https://github.com/glotzerlab/spatula

Python package for calculation of symmetry based order parameters in molecular simulation systems.
https://github.com/glotzerlab/spatula

Last synced: 8 months ago
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Python package for calculation of symmetry based order parameters in molecular simulation systems.

• Host: GitHub
• URL: https://github.com/glotzerlab/spatula
• Owner: glotzerlab
• License: bsd-3-clause
• Created: 2022-08-05T18:51:26.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2025-10-02T06:13:04.000Z (8 months ago)
• Last Synced: 2025-10-02T08:26:04.947Z (8 months ago)
• Language: Python
• Homepage: https://spatula.readthedocs.io
• Size: 6.55 MB
• Stars: 2
• Watchers: 9
• Forks: 0
• Open Issues: 4
• Metadata Files:
  • Readme: README.rst
  • Changelog: changelog.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE
  • Authors: AUTHORS.rst

Awesome Lists containing this project

README

          
=======

SPATULA

=======

Overview

--------

``SPATULA`` (Symmetry Pattern Analysis Toolkit for Understanding Local Arrangements) is a Python package for computing the continuous symmetry ordering of the neighbors of a point in space.

In general, this is to compute the local ordering of particles (molecules) in simulations or experiments over time.

The package serves as an extension of `freud `__ with a new order parameter.

``spatula`` currently supports all point groups of finite order:

- All crystallographic point groups

- Cyclical groups :math:`C_n`

- Cyclical groups with vertical reflection :math:`C_{nv}`

- Cyclical groups with horizontal reflection :math:`C_{nh}`

- Dihedral groups :math:`D_n`

- Dihedral groups with horizontal reflection :math:`D_{nh}`

- Dihedral groups with diagonal reflections :math:`D_{nd}`

- Polyhedral groups :math:`T, T_h, T_d, O, O_h, I, I_h`

- Rotoreflection groups :math:`S_n`

- Inversion group: :math:`C_i`

- Reflection group: :math:`C_s`

Resources

=========

- `Reference Documentation `__: Examples, tutorials, and package Python APIs.

- `Installation Guide `__: Instructions for installing and compiling **spatula**.

- `GitHub repository `__: Download the **spatula** source code.

- `Issue tracker `__: Report issues or request features.

Related Tools

=============

- `HOOMD-blue `__: Perform MD / MC simulations that

  can be analyzed with **spatula**.

- `freud `__: Analyze particle simulations.

- `signac `__: Manage your workflow with **signac**.

Citation

========

When using **spatula** to process data for publication, please refer to the `documentation instructions

`__.

Installation

============

**Spatula** is available on PyPI and conda-forge.

See the Installation Guide for more information.

Example

-------

.. code-block:: python

    import freud

    import spatula

    system = freud.data.UnitCell.fcc().generate_system(3)

    optimizer = spatula.optimize.Union.with_step_gradient_descent(

        optimizer=spatula.optimize.Mesh.from_grid()

    )

    PGOP_Oh_Ih = spatula.PGOP(["Oh","Ih"], optimizer)

    PGOP_Oh_Ih.compute(system, sigmas=None, neighbors={"r_max": 1.2, "exclude_ii": True})

    print(PGOP_Oh_Ih.order)