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Extracopularity in 3D Particle Packings

Code for computing extracopularity coefficients in three-dimensional particle packings.

Description

The extracopularity coefficient is a local orientational order parameter for systems of interacting particles useful in the structural analysis of molecular dynamics simulations. In this repository, we provide implementations of our algorithm for computing extracopularity coefficients in three-dimensional particle packings. A MATLAB implementation is currently available, and a C++ implementation is under development. Our code accepts LAMMPS dump file inputs, which are easily visualized in OVITO. Renderings of simulations analyzed by our code can be found on YouTube.

Getting started

1. Installation: Place the function file extracopularity.m anywhere in the MATLAB search path or present working directory.
2. Execution: Pass the full path of the target LAMMPS dump file as a string into the function. If the data is in another file format, simply import it into OVITO and export it as a LAMMPS dump file before doing so.
3. Visualization: Import the output of the code into OVITO and use the color coding modifier with the input property set to c_extra. Use the slice modifier to remove external surfaces if the simulation had been performed with periodic boundary conditions, as they are not recognized by current versions of the code.
4. Postprocessing: Use the smooth trajectory modifier in OVITO to reduce temporal noise. This must be placed lowest in the list of modifiers for it to produce the desired effect.

For further documentation, see the header comment of extracopularity.m

Versions

The latest version performs "bond angle discretization" as per [2] if a "commonly encountered geometry" cannot be found as per [1]. A version that adheres strictly to [1] is preserved in the legacy branch.

Citation

If this software is used in the preparation of work that is to be published, please cite the following:

1. John Çamkıran, Fabian Parsch, and Glenn D. Hibbard , "A local orientational order parameter for systems of interacting particles", J. Chem. Phys. 156, 091101 (2022)

2. John Çamkıran, Fabian Parsch, and Glenn D. Hibbard , "On the topology of the space of coordination geometries", Eur. Phys. J. B 96, 72 (2023)

Licenses

This software is distributed under the BSD-3-Clause License. For more details see the LICENSE file.