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structuretoolkit

build, analyse and visualise atomistic structures for materials science

https://github.com/pyiron/structuretoolkit

Science Score: 44.0%

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.6%) to scientific vocabulary

Keywords

ase atomistic materials-science pyiron
Last synced: 6 months ago · JSON representation ·

Repository

build, analyse and visualise atomistic structures for materials science

Basic Info
  • Host: GitHub
  • Owner: pyiron
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 46.6 MB
Statistics
  • Stars: 8
  • Watchers: 5
  • Forks: 1
  • Open Issues: 20
  • Releases: 33
Topics
ase atomistic materials-science pyiron
Created almost 3 years ago · Last pushed 6 months ago
Metadata Files
Readme License Code of conduct Citation Codeowners

README.md

structuretoolkit

Pipeline codecov

Originally developed as part of the pyiron_atomistics module the structuretoolkit was release as standalone library for analysing, building and visualising atomistic structures. Internally it uses the ase.atoms.Atoms class to represent atomistic structures in python. The structuretoolkit is integrated inside pyiron_atomistics.

Disclaimer

The structuretoolkit is currently under development.

Example

```python import structuretoolkit as stk from ase.build import bulk

structure = bulk("Al", cubic=True) stk.analyse.getadaptivecna_descriptors(structure) stk.plot3d(structure) ```

Features

Analysis

  • stk.analyse.get_neighbors()
  • stk.analyse.get_neighborhood()
  • stk.analyse.get_equivalent_atoms()
  • stk.analyse.get_steinhardt_parameters()
  • stk.analyse.get_centro_symmetry_descriptors()
  • stk.analyse.get_diamond_structure_descriptors()
  • stk.analyse.get_adaptive_cna_descriptors()
  • stk.analyse.get_voronoi_volumes()
  • stk.analyse.find_solids()
  • stk.analyse.get_mean_positions()
  • stk.analyse.get_average_of_unique_labels()
  • stk.analyse.get_interstitials()
  • stk.analyse.get_layers()
  • stk.analyse.get_voronoi_vertices()
  • stk.analyse.get_voronoi_neighbors()
  • stk.analyse.get_delaunay_neighbors()
  • stk.analyse.get_cluster_positions()
  • stk.analyse.get_strain()

Build

  • stk.build.get_grainboundary_info()
  • stk.build.grainboundary()
  • stk.build.high_index_surface()
  • stk.build.get_high_index_surface_info()
  • stk.build.sqs_structures()
  • stk.build.pyxtal()
  • stk.build.B2()
  • stk.build.C14()
  • stk.build.C15()
  • stk.build.C36()
  • stk.build.D03()

Visualize

  • stk.visualize.plot3d()

Common

  • stk.common.ase_to_pymatgen()
  • stk.common.pymatgen_to_ase()
  • stk.common.pymatgen_read_from_file()
  • stk.common.ase_to_pyscal()
  • stk.common.apply_strain()
  • stk.common.center_coordinates_in_unit_cell()
  • stk.common.get_extended_positions()
  • stk.common.get_vertical_length()
  • stk.common.get_wrapped_coordinates()
  • stk.common.select_index()

Owner

  • Name: pyiron
  • Login: pyiron
  • Kind: organization

pyiron - an integrated development environment (IDE) for materials science.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors: 
- family-names: "Janssen"
  given-names: "Jan"
  orcid: "https://orcid.org/0000-0001-9948-7119"
- family-names: "Surendralal"
  given-names: "Sudarsan"
  orcid: "https://orcid.org/0000-0003-0362-7549"
- family-names: "Lysogorskiy"
  given-names: "Yury"
  orcid: "https://orcid.org/000-0003-4617-3188"
- family-names: "Todorova"
  given-names: "Mira"
  orcid: "https://orcid.org/0000-0002-8053-9350"
- family-names: "Hickel"
  given-names: "Tilmann"
  orcid: "https://orcid.org/0000-0003-0698-4891"
- family-names: "Drautz"
  given-names: "Ralf"
  orcid: "https://orcid.org/0000-0001-7101-8804"
- family-names: "Neugebauer"
  given-names: "Joerg"
  orcid: "https://orcid.org/0000-0002-7903-2472"
title: "pyiron: An integrated development environment for computational materials science"
version: 0.1.8
doi: 10.1016/j.commatsci.2018.07.043
date-released: 2019-06-01
license: "BSD-3-Clause"
url: "http://github.com/pyiron"

GitHub Events

Total
  • Release event: 4
  • Delete event: 102
  • Issue comment event: 177
  • Push event: 232
  • Pull request review comment event: 16
  • Pull request review event: 14
  • Pull request event: 212
  • Create event: 101
Last Year
  • Release event: 4
  • Delete event: 102
  • Issue comment event: 177
  • Push event: 232
  • Pull request review comment event: 16
  • Pull request review event: 14
  • Pull request event: 212
  • Create event: 101

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 21
  • Total pull requests: 520
  • Average time to close issues: 10 days
  • Average time to close pull requests: 7 days
  • Total issue authors: 7
  • Total pull request authors: 11
  • Average comments per issue: 1.76
  • Average comments per pull request: 1.18
  • Merged pull requests: 423
  • Bot issues: 0
  • Bot pull requests: 332
Past Year
  • Issues: 0
  • Pull requests: 185
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 0
  • Pull request authors: 5
  • Average comments per issue: 0
  • Average comments per pull request: 1.55
  • Merged pull requests: 150
  • Bot issues: 0
  • Bot pull requests: 161
View more stats
Top Authors
Issue Authors
  • jan-janssen (10)
  • ahmedabdelkawy (3)
  • mbruns91 (3)
  • samwaseda (2)
  • dependabot[bot] (2)
  • pmrv (1)
  • liamhuber (1)
  • superstar54 (1)
Pull Request Authors
  • dependabot[bot] (275)
  • jan-janssen (148)
  • pre-commit-ci[bot] (84)
  • samwaseda (22)
  • pmrv (7)
  • ligerzero-ai (3)
  • srmnitc (2)
  • liamhuber (2)
  • pyiron-runner (1)
  • niklassiemer (1)
  • ahmedabdelkawy (1)
Top Labels
Issue Labels
bug (3) dependencies (2) patch (2) format_black (1) enhancement (1)
Pull Request Labels
dependencies (275) patch (79) minor (76) python (26) format_black (22) major (18) enhancement (7) bug (3)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 2,329 last-month
  • Total dependent packages: 3
  • Total dependent repositories: 0
  • Total versions: 34
  • Total maintainers: 2
pypi.org: structuretoolkit

build, analyse and visualise atomistic structures for materials science

  • Homepage: https://github.com/pyiron/structuretoolkit
  • Documentation: https://github.com/pyiron/structuretoolkit
  • License: BSD 3-Clause License Copyright (c) 2018, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  • Latest release: 0.0.34
    published 6 months ago
  • Versions: 34
  • Dependent Packages: 3
  • Dependent Repositories: 0
  • Downloads: 2,329 Last month
  • Docker Downloads: 0
Rankings
Dependent packages count: 7.0%
Average: 18.7%
Dependent repos count: 30.5%
Maintainers (2)
jan-janssen pyiron
Last synced: 6 months ago

Dependencies

.github/workflows/black.yml actions
  • actions/checkout v2 composite
  • psf/black stable composite
.github/workflows/deploy.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish master composite
.github/workflows/mini.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/pypicheck.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/unittests.yml actions
  • actions/checkout v2 composite
  • conda-incubator/setup-miniconda v2 composite
setup.py pypi
  • ase ==3.22.1
  • matplotlib ==3.7.1
  • numpy ==1.24.3
  • scipy ==1.10.1
.ci_support/environment.yml pypi