 39.2%
Last synced: 7 months ago

Dependencies

.github/workflows/CI.yml actions
  • actions/cache v1 composite
  • actions/checkout v2 composite
  • codecov/codecov-action v1 composite
  • julia-actions/julia-buildpkg v1 composite
  • julia-actions/julia-docdeploy v1 composite
  • julia-actions/julia-processcoverage v1 composite
  • julia-actions/julia-runtest v1 composite
  • julia-actions/setup-julia v1 composite
.github/workflows/TagBot.yml actions
  • JuliaRegistries/TagBot v1 composite