crystals 1.2.2

Data structures for crystallography

crystals

crystals is a library of data structure and algorithms to manipulate abstract crystals in a Pythonic way. crystals helps with reading crystallographic files (like .cif and .pdb), provides access to atomic positions, scattering utilities, and allows for symmetry determination. Although crystals can be used on its own, it was made to be integrated into larger projects (like scikit-ued).

Take a look at the documentation for more information.

Usage example

crystals is all about constructing crystals and getting information about the resulting object. Crystals can be built from a variety of sources:

• From files on disk, such as Crystallography Information Files (CIF) or Place-Wave Self-Consistent Field calculations (PWSCF);
• From the internal database of over 90 structure files (mostly elemental crystals);
• From online databases, such as the RCSB Protein DataBank or the Crystallography Open Database.

Here's a quick example of building a crystal from the internal database:

>>> from crystals import Crystal
>>>
>>> Crystal.from_database('vo2-m1')
< Crystal object with following unit cell:
    Atom O  @ (0.10, 0.21, 0.20)
    Atom O  @ (0.10, 0.29, 0.70)
    Atom O  @ (0.39, 0.69, 0.29)
    Atom O  @ (0.39, 0.81, 0.79)
    Atom O  @ (0.61, 0.19, 0.21)
    Atom O  @ (0.61, 0.31, 0.71)
    Atom O  @ (0.90, 0.71, 0.30)
    Atom O  @ (0.90, 0.79, 0.80)
    Atom V  @ (0.24, 0.53, 0.53)
    Atom V  @ (0.24, 0.97, 0.03)
    Atom V  @ (0.76, 0.03, 0.97)
    Atom V  @ (0.76, 0.48, 0.47)
Lattice parameters:
    a=5.743Å, b=4.517Å, c=5.375Å
    α=90.000°, β=122.600°, γ=90.000°
Chemical composition:
    O: 66.667%
    V: 33.333% >

Symmetry information is also readily available:

>>> from crystals import Crystal
>>> from pprint import pprint # pretty printing
>>>
>>> vo2 = Crystal.from_database('vo2-m1')
>>> pprint(vo2.symmetry())
{'centering': <CenteringType.primitive: 'P'>,
 'hall_number': 81,
 'hall_symbol': '-P 2ybc',
 'hm_symbol': 'P121/c1',
 'international_full': 'P 1 2_1/c 1',
 'international_number': 14,
 'international_symbol': 'P2_1/c',
 'pointgroup': '2/m'}

Command-line script

crystals comes with command-line utilities. The most important of them is the crystals info command-line program, which will give you information on a crystal.

For example, the equivalent of the usage example above is as follows:

    > crystals info vo2-m1
    Crystal object with following unit cell:
        Atom O  @ (0.10, 0.29, 0.70) | [1s²2s²2p⁴]
        Atom O  @ (0.10, 0.21, 0.20) | [1s²2s²2p⁴]
        Atom O  @ (0.90, 0.71, 0.30) | [1s²2s²2p⁴]
        Atom O  @ (0.90, 0.79, 0.80) | [1s²2s²2p⁴]
        Atom O  @ (0.39, 0.69, 0.29) | [1s²2s²2p⁴]
        Atom O  @ (0.39, 0.81, 0.79) | [1s²2s²2p⁴]
        Atom O  @ (0.61, 0.19, 0.21) | [1s²2s²2p⁴]
        Atom O  @ (0.61, 0.31, 0.71) | [1s²2s²2p⁴]
        Atom V  @ (0.24, 0.97, 0.03) | [1s²2s²2p⁶3s²3p⁶4s²3d³]
        Atom V  @ (0.76, 0.03, 0.97) | [1s²2s²2p⁶3s²3p⁶4s²3d³]
        Atom V  @ (0.24, 0.53, 0.53) | [1s²2s²2p⁶3s²3p⁶4s²3d³]
        Atom V  @ (0.76, 0.48, 0.47) | [1s²2s²2p⁶3s²3p⁶4s²3d³]
    Lattice parameters:
        a=5.743Å, b=4.517Å, c=5.375Å
        α=90.000°, β=122.600°, γ=90.000°
    Chemical composition:
        V: 33.333%
    Source:
        (...omitted...)\crystals\crystals\cifs\vo2-m1.cif
    Symmetry information:
        International symbol
                    (short) ..... P2_1/c
                    (full) ...... P 1 2_1/c 1
        International number .... 14
        Hermann-Mauguin symbol .. P121/c1
        Pointgroup .............. 2/m
        Hall Number ............. 81
        Centering ............... CenteringType.primitive

crystals will guess what the input means. You can pass a filename, or database entry. See crystals --help for more details.

Installation

crystals is available on the Python Package Index:

pip install crystals

For users of the conda package manager, crystals is also available from the conda-forge channel:

conda install -c conda-forge crystals

From source

crystals can also be installed from source:

git clone https://github.com/LaurentRDC/crystals.git
cd crystals
python setup.py install

You can install the latest development version using pip as well:

python -m pip install git+git://github.com/LaurentRDC/crystals.git

To build documentation, you will need a few more packages, listed in dev-requirements.txt. For example, to build documentation from source:

git clone https://github.com/LaurentRDC/crystals.git
cd crystals
pip install -r dev-requirements.txt
python setup.py build_sphinx

Documentation

The documentation, including a user guide as well as detailed reference, is available here: https://crystals.readthedocs.io/

Development

Tests can be run with the standard library's unittest module:

python -m unittest discover

Some optional tests might be skipped if dependencies are not installed, e.g. ASE.

Citations

As this package is a spinoff from scikit-ued, please consider citing the following publication if you find crystals useful:

L. P. René de Cotret, M. R. Otto, M. J. Stern. and B. J. Siwick, An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data, Advanced Structural and Chemical Imaging 4:11 (2018) DOI: 10.1186/s40679-018-0060-y.

Underlying algorithms provided by spglib are described in the following publication:

A. Togo and I. Tanaka, spglib: a software library for crystal symmetry search. https://arxiv.org/abs/1808.01590 (written at version 1.10.4).

Structure parsing from CIF files has been tested for correctness against CIF2CELL, detailed here:

Torbjorn Bjorkman, CIF2Cell: Generating geometries for electronic structure programs, Computer Physics Communications 182, 1183-1186 (2011) DOI: 10.1016/j.cpc.2011.01.013

Structure parsing from PDB files has been tested for correctness against Bio.PDB, detailed here:

Hamelryck, T., Manderick, B. PDB parser and structure class implemented in Python. Bioinformatics 19: 2308–2310 (2003)

Atomic weights are reported in the following publication:

Meija, J., Coplen, T., Berglund, M., et al. (2016). Atomic weights of the elements 2013 (IUPAC Technical Report). Pure and Applied Chemistry, 88(3), pp. 265-291. Retrieved 30 Nov. 2016, DOI:10.1515/pac-2015-0305

Aknowledgements

This package depends on the work of some amazing people. Of note are the spglib contributors.

Support / Report Issues

All support requests and issue reports should be filed on Github as an issue.

License

crystals is made available under the BSD 3-clause license. For more details, see LICENSE.

Related projects

• Streaming operations on NumPy arrays are available in the npstreams package.
• Interactive exploration of ultrafast electron diffraction data with the iris-ued package.
• Data structures and algorithms to handle ultrafast electron scattering data in the scikit-ued package.