Overview

This repository is intended to highlight both simple and visually-interesting examples of systems rendered using plato. Note that many of these are more "rough and dirty," but realistically useful, scenes; there are many other simpler examples located in the plato test demo scenes.

Live examples are available through mybinder.org, although it may be preferable to run more complex examples on your own computer.

For ease of use, data are currently stored directly in the repository alongside the notebooks to render them.

Examples use the libgetar library for storing trajectory data. Some examples compute things using the freud library.

Tutorial-Style Simple Examples

These showcase the basics of creating and displaying plato scenes and primitives.

• Basic overview
• Arrows2D primitive
• ConvexPolyhedra primitive
• SpherePoints primitive

Live Simulation Examples

These examples are generated from live hoomd-blue simulations using the hoomd_flowws project and analyzed using freud.

Rounded Pentagons

Repulsive Spheres

Rounded Cubes

Hard Icosahedra

Realistic Examples

Binary tetrahedra-octahedra crystal

This notebook generates an image similar to that found in a Soft Matter cover associated with the paper Self-assembly of a space-tessellating structure in the binary system of hard tetrahedra and octahedra by Cadotte, Dshemuchadse, Damasceno, Newman, and Glotzer.

Protein

This notebook renders a cartoon-style image of the protein glutathione s-transferase.

Hexatic Polygons

These are data from the study Shape and Symmetry Determine Two-Dimensional Melting Transitions of Hard Regular Polygons. A selection of the data from the paper are available at Deep Blue under the Creative Commons Attribution 4.0 license.

The hexatic order parameter $\psi_6$ for each particle is computed using freud. The angle of $\psi_6$ for each particle, corresponding to the orientation of each particle's nearest 6-neighbor environment, is mapped to the color for the particle.

Active Squares

This notebook renders a set of rotationally-driven, rounded squares using the Discrete Element Method (DEM) component of hoomd-blue. Particles are colored according to the orientation of their hexatic order parameter $\psi_6$ by freud, showing the hexagonally-ordered domains of the crystal.

Contact-triggered Active Particles

These results are from the paper Tunable emergent structures and traveling waves in mixtures of passive and contact-triggered-active particles by Agrawal, Bruss, and Glotzer. In this image, contact-triggered active particles (red) and passive particles (blue) assemble two different ordered structures.

Crystallization

This notebook shows a process of nucleation and growth of a somewhat complex crystal structure ($tP30-\text{CrFe}$). Individual particles were identified as being in the fluid or solid phase using pythia.