Work Description

Data for: Tunable Assembly of Host–Guest Colloidal Crystals

Tobias Dwyer, Timothy C. Moore, Joshua A. Anderson & Sharon C. Glotzer

Method

We produced this data via hard particle monte carlo (HPMC) simulations at constant pressure using HOOMD-blue 3.5 on the ACCESS Bridges 2 supercomputer.
Simulation trajectories were saved in the gsd format. Structure characterization of the self-assembly simulations (correlation functions, structure factor, orientation distributions, and hexatic bond order distributions) were computed with the freud analysis package. Visualization of all simulation snapshots was conducted in ovito. Data was generated and managed with the signac data management tool. Shape based calculations, such as the area of the star particles were conducted with coxeter.

Relevant documentation:

• HOOMD-blue - version 3.5.0 - https://hoomd-blue.readthedocs.io/en/
• signac - version 1.7.0 - https://docs.signac.io/en/latest/
• freud - version 2.11.0 - https://freud.readthedocs.io/en/latest/index.html
• ovito - https://www.ovito.org/about/
• gsd - version 2.6.0 - https://gsd.readthedocs.io/en/stable/python-api.html
• numpy - version 1.23.3 - https://numpy.org/doc/stable/user/index.html
• coxeter - version 0.6.1 - https://coxeter.readthedocs.io/en/latest/

References:

• J. A. Anderson, J. Glaser, and S. C. Glotzer. HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations. Computational Materials Science 173: 109363, Feb 2020. 10.1016/j.commatsci.2019.109363
• Carl S. Adorf, Paul M. Dodd, Vyas Ramasubramani, and Sharon C. Glotzer. Simple data and workflow management with the signac framework. Comput. Mater. Sci., 146(C):220–229, 2018. doi:10.1016/j.commatsci.2018.01.035.
• V. Ramasubramani, B. D. Dice, E. S. Harper, M. P. Spellings, J. A. Anderson, and S. C. Glotzer. freud: A Software Suite for High Throughput Analysis of Particle Simulation Data. Computer Physics Communications Volume 254, September 2020, 107275. doi:10.1016/j.cpc.2020.107275.
• A. Stukowski. Visualization and analysis of atomistic simulation data with OVITO – the Open Visualization Tool, Modelling Simul. Mater. Sci. Eng. 18 (2010), 015012. doi:10.1088/0965-0393/18/1/015012
• Ramasubramani, V., Dice, B., Dwyer, T. & Glotzer, S. coxeter: A Python package for working with shapes. JOSS 6, 3098 (2021). doi:10.21105/joss.03098

Description

This dataset was generated for our work: "Tunable Assembly of Host–Guest Colloidal Crystals". The data set comes in two parts: Simulations and Free Volume Calculations. The Simulation data set contains 2 different kinds of data: Simulation data and corresponding python scripts. First, simulation trajectories for 5 different binary systems of star particles and convex guests, and one system of only star particles. All simulation were performed at constant pressure. The data set contains GSD files for each of the simulations used in this work. Second data type is the corresponding python code used to produce the simulations which is organized in a separate set of directories.

1. Simulation data:

   • stars_only.gsd - star particle only simulation trajectory used in the SI of this work.
   • squares_small.gsd - simulation trajectory of squares and star particles used in figure 2 of this work.
   • hexagons_large.gsd - simulation trajectory of large hexagons and star particles used in figure 4 of this work.
   • hexagons_small.gsd - simulation trajectory of large hexagons and star particles used in figure 2 of this work.
   • sheild.gsd - simulation trajectory of large hexagons and star particles used in figure 4 of this work.
   • large_rectangles.gsd - simulation trajectory of large hexagons and star particles used in figure 4 of this work.

2. workspaces_for_HPMC_simulations directory:

   • Contains Readme.txt file with additional help to initialize and run the code.
   • Contains a directory for each shape that corresponds to the python code that was used to produce the above Simulation data(rectangle, stars_only, square, small_hexagon, shield, and large_hexagon).
     • init.py - initializes the signac workspace.
     • project.py - contains the operation that is used to run the simulation

The other data set generated is for the Free Volume calculations conducted using HOOMD-blue. Each directory contains the data used to calculate the free volume for each system analyzed in figure 5 along with the corresponding signac workspace. In addition, the directory also contains the Jupyter notebook used to analyze the data as well as the Free volume analysis outputs for each guest shape as a .svg file.

1. Free_volume_calculations_and_analysis directory:
   • Readme.txt file with additional help to initialize and run the code.
   • free_volume_analysis.ipynb - Jupyter notebook that analyzes hoomd acceptance ratio outputs and converts the data in free volume.
   • large_rectangle_full_comparison.svg - plot of the free volume analysis for the large rectangle guest which is the output of free_volume_analysis.ipynb
   • large_hexagon_full_comparison.svg - plot of the free volume analysis for the large hexagon guest which is the output of free_volume_analysis.ipynb
   • small_square_full_comparison.svg - plot of the free volume analysis for the small square guest which is the output of free_volume_analysis.ipynb
   • small_hexagon_full_comparison.svg- plot of the free volume analysis for the small hexagon guest which is the output of free_volume_analysis.ipynb
   • Shape directory - where Shape is: hexagon-star-large, hexagon-star-small, or square-star, rectangle-star.
     
     • mc_ratioX.txt - HPMC move ratio for guest particles in the hexagon unit cell which are converted to free volume in free_volume_analysis.ipynb, where X is the repeat number (from 1-5).
     • mc_ratioX_host.txt - HPMC move ratio for host particles in the hexagon unit cell which are converted to free volume in free_volume_analysis.ipynb, where X is the repeat number (from 1-5).
     • mc_ratioX_sheared.txt -HPMC move ratio for guest particles in the stretched unit cell which are converted to free volume in free_volume_analysis.ipynb, where X is the repeat number (from 1-5).
     • mc_ratioX_sheared_host.txt - HPMC move ratio for host particles in the stretched unit cell which are converted to free volume in free_volume_analysis.ipynb, where X is the repeat number (from 1-5).
     • orientations.txt - orientations used for the free volume calculations for the guest particles in the hexagon unit cell.
     • orientations_host.txt - orientations used for the free volume calculations for the host particles in the hexagon unit cell.
     • orientations_sheared.txt - orientations used for the free volume calculations for the guest particles in the stretched unit cell.
     • orientations_sheared_host.txt - orientations used for the free volume calculations for the host particles in the stretched unit cell.
     • project.py - code used run free volume calculations which output the above .txt files.
     • init.py - code used to initialize the signac workspace
     • unit_cell.py - Code used to construct hexagon and stretched unit cells for each system.
       
     • workspace directory - Contains output files from from HOOMD-blue simulations used to calculate acceptance ratios at each particle orientation.

Corresponding Author: Sharon Glotzer: email: sglotzerkjc@umich.edu

Depositing Author: Tobias Dwyer: email: ttdwyer@umich.edu

Date Written: August 23rd, 2023