spatula-analysis 0.2.0

Point group symmetry analysis of local environments for point cloud data.

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 \(C_n\)

• Cyclical groups with vertical reflection \(C_{nv}\)

• Cyclical groups with horizontal reflection \(C_{nh}\)

• Dihedral groups \(D_n\)

• Dihedral groups with horizontal reflection \(D_{nh}\)

• Dihedral groups with diagonal reflections \(D_{nd}\)

• Polyhedral groups \(T, T_h, T_d, O, O_h, I, I_h\)

• Rotoreflection groups \(S_n\)

• Inversion group: \(C_i\)

• Reflection group: \(C_s\)

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

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)