AtomMan
=======
Atomistic Manipulation Toolkit
AtomMan: the Atomistic Manipulation Toolkit is a Python library for
creating, representing, manipulating, and analyzing large-scale atomic
systems of atoms. The focus of the package is to facilitate the rapid design
and development of simulations that are fully documented and easily adaptable
to new potentials, configurations, etc. The code has no requirements that
limit which systems it can be used on, i.e. it should work on Linux, Mac and
Windows computers.
Features:
1. Allows for efficient and fast calculations on millions of atoms, each with
many freely defined per-atom properties.
2. Built-in tools for generating and analyzing crystalline defects, such as
point defects, stacking faults, and dislocations.
4. Call LAMMPS directly from Python and instantly retrieve the resulting data
or LAMMPS error statement.
5. Easily convert systems to/from the other Python atomic representations, such
as ase.Atoms and pymatgen.Structure.
6. Can read and dump crystal structure information from a number of formats,
such as LAMMPS data and dump files, and POSCAR.
7. Built-in unit conversions.
Installation
------------
The atomman package is compatible with Python 3.7+.
The latest release can be installed using pip::
pip install atomman
or using conda from the conda-forge channel::
conda install -c conda-forge atomman
For Windows users, it is recommended to use an Anaconda distribution and use
conda to install numpy, scipy, matplotlib, pandas and cython prior to
installing atomman.
Alternatively, all code and documentation can be downloaded from GitHub.
- The stable releases are available at
`https://github.com/usnistgov/atomman <https://github.com/usnistgov/atomman>`__.
- The working development versions are at
`https://github.com/lmhale99/atomman <https://github.com/lmhale99/atomman>`__.
Documentation
-------------
Web-based documentation for the atomman package is available at
`https://www.ctcms.nist.gov/potentials/atomman <https://www.ctcms.nist.gov/potentials/atomman>`__.
Source code for the documentation can be found in the
`github doc directory <https://github.com/usnistgov/atomman/tree/master/doc/>`__.
The doc directory contains the information both as the source RestructuredText
files and as unformatted HTML. If you download a copy, you can view the HTML
version offline by
cd {atomman_path}/doc/html
python -m http.server
Then, opening localhost:8000 in a web browser.
The documentation consists of two main components:
1. **Tutorial Jupyter Notebooks:**
`Online html version <https://www.ctcms.nist.gov/potentials/atomman/tutorial/index.html>`__,
`Downloadable Notebook version <https://github.com/usnistgov/atomman/tree/master/doc/tutorial>`__.
The tutorials starting with ##. provide a general overview/example of the
various capabilities. The tutorials starting with ##.#. give more detailed
descriptions and list options available to the tools mentioned in the
overview tutorials.
2. **Code Documentation:**
`Online html version <https://www.ctcms.nist.gov/potentials/atomman/atomman.html>`__.
This provides a rendering of the Python docstrings for the included
functions and classes.
Optional packages
-----------------
This is a list of additional Python packages that are needed for some of the
optional features of the package.
- `diffpy.Structure <http://www.diffpy.org/diffpy.Structure/>`__:
CIF reader. Required for loading systems from CIF files.
- `ase <https://wiki.fysik.dtu.dk/ase/>`__:
The Atomic Simulation Environment for interacting with small systems
and DFT calculations. Required for converting to/from ase.Atoms objects.
- `pymatgen <http://pymatgen.org/>`__:
The Python Materials Genomics package used by the Materials
Project for DFT calculations. Required for converting to/from
pymatgen.Structure objects.
- `spglib <https://atztogo.github.io/spglib/python-spglib.html>`__:
A Python interface to the spglib spacegroup analysis code. spglib
can be used to analyze and determine the spacegroup for an atomic system.
Required for converting to/from spglib.cell objects.
Raw data
{
"_id": null,
"home_page": "https://github.com/usnistgov/atomman/",
"name": "atomman",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "atom,atomic,atomistic,molecular dynamics",
"author": "Lucas Hale",
"author_email": "lucas.hale@nist.gov",
"download_url": "https://files.pythonhosted.org/packages/dd/09/b0647d156479815d8d430b5124cab736540d34a1481c80ff57856c8d4a14/atomman-1.4.10.tar.gz",
"platform": null,
"description": "AtomMan\r\n=======\r\n\r\nAtomistic Manipulation Toolkit\r\n\r\nAtomMan: the Atomistic Manipulation Toolkit is a Python library for\r\ncreating, representing, manipulating, and analyzing large-scale atomic\r\nsystems of atoms. The focus of the package is to facilitate the rapid design\r\nand development of simulations that are fully documented and easily adaptable\r\nto new potentials, configurations, etc. The code has no requirements that\r\nlimit which systems it can be used on, i.e. it should work on Linux, Mac and\r\nWindows computers.\r\n\r\nFeatures:\r\n\r\n1. Allows for efficient and fast calculations on millions of atoms, each with\r\n many freely defined per-atom properties.\r\n\r\n2. Built-in tools for generating and analyzing crystalline defects, such as\r\n point defects, stacking faults, and dislocations.\r\n\r\n4. Call LAMMPS directly from Python and instantly retrieve the resulting data\r\n or LAMMPS error statement.\r\n\r\n5. Easily convert systems to/from the other Python atomic representations, such\r\n as ase.Atoms and pymatgen.Structure.\r\n\r\n6. Can read and dump crystal structure information from a number of formats,\r\n such as LAMMPS data and dump files, and POSCAR.\r\n\r\n7. Built-in unit conversions.\r\n\r\nInstallation\r\n------------\r\n\r\nThe atomman package is compatible with Python 3.7+.\r\n\r\nThe latest release can be installed using pip::\r\n\r\n pip install atomman\r\n\r\nor using conda from the conda-forge channel::\r\n\r\n conda install -c conda-forge atomman\r\n\r\nFor Windows users, it is recommended to use an Anaconda distribution and use\r\nconda to install numpy, scipy, matplotlib, pandas and cython prior to\r\ninstalling atomman.\r\n\r\nAlternatively, all code and documentation can be downloaded from GitHub.\r\n\r\n- The stable releases are available at\r\n `https://github.com/usnistgov/atomman <https://github.com/usnistgov/atomman>`__.\r\n\r\n- The working development versions are at\r\n `https://github.com/lmhale99/atomman <https://github.com/lmhale99/atomman>`__.\r\n \r\nDocumentation\r\n-------------\r\n\r\nWeb-based documentation for the atomman package is available at\r\n`https://www.ctcms.nist.gov/potentials/atomman <https://www.ctcms.nist.gov/potentials/atomman>`__.\r\n\r\nSource code for the documentation can be found in the\r\n`github doc directory <https://github.com/usnistgov/atomman/tree/master/doc/>`__.\r\nThe doc directory contains the information both as the source RestructuredText\r\nfiles and as unformatted HTML. If you download a copy, you can view the HTML\r\nversion offline by\r\n\r\n cd {atomman_path}/doc/html\r\n python -m http.server\r\n\r\nThen, opening localhost:8000 in a web browser.\r\n\r\nThe documentation consists of two main components:\r\n\r\n1. **Tutorial Jupyter Notebooks:**\r\n `Online html version <https://www.ctcms.nist.gov/potentials/atomman/tutorial/index.html>`__,\r\n `Downloadable Notebook version <https://github.com/usnistgov/atomman/tree/master/doc/tutorial>`__.\r\n The tutorials starting with ##. provide a general overview/example of the\r\n various capabilities. The tutorials starting with ##.#. give more detailed\r\n descriptions and list options available to the tools mentioned in the\r\n overview tutorials.\r\n\r\n2. **Code Documentation:**\r\n `Online html version <https://www.ctcms.nist.gov/potentials/atomman/atomman.html>`__.\r\n This provides a rendering of the Python docstrings for the included\r\n functions and classes.\r\n\r\n\r\nOptional packages\r\n-----------------\r\n\r\nThis is a list of additional Python packages that are needed for some of the\r\noptional features of the package.\r\n\r\n- `diffpy.Structure <http://www.diffpy.org/diffpy.Structure/>`__:\r\n CIF reader. Required for loading systems from CIF files.\r\n\r\n- `ase <https://wiki.fysik.dtu.dk/ase/>`__:\r\n The Atomic Simulation Environment for interacting with small systems\r\n and DFT calculations. Required for converting to/from ase.Atoms objects.\r\n\r\n- `pymatgen <http://pymatgen.org/>`__:\r\n The Python Materials Genomics package used by the Materials\r\n Project for DFT calculations. Required for converting to/from\r\n pymatgen.Structure objects.\r\n\r\n- `spglib <https://atztogo.github.io/spglib/python-spglib.html>`__:\r\n A Python interface to the spglib spacegroup analysis code. spglib\r\n can be used to analyze and determine the spacegroup for an atomic system.\r\n Required for converting to/from spglib.cell objects.\r\n",
"bugtrack_url": null,
"license": "",
"summary": "Atomistic Manipulation Toolkit",
"version": "1.4.10",
"project_urls": {
"Homepage": "https://github.com/usnistgov/atomman/"
},
"split_keywords": [
"atom",
"atomic",
"atomistic",
"molecular dynamics"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "2ca9a25065f77684ca4d248e9ef5084fff0740fdee5a75de7a542cbfd19c0e15",
"md5": "be58d6730e91d56f79381dd19fd749ba",
"sha256": "f12b95aee65a0fb6f651ba165c54c8aa123aebff8694a344b2e7e5045ce878a9"
},
"downloads": -1,
"filename": "atomman-1.4.10-cp310-cp310-win_amd64.whl",
"has_sig": false,
"md5_digest": "be58d6730e91d56f79381dd19fd749ba",
"packagetype": "bdist_wheel",
"python_version": "cp310",
"requires_python": null,
"size": 2186029,
"upload_time": "2023-07-30T03:04:47",
"upload_time_iso_8601": "2023-07-30T03:04:47.029024Z",
"url": "https://files.pythonhosted.org/packages/2c/a9/a25065f77684ca4d248e9ef5084fff0740fdee5a75de7a542cbfd19c0e15/atomman-1.4.10-cp310-cp310-win_amd64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "7064f244757dce369aa44be69f7f2c60d0faaa2bb5cbb8c3f410335a524a6d42",
"md5": "4b90af85b22c27815221ec3dbfdea937",
"sha256": "c12bb68dfcd7f0d23adfab0189d296ff7c899b2b21afb1fa188ef12f861011d3"
},
"downloads": -1,
"filename": "atomman-1.4.10-cp311-cp311-win_amd64.whl",
"has_sig": false,
"md5_digest": "4b90af85b22c27815221ec3dbfdea937",
"packagetype": "bdist_wheel",
"python_version": "cp311",
"requires_python": null,
"size": 2188421,
"upload_time": "2023-07-30T03:04:50",
"upload_time_iso_8601": "2023-07-30T03:04:50.444314Z",
"url": "https://files.pythonhosted.org/packages/70/64/f244757dce369aa44be69f7f2c60d0faaa2bb5cbb8c3f410335a524a6d42/atomman-1.4.10-cp311-cp311-win_amd64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "ec2c531dc5f8276b67a0058a6096f22684aa4b11fd349a89a920275661843a32",
"md5": "863b4d2fa423050ab7518ff2676140c3",
"sha256": "36942ccaf159891df5062ce5f5b941a37c78317dd70c91fbb50e9c07dd9ceac2"
},
"downloads": -1,
"filename": "atomman-1.4.10-cp38-cp38-win_amd64.whl",
"has_sig": false,
"md5_digest": "863b4d2fa423050ab7518ff2676140c3",
"packagetype": "bdist_wheel",
"python_version": "cp38",
"requires_python": null,
"size": 2189214,
"upload_time": "2023-07-30T03:04:53",
"upload_time_iso_8601": "2023-07-30T03:04:53.225796Z",
"url": "https://files.pythonhosted.org/packages/ec/2c/531dc5f8276b67a0058a6096f22684aa4b11fd349a89a920275661843a32/atomman-1.4.10-cp38-cp38-win_amd64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "74fecf6fe36be6cda83e04af93a4fe013378aad98d20cf0df2020931b82698ce",
"md5": "9c4150ff4ce52c9007920a5606007fda",
"sha256": "f034d37154f5faf4c8e33f9120d4faf24fa7679969bb20ca837152750b15d40a"
},
"downloads": -1,
"filename": "atomman-1.4.10-cp39-cp39-win_amd64.whl",
"has_sig": false,
"md5_digest": "9c4150ff4ce52c9007920a5606007fda",
"packagetype": "bdist_wheel",
"python_version": "cp39",
"requires_python": null,
"size": 2187764,
"upload_time": "2023-07-30T03:04:56",
"upload_time_iso_8601": "2023-07-30T03:04:56.237635Z",
"url": "https://files.pythonhosted.org/packages/74/fe/cf6fe36be6cda83e04af93a4fe013378aad98d20cf0df2020931b82698ce/atomman-1.4.10-cp39-cp39-win_amd64.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "dd09b0647d156479815d8d430b5124cab736540d34a1481c80ff57856c8d4a14",
"md5": "2c7294578d816bed43b8db49986bec09",
"sha256": "d5b6920bc713f48127ddbf8d8d472d5312ce8331c6e0f540448cc7b6545b55cd"
},
"downloads": -1,
"filename": "atomman-1.4.10.tar.gz",
"has_sig": false,
"md5_digest": "2c7294578d816bed43b8db49986bec09",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 1871342,
"upload_time": "2023-07-30T03:04:58",
"upload_time_iso_8601": "2023-07-30T03:04:58.675186Z",
"url": "https://files.pythonhosted.org/packages/dd/09/b0647d156479815d8d430b5124cab736540d34a1481c80ff57856c8d4a14/atomman-1.4.10.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-07-30 03:04:58",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "usnistgov",
"github_project": "atomman",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"requirements": [],
"lcname": "atomman"
}
JSON
