Welcome to spatula documentation¶

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 $C_n$
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.

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)

Table of Contents¶

Contents: