pyiron_atomistics

pyiron_atomistics - an integrated development environment (IDE) for atomistic simulation in computational materials science.

https://github.com/pyiron/pyiron_atomistics

Science Score: 77.0%

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
Found 2 DOI reference(s) in README
✓
Academic publication links
Links to: sciencedirect.com
✓
Committers with academic emails
5 of 68 committers (7.4%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (15.4%) to scientific vocabulary

Keywords

dft gaussian lammps pyiron python vasp

Keywords from Contributors

ab-initio molecular-dynamics ase development-environment hdf5 ide workflow-automation workflow-engine workflow-management thermodynamic-calculations

Last synced: 4 months ago · JSON representation ·

Repository

pyiron_atomistics - an integrated development environment (IDE) for atomistic simulation in computational materials science.

Basic Info

Host: GitHub
Owner: pyiron
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://pyiron-atomistics.readthedocs.io
Size: 55.7 MB

Statistics

Stars: 46
Watchers: 8
Forks: 18
Open Issues: 146
Releases: 140

Topics

dft gaussian lammps pyiron python vasp

Created about 5 years ago · Last pushed 4 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

pyiron_atomistics

Anaconda Release

pyiron - an integrated development environment (IDE) for computational materials science. It combines several tools in a common platform:

Atomic structure objects – compatible to the Atomic Simulation Environment (ASE).
Atomistic simulation codes – like LAMMPS and VASP.
Feedback Loops – to construct dynamic simulation life cycles.
Hierarchical data management – interfacing with storage resources like SQL and HDF5.
Integrated visualization – based on NGLview.
Interactive simulation protocols - based on Jupyter notebooks.
Object-oriented job management – for scaling complex simulation protocols from single jobs to high-throughput simulations.

Screenshot of pyiron_atomistics running inside jupyterlab.

pyiron (called pyron) is developed in the Computational Materials Design department of Joerg Neugebauer at the Max Planck Institut für Eisenforschung (Max Planck Institute for iron research). While its original focus was to provide a framework to develop and run complex simulation protocols as needed for ab initio thermodynamics it quickly evolved into a versatile tool to manage a wide variety of simulation tasks. In 2016 the Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) joined the development of the framework with a specific focus on high throughput applications. In 2018 pyiron was released as open-source project.

pyiron_atomistics: This is the documentation page for the basic infrastructure moduls of pyiron. If you're new to pyiron and want to get an overview head over to pyiron. If you're looking for the API docs of pyiron_base check pyiron_base.

Explore pyiron_atomistics

We provide various options to install, explore and run pyiron_atomistics:

Workstation Installation (recommeded): for Windows, Linux or Mac OS X workstations (interface for local VASP executable, support for the latest jupyterlab based GUI)
Mybinder.org (beta): test pyiron directly in your browser (no VASP license, no visualization, only temporary data storage)
Docker (for demonstration): requires Docker installation (no VASP license, only temporary data storage)

Join the development

Please contact us if you are interested in using pyiron:

to interface your simulation code or method
implementing high-throughput approaches based on atomistic codes
to learn more about method development and Big Data in material science.

Please also check out the pyiron_atomistics contributing guidelines.

Citing

If you use pyiron in your research, please consider citing the following work:

@article{pyiron-paper, title = {pyiron: An integrated development environment for computational materials science}, journal = {Computational Materials Science}, volume = {163}, pages = {24 - 36}, year = {2019}, issn = {0927-0256}, doi = {https://doi.org/10.1016/j.commatsci.2018.07.043}, url = {http://www.sciencedirect.com/science/article/pii/S0927025618304786}, author = {Jan Janssen and Sudarsan Surendralal and Yury Lysogorskiy and Mira Todorova and Tilmann Hickel and Ralf Drautz and Jörg Neugebauer}, keywords = {Modelling workflow, Integrated development environment, Complex simulation protocols}, }

Owner

Name: pyiron
Login: pyiron
Kind: organization

Website: http://pyiron.org
Twitter: pyiron
Repositories: 34
Profile: https://github.com/pyiron

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"

Committers

Last synced: over 2 years ago

All Time

Total Commits: 7,850
Total Committers: 68
Avg Commits per committer: 115.441
Development Distribution Score (DDS): 0.802

Past Year

Commits: 790
Committers: 27
Avg Commits per committer: 29.259
Development Distribution Score (DDS): 0.823

Top Committers

Name	Email	Commits
Jan Janssen	j**n@u**m	1,555
Jan Janßen	j**n@m**e	1,554
sudarsan1989	s**l@m**e	1,223
Sam Waseda	o**a@m**e	1,106
Marvin Poul	p**r@c**e	327
Liam Huber	l**r@g**m	305
pyiron-runner	p**n@m**e	223
Niklas Siemer	7**r@u**m	206
dependabot[bot]	4**]@u**m	164
Osamu Waseda	s**d@c**e	121
FeLoch	l**m@g**e	120
Marvin Poul	p**l@m**e	96
Osamu Waseda	w**a@m**e	96
Niklas Leimeroth	l**h@m**e	72
Sarath Menon	s**n@m**g	55
srmnitc	s**n@g**m	45
Christoph Freysoldt	f**t@m**e	44
Jan Janssen	j**n@o**m	44
Sam Dareska	3**a@u**m	36
dependabot-preview[bot]	2**]@u**m	35
Ahmed-Aslam	a**m@g**m	35
Felix	l**r@m**e	32
Sander Borgmans	s**s@u**e	30
Michael Ashton	a**n@m**e	28
Raynol Dsouza	d**a@m**e	27
Michael Ashton	a**n@c**l	23
Han Mai	h**i@m**e	23
skatnagallu	s**u@m**e	21
Jan Janssen	j**n@l**v	20
Ali Zendegani	z**i@u**m	13
and 38 more...

Committer Domains (Top 20 + Academic)

mpie.de: 17 gmx.de: 3 cmmc001.bc.rzg.mpg.de: 2 markuss-mbp.mpie.de: 1 ufl.edu: 1 greyhavensolutions.com: 1 rub.de: 1 codacy.com: 1 sarathmenon.me: 1 ymail.com: 1 cmmb31.fritz.box: 1 lanl.gov: 1 ugent.be: 1 mailbox.org: 1 mm.tu-darmstadt.de: 1 creshal.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 124
Total pull requests: 915
Average time to close issues: about 2 months
Average time to close pull requests: 10 days
Total issue authors: 37
Total pull request authors: 20
Average comments per issue: 4.2
Average comments per pull request: 1.68
Merged pull requests: 686
Bot issues: 2
Bot pull requests: 392

Past Year

Issues: 24
Pull requests: 196
Average time to close issues: 5 days
Average time to close pull requests: 3 days
Issue authors: 16
Pull request authors: 8
Average comments per issue: 2.38
Average comments per pull request: 1.12
Merged pull requests: 126
Bot issues: 2
Bot pull requests: 145

View more stats

Top Authors

Issue Authors

samwaseda (17)
lfzhu-phys (13)
Leimeroth (10)
liamhuber (10)
jyang2009 (8)
jan-janssen (7)
pmrv (7)
usaikia (4)
ahmedabdelkawy (4)
ligerzero-ai (4)
skatnagallu (3)
freyso (3)
yuyuanjingxuan (3)
RhettZhou (3)
sinazadeh (3)

Pull Request Authors

dependabot[bot] (339)
jan-janssen (301)
pmrv (78)
samwaseda (66)
pre-commit-ci[bot] (53)
liamhuber (19)
skatnagallu (13)
niklassiemer (12)
ligerzero-ai (6)
Leimeroth (6)
srmnitc (5)
ahmedabdelkawy (4)
jyang2009 (3)
freyso (2)
raynol-dsouza (2)

Top Labels

Issue Labels

bug (62) enhancement (13) question (6) code_smell (3) good first issue (2) documentation (2) help wanted (1) major (1) dependencies (1) minor (1)

Pull Request Labels

dependencies (341) format_black (114) patch (101) integration (66) minor (53) bug (50) python (35) enhancement (28) stale (19) major (15) code_smell (5) help wanted (3) documentation (1)

Packages

Total packages: 2
Total downloads:
- pypi 1,926 last-month

Total dependent packages: 13
(may contain duplicates)
Total dependent repositories: 22
(may contain duplicates)
Total versions: 209
Total maintainers: 5

pypi.org: pyiron-atomistics

An interface to atomistic simulation codes including but not limited to GPAW, LAMMPS, S/Phi/nX and VASP.

Homepage: https://pyiron.org
Documentation: https://pyiron.readthedocs.io
License: BSD 3-Clause License Copyright (c) 2021, 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: 0.7.16
published 5 months ago

Versions: 149
Dependent Packages: 8
Dependent Repositories: 1
Downloads: 1,926 Last month
Docker Downloads: 0

Rankings

Dependent packages count: 1.1%

Docker downloads count: 1.9%

Average: 9.5%

Downloads: 9.8%

Forks count: 10.5%

Stargazers count: 11.9%

Dependent repos count: 21.6%

Maintainers (5)

jan-janssen pyiron niklassiemer srmnitc mpmpie

Last synced: 4 months ago

conda-forge.org: pyiron_atomistics

pyiron was initially developed in the Computational Materials Design department of Joerg Neugebauer at the Max Planck Insitut für Eisenforschung (Max Planck Insitute for iron research) as a framework for ab initio thermodynamics. In collaboration with the Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) the framework was recently extended for high throughput applications resulting in the opensource release of pyiron.

Homepage: https://github.com/pyiron/pyiron_atomistics
License: BSD-3-Clause
Latest release: 0.2.59
published about 3 years ago

Versions: 60
Dependent Packages: 5
Dependent Repositories: 21

Rankings

Dependent repos count: 7.9%

Dependent packages count: 10.4%

Average: 27.5%

Forks count: 43.8%

Stargazers count: 48.0%

Last synced: 4 months ago

Dependencies

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.ci_support/environment.yml conda

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matplotlib-base 3.6.3.*
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pandas 1.5.3.*
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pint 0.20.1.*
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binder/environment.yml conda

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pyiron
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pyiron_atomistics >=0.2.0
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setup.py pypi

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defusedxml ==0.7.1
h5py ==3.8.0
matplotlib ==3.6.3
mendeleev ==0.12.1
mp-api ==0.30.9
numpy ==1.24.2
pandas ==1.5.3
phonopy ==2.17.1
pint ==0.20.1
pyiron_base ==0.5.31
pymatgen ==2022.11.7
scikit-learn ==1.2.1
scipy ==1.10.0
seekpath ==2.0.1
spglib ==2.0.2

pyiron_atomistics

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

pyiron_atomistics

Explore pyiron_atomistics

Join the development

Citing

Owner

Citation (CITATION.cff)

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: pyiron-atomistics

Rankings

Maintainers (5)

conda-forge.org: pyiron_atomistics

Rankings

Dependencies