| Name | pyiron-atomistics JSON |
| Version |
0.5.1
JSON |
| download |
| home_page | None |
| Summary | An interface to atomistic simulation codes including but not limited to GPAW, LAMMPS, S/Phi/nX and VASP. |
| upload_time | 2024-04-14 12:48:31 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| 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. |
| keywords |
pyiron
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
pyiron
======
.. image:: https://coveralls.io/repos/github/pyiron/pyiron_atomistics/badge.svg?branch=main
:target: https://coveralls.io/github/pyiron/pyiron_atomistics?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_atomistics/badges/latest_release_date.svg
:target: https://anaconda.org/conda-forge/pyiron_atomistics/
:alt: Release_Date
.. image:: https://github.com/pyiron/pyiron_atomistics/workflows/Python%20package/badge.svg
:target: https://github.com/pyiron/pyiron_atomistics/actions
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.. image:: https://anaconda.org/conda-forge/pyiron_atomistics/badges/downloads.svg
:target: https://anaconda.org/conda-forge/pyiron_atomistics/
: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) <https://wiki.fysik.dtu.dk/ase/>`_.
- Atomistic simulation codes – like `LAMMPS <http://lammps.sandia.gov>`_ and `VASP <https://www.vasp.at>`_.
- Feedback Loops – to construct dynamic simulation life cycles.
- Hierarchical data management – interfacing with storage resources like SQL and `HDF5 <https://support.hdfgroup.org/HDF5/>`_.
- Integrated visualization – based on `NGLview <https://github.com/arose/nglview>`_.
- Interactive simulation protocols - based on `Jupyter notebooks <http://jupyter.org>`_.
- 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 <https://www.mpie.de/CM>`_ of `Joerg Neugebauer <https://www.mpie.de/person/43010/2763386>`_ at the `Max Planck Institut für Eisenforschung (Max Planck Institute for iron research) <https://www.mpie.de/2281/en>`_. 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) <http://www.icams.de>`_ 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 <http://pyiron.org>`_ page for more details.
Installation
------------
You can test pyiron on `Mybinder.org (beta) <https://mybinder.org/v2/gh/pyiron/pyiron_atomistics/main?urlpath=lab>`_.
For a local installation we recommend to install pyiron inside an `anaconda <https://www.anaconda.com>`_ 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 <https://pyiron.readthedocs.io/en/latest/source/installation.html>`_ page for more details.
Example
-------
After the successful configuration you can start your first pyiron calculation. Navigate to 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_atomistics 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_atomistics/main
:alt: mybinder
License and Acknowledgments
---------------------------
``pyiron`` is licensed under the BSD license.
If you use pyiron in your scientific work, `please consider citing <http://www.sciencedirect.com/science/article/pii/S0927025618304786>`_ ::
@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},
}
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"description": "pyiron\n======\n\n.. image:: https://coveralls.io/repos/github/pyiron/pyiron_atomistics/badge.svg?branch=main\n :target: https://coveralls.io/github/pyiron/pyiron_atomistics?branch=main\n :alt: Coverage Status\n\n.. image:: https://api.codacy.com/project/badge/Grade/c513254f10004df5a1f5c76425c6584b\n :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\n :alt: Codacy Badge\n\n.. image:: https://anaconda.org/conda-forge/pyiron_atomistics/badges/latest_release_date.svg\n :target: https://anaconda.org/conda-forge/pyiron_atomistics/\n :alt: Release_Date\n\n.. image:: https://github.com/pyiron/pyiron_atomistics/workflows/Python%20package/badge.svg\n :target: https://github.com/pyiron/pyiron_atomistics/actions\n :alt: Build Status\n\n.. image:: https://anaconda.org/conda-forge/pyiron_atomistics/badges/downloads.svg\n :target: https://anaconda.org/conda-forge/pyiron_atomistics/\n :alt: Downloads\n\n.. image:: https://readthedocs.org/projects/pyiron/badge/?version=latest\n :target: https://pyiron.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n\n.. image:: docs/_static/screenshot.png\n :align: center\n :alt: Screenshot of pyiron running inside jupyterlab.\n\n\npyiron - an integrated development environment (IDE) for computational materials science. It combines several tools in a common platform:\n\n - Atomic structure objects \u2013 compatible to the `Atomic Simulation Environment (ASE) <https://wiki.fysik.dtu.dk/ase/>`_.\n - Atomistic simulation codes \u2013 like `LAMMPS <http://lammps.sandia.gov>`_ and `VASP <https://www.vasp.at>`_.\n - Feedback Loops \u2013 to construct dynamic simulation life cycles.\n - Hierarchical data management \u2013 interfacing with storage resources like SQL and `HDF5 <https://support.hdfgroup.org/HDF5/>`_.\n - Integrated visualization \u2013 based on `NGLview <https://github.com/arose/nglview>`_.\n - Interactive simulation protocols - based on `Jupyter notebooks <http://jupyter.org>`_.\n - Object oriented job management \u2013 for scaling complex simulation protocols from single jobs to high-throughput simulations.\n\npyiron (called pyron) is developed in the `Computational Materials Design department <https://www.mpie.de/CM>`_ of `Joerg Neugebauer <https://www.mpie.de/person/43010/2763386>`_ at the `Max Planck Institut f\u00fcr Eisenforschung (Max Planck Institute for iron research) <https://www.mpie.de/2281/en>`_. 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) <http://www.icams.de>`_ joined the development of the framework with a specific focus on high throughput applications. In 2018 pyiron was released as open-source project.\nSee the `Documentation <http://pyiron.org>`_ page for more details.\n\n\nInstallation\n------------\nYou can test pyiron on `Mybinder.org (beta) <https://mybinder.org/v2/gh/pyiron/pyiron_atomistics/main?urlpath=lab>`_.\nFor a local installation we recommend to install pyiron inside an `anaconda <https://www.anaconda.com>`_ environment::\n\n conda install -c conda-forge pyiron\n\n\nAfter the installation of pyiron you need to configure pyiron. The default configuration can be generated automatically. Start a new Python session and import pyiron::\n\n > import pyiron\n > pyiron.install()\n >>> It appears that pyiron is not yet configured, do you want to create a default start configuration (recommended: yes). [yes/no]:\n > yes\n > exit()\n\n\nSee the `Documentation-Installation <https://pyiron.readthedocs.io/en/latest/source/installation.html>`_ page for more details.\n\n\nExample\n-------\nAfter the successful configuration you can start your first pyiron calculation. Navigate to the projects directory and start a jupyter notebook or jupyter lab session correspondingly::\n\n cd ~/pyiron/projects\n jupyter notebook\n\nOpen 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::\n\n from pyiron_atomistics import Project\n pr = Project('test')\n structure = pr.create_structure('Fe', 'bcc', 2.78)\n structure.plot3d()\n\nFinally a first lammps calculation can be executed by::\n\n job = pr.create_job(job_type=pr.job_type.Lammps, job_name='lammpstestjob')\n job.structure = structure\n job.potential = job.list_potentials()[0]\n job.run()\n\n\nGetting started:\n----------------\nTest pyiron with mybinder:\n\n.. image:: https://mybinder.org/badge_logo.svg\n :target: https://mybinder.org/v2/gh/pyiron/pyiron_atomistics/main\n :alt: mybinder\n\n\nLicense and Acknowledgments\n---------------------------\n``pyiron`` is licensed under the BSD license.\n\nIf you use pyiron in your scientific work, `please consider citing <http://www.sciencedirect.com/science/article/pii/S0927025618304786>`_ ::\n\n @article{pyiron-paper,\n title = {pyiron: An integrated development environment for computational materials science},\n journal = {Computational Materials Science},\n volume = {163},\n pages = {24 - 36},\n year = {2019},\n issn = {0927-0256},\n doi = {https://doi.org/10.1016/j.commatsci.2018.07.043},\n url = {http://www.sciencedirect.com/science/article/pii/S0927025618304786},\n author = {Jan Janssen and Sudarsan Surendralal and Yury Lysogorskiy and Mira Todorova and Tilmann Hickel and Ralf Drautz and J\u00f6rg Neugebauer},\n keywords = {Modelling workflow, Integrated development environment, Complex simulation protocols},\n }\n",
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