pyiron

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

https://github.com/pyiron/pyiron

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
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
Links to: sciencedirect.com
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Committers with academic emails
5 of 56 committers (8.9%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary

Keywords

ab-initio ase development-environment dft hdf5 ide lammps molecular-dynamics pyiron python simulation vasp

Keywords from Contributors

workflow-automation workflow-engine workflow-management graph-generation multiprocessing slurm mpi4py mpi flux mesh

Last synced: 4 months ago · JSON representation ·

Repository

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

Basic Info

Host: GitHub
Owner: pyiron
License: bsd-3-clause
Language: Jupyter Notebook
Default Branch: main
Homepage: http://pyiron.org
Size: 45.1 MB

Statistics

Stars: 417
Watchers: 15
Forks: 54
Open Issues: 6
Releases: 14

Topics

ab-initio ase development-environment dft hdf5 ide lammps molecular-dynamics pyiron python simulation vasp

Created almost 8 years ago · Last pushed 4 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

README.rst

pyiron
======

.. image:: https://coveralls.io/repos/github/pyiron/pyiron/badge.svg?branch=main
    :target: https://coveralls.io/github/pyiron/pyiron?branch=main
    :alt: Coverage Status

.. image:: https://api.codacy.com/project/badge/Grade/c513254f10004df5a1f5c76425c6584b
    :target: https://app.codacy.com/app/pyiron-runner/pyiron?utm_source=github.com&utm_medium=referral&utm_content=pyiron/pyiron&utm_campaign=Badge_Grade_Settings
    :alt: Codacy Badge

.. image:: https://anaconda.org/conda-forge/pyiron/badges/latest_release_date.svg
    :target: https://anaconda.org/conda-forge/pyiron/
    :alt: Release_Date

.. image:: https://github.com/pyiron/pyiron/workflows/Python%20package/badge.svg
    :target: https://github.com/pyiron//pyiron/actions
    :alt: Build Status

.. image:: https://anaconda.org/conda-forge/pyiron/badges/downloads.svg
    :target: https://anaconda.org/conda-forge/pyiron/
    :alt: Downloads

.. image:: https://readthedocs.org/projects/pyiron/badge/?version=latest
    :target: https://pyiron.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status


.. image:: docs/_static/screenshot.png
    :align: center
    :alt: Screenshot of pyiron running inside jupyterlab.


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.

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.
See the `Documentation `_ page for more details.

.. note::
   **pyiron**: This is the documentation page for the pyiron meta package, that combines the other packages in a common
   interface.  The API documentation for `pyiron_base `_ and
   `pyiron_atomistics `_ are available as separate pages.


Installation
------------
You can test pyiron on `Mybinder.org (beta) `_.
For a local installation we recommend to install pyiron inside an `anaconda `_  environment::

    conda install -c conda-forge pyiron


After the installation of pyiron you need to configure pyiron. The default configuration can be generated automatically. Start a new Python session and import pyiron::

   > import pyiron
   > pyiron.install()
   >>> It appears that pyiron is not yet configured, do you want to create a default start configuration (recommended: yes). [yes/no]:
   > yes
   > exit()


See the `Documentation-Installation `_ page for more details.


Example
-------
After the successful configuration you can start your first pyiron calculation. Navigate to the the projects directory and start a jupyter notebook or jupyter lab session correspondingly::

    cd ~/pyiron/projects
    jupyter notebook

Open a new jupyter notebook and inside the notebook you can now validate your pyiron calculation by creating a test project, setting up an initial structure of bcc Fe and visualize it using NGLview::

    from pyiron import Project
    pr = Project('test')
    structure = pr.create_structure('Fe', 'bcc', 2.78)
    structure.plot3d()

Finally a first lammps calculation can be executed by::

    job = pr.create_job(job_type=pr.job_type.Lammps, job_name='lammpstestjob')
    job.structure = structure
    job.potential = job.list_potentials()[0]
    job.run()


Getting started:
----------------
Test pyiron with mybinder:

.. image:: https://mybinder.org/badge_logo.svg
     :target: https://mybinder.org/v2/gh/pyiron/pyiron/main
     :alt: mybinder


License and Acknowledgments
---------------------------
``pyiron`` is licensed under the BSD license.

If you use pyiron in your scientific work, `please consider citing `_ ::

  @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"

GitHub Events

Total

Issues event: 5
Watch event: 47
Delete event: 16
Issue comment event: 12
Push event: 43
Pull request event: 37
Fork event: 5
Create event: 13

Last Year

Issues event: 5
Watch event: 47
Delete event: 16
Issue comment event: 12
Push event: 43
Pull request event: 37
Fork event: 5
Create event: 13

Committers

Last synced: almost 2 years ago

All Time

Total Commits: 5,863
Total Committers: 56
Avg Commits per committer: 104.696
Development Distribution Score (DDS): 0.738

Past Year

Commits: 106
Committers: 11
Avg Commits per committer: 9.636
Development Distribution Score (DDS): 0.689

Top Committers

Name	Email	Commits
Jan Janßen	j**n@m**e	1,538
Jan Janssen	j****n	1,467
sudarsan1989	s**l@m**e	960
Sam Waseda	o**a@m**e	712
Liam Huber	l**r@g**m	199
Marvin Poul	p**r@c**e	127
Osamu Waseda	s**d@c**e	121
FeLoch	l**m@g**e	120
Osamu Waseda	w**a@m**e	95
Niklas Siemer	7****r	47
dependabot[bot]	4****]	43
Ahmed-Aslam	a**m@g**m	35
Han	h**i@m**e	33
Felix	l**r@m**e	32
pyiron-runner	p**n@m**e	31
Sander Borgmans	s**s@u**e	30
Jan Janssen	j**n@o**m	29
Michael Ashton	a**n@m**e	28
tnecnivkcots	8****s	23
Michael Ashton	a**n@c**l	23
Sam Waseda	3****a	15
Raynol Dsouza	d**a@m**e	13
Michael Ashton	a**n@c**x	12
Leimeroth	n**h@g**e	10
alaukik	s**3@g**m	10
dependabot-preview[bot]	2****]	9
Markus Peter Tautschnig	m**3@c**e	8
Han	6****i	8
Sudarsan Surendralal	s**l@g**m	7
srmnitc	s**n@g**m	7
and 26 more...

Committer Domains (Top 20 + Academic)

mpie.de: 15 gmx.de: 3 cmmc001.bc.rzg.mpg.de: 2 markuss-mbp.mpie.de: 1 mm.tu-darmstadt.de: 1 ufl.edu: 1 greyhavensolutions.com: 1 mailbox.org: 1 andrew.cmu.edu: 1 rub.de: 1 codacy.com: 1 cmmb31.fritz.box: 1 ugent.be: 1 creshal.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 44
Total pull requests: 213
Average time to close issues: about 1 month
Average time to close pull requests: 6 days
Total issue authors: 25
Total pull request authors: 12
Average comments per issue: 5.25
Average comments per pull request: 0.7
Merged pull requests: 177
Bot issues: 0
Bot pull requests: 90

Past Year

Issues: 4
Pull requests: 36
Average time to close issues: 3 months
Average time to close pull requests: 1 day
Issue authors: 4
Pull request authors: 3
Average comments per issue: 1.25
Average comments per pull request: 0.17
Merged pull requests: 25
Bot issues: 0
Bot pull requests: 24

View more stats

Top Authors

Issue Authors

sinazadeh (6)
lfzhu-phys (5)
samwaseda (4)
jan-janssen (3)
jkitchin (3)
mostafajoulaian (2)
edmen-dev (2)
tnecnivkcots (2)
dhoulek (1)
ligerzero-ai (1)
JonathanSchmidt1 (1)
Arslanzulfqar5 (1)
BaoyingDou (1)
LekshmiSreekala (1)
sravankumarkb (1)

Pull Request Authors

dependabot[bot] (96)
jan-janssen (72)
ligerzero-ai (24)
niklassiemer (8)
samwaseda (6)
tnecnivkcots (4)
pmrv (2)
aminsakic (2)
neil51 (1)
liamhuber (1)
jkitchin (1)
dependabot-preview[bot] (1)

Top Labels

Issue Labels

bug (19) enhancement (8) priority: medium (1) question (1)

Pull Request Labels

dependencies (97) patch (37) python (15) stale (4) documentation (3) priority: low (2) enhancement (1) priority: medium (1)

Packages

Total packages: 1
Total downloads:
- pypi 375 last-month

Total dependent packages: 1
Total dependent repositories: 2
Total versions: 57
Total maintainers: 5

pypi.org: pyiron

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

Homepage: https://github.com/pyiron/pyiron
Documentation: https://pyiron.readthedocs.io/
License: BSD
Latest release: 0.5.2
published almost 2 years ago

Versions: 57
Dependent Packages: 1
Dependent Repositories: 2
Downloads: 375 Last month
Docker Downloads: 0

Rankings

Docker downloads count: 1.9%

Stargazers count: 3.6%

Forks count: 6.2%

Average: 7.1%

Downloads: 9.0%

Dependent packages count: 10.1%

Dependent repos count: 11.5%

Maintainers (5)

jan-janssen pyiron niklassiemer srmnitc mpmpie

Last synced: 4 months ago

Dependencies

.github/workflows/UpdateDependabotPR.yml actions

actions/checkout v2 composite
ad-m/github-push-action main composite

.github/workflows/codeql-analysis.yml actions

actions/checkout v2 composite
github/codeql-action/analyze v1 composite
github/codeql-action/init v1 composite

.github/workflows/deploy.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/docs.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2.2.0 composite

.github/workflows/notebooks.yml actions

actions/checkout v2.2.0 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/pypicheck.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2.2.0 composite

.ci_support/environment.yml conda

codacy-coverage
coverage
coveralls
pyiron_atomistics 0.2.62.*

binder/environment.yml conda

gpaw
iprpy-data
jupyterlab
lammps
nglview
pyiron
pyiron-data >=0.0.5
pyiron_atomistics
pyiron_base
pymatgen
pyscal
python
seaborn
sphinxdft >=2.7.0
sphinxdft-data
sqsgenerator

docs/environment.yml conda

nbsphinx
pyiron

.devcontainer/Dockerfile docker

mcr.microsoft.com/vscode/devcontainers/anaconda dev-3 build

setup.py pypi

pyiron_atomistics ==0.2.62