https://github.com/glotzerlab/fedorov
A python package to initialize different crystal structures
https://github.com/glotzerlab/fedorov
Last synced: about 1 year ago
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A python package to initialize different crystal structures
- Host: GitHub
- URL: https://github.com/glotzerlab/fedorov
- Owner: glotzerlab
- License: bsd-3-clause
- Created: 2020-03-28T01:23:59.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2022-05-23T18:52:54.000Z (about 4 years ago)
- Last Synced: 2025-01-21T06:46:43.778Z (over 1 year ago)
- Language: Python
- Homepage:
- Size: 234 KB
- Stars: 1
- Watchers: 8
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- Changelog: ChangeLog.rst
- Contributing: CONTRIBUTING.md
- License: License.txt
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README
########################################
Fedorov
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A Python package to initialize different crystal structures. Named after the Russian mathematician, crystallographer and mineralogist: `Evgraf Fedorov `_. This package provides methods to generate any user defined crystal structures in both 2D and 3D systems, and includes access to 590 known crystal structures defined in `Aflow `_. Users can use this package to obtain the necessary data in form of numpy array to use for softwares such as `HOOMD-blue `_ to construct any systems with specific crystal structure for simulation and analysis. In addition, the package also provides access to all the 3D space group, 2D plane group as well as point group operations that allows user to apply different symmetry operations.
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Installation
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Install with pip
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To install the package with the package manager pip_, execute
.. code:: bash
$ pip install fedorov --user
To upgrade the package, simply execute the same command with the ``--upgrade`` option.
.. code:: bash
$ pip install fedorov --user --upgrade
.. _pip: https://pip.pypa.io/en/stable/
Install from source
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Alternatively you can clone the `git repository `_ and execute the ``setup.py`` script to install the package.
.. code:: bash
git clone https://github.com/glotzerlab/fedorov.git
cd fedorov
python setup.py install --user
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Documentation
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- Documentation for the most recent release can be found here: `fedorov stable `_
- Documentation with the latest changes can be found here: `fedorov latest `_
You can also build the documentation with sphinx:
You can install sphinx using conda:
.. code-block:: bash
conda install sphinx
or pip:
.. code-block:: bash
pip install sphinx
To build the documentation, run the following commands in the source directory:
.. code-block:: bash
cd doc
make html
# Then open _build/html/index.html
To build a PDF of the documentation (requires LaTeX and/or PDFLaTeX):
.. code-block:: bash
cd doc
make latexpdf
# Then open _build/latex/fedorov.pdf
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Quickstart
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This package provides methods to generate known or user defined crystal structures. For example, to generate any known crystal structures from this `list `_:
.. code-block:: python
import numpy as np
from fedorov import SpaceGroup, Prototype, AflowPrototype
from fedorov import convert_to_box
# generate the exact prototype provided by Aflow, use prototype_index [0, 589]
prototype_index = 5
new_structure = AflowPrototype(prototype_index=prototype_index, print_info=True,
set_type=True)
basis_vectors, type_list = new_structure.get_basis_vectors()
lattice_vectors = new_structure.get_lattice_vectors()
Lx, Ly, Lz, xy, xz, yz = convert_to_box(lattice_vectors)
More examples can be found `here `_.
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Testing
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You can test this package by executing:
.. code-block:: bash
python -m pytest tests/
within the repository root directory.
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Credits
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See `Credits `_.