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pyscal- A python module for structural analysis of atomic environments
======================================================================

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**pyscal** is a python module for the calculation of local atomic
structural environments including `Steinhardt's bond orientational order
parameters <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.28.784>`__
during post-processing of atomistic simulation data. The core
functionality of pyscal is written in C++ with python wrappers using
`pybind11 <https://pybind11.readthedocs.io/en/stable/intro.html>`__
which allows for fast calculations with possibilities for easy expansion
in python.

Steinhardt's order parameters are widely used for `identification of
crystal
structures <https://aip.scitation.org/doi/full/10.1063/1.4774084>`__.
They are also used to identify if an atom is `solid or
liquid <https://link.springer.com/chapter/10.1007/b99429>`__. pyscal is
inspired by
`BondOrderAnalysis <https://homepage.univie.ac.at/wolfgang.lechner/bondorderparameter.html>`__
code, but has since incorporated many additions and modifications.
pyscal module includes the following functionality-

Highlights
----------

-  fast and efficient calculations using C++ and expansion using python.
-  calculation of Steinhardt's order parameters and their `averaged
   version <https://aip.scitation.org/doi/full/10.1063/1.2977970>`__ and
   `disorder parameters <https://doi.org/10.1063/1.3656762>`__.
-  links with `Voro++ <http://math.lbl.gov/voro++/>`__ code, for
   calculation of `Steinhardt parameters weighted using face area of
   Voronoi
   polyhedra <https://aip.scitation.org/doi/full/10.1063/1.4774084>`__.
-  classification of atoms as `solid or
   liquid <https://link.springer.com/chapter/10.1007/b99429>`__.
-  clustering of particles based on a user defined property.
-  methods for calculating radial distribution function, voronoi volume
   of particles, number of vertices and face area of voronoi polyhedra
   and coordination number.
-  calculation of angular parameters such as `for identification of
   diamond
   structure <https://journals.aps.org/prb/abstract/10.1103/PhysRevB.47.15717>`__
   and `Ackland-Jones <https://doi.org/10.1103/PhysRevB.73.054104>`__
   angular parameters.
-  `Centrosymmetry
   parameter <https://doi.org/10.1103/PhysRevB.58.11085>`__ for
   identification of defects.
-  `Adaptive common neighbor
   analysis <https://iopscience.iop.org/article/10.1088/0965-0393/20/4/045021>`__
   for identification of crystal structures.

Documentation
-------------

.. toctree::

    downloadandinstall
    prologue/news
    methodsandexamples
    modules
    pubsandprojects
    prologue/extending
    prologue/helpandsupport
    prologue/citing
    prologue/acknowledgements
    prologue/license