fedorov 0.1.0

A python code repo to initialize different crystal structures based on Pearson symbol or space group

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.

Installation

Install with pip

To install the package with the package manager pip, execute

$ pip install fedorov --user

To upgrade the package, simply execute the same command with the --upgrade option.

$ pip install fedorov --user --upgrade

Install from source

Alternatively you can clone the git repository and execute the setup.py script to install the package.

git clone https://github.com/glotzerlab/fedorov.git
cd fedorov
python setup.py install --user

Documentation

• Documentation link: Website link to be added

You can also build the documentation with sphinx:

You can install sphinx using conda:

conda install sphinx

or pip:

pip install sphinx

To build the documentation, run the following commands in the source directory:

cd doc
make html
# Then open _build/html/index.html

To build a PDF of the documentation (requires LaTeX and/or PDFLaTeX):

cd doc
make latexpdf
# Then open _build/latex/fedorov.pdf

Quickstart

This package provides methods to generate known or user defined crystal structures. For example, to generate any known crystal structures from this list:

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 example can be found here.

Testing

You can test this package by executing:

python -m pytest tests/

within the repository root directory.

Credits

See Credits.