References#

CPC+11

Vania Calandrini, Eric Pellegrini, Paolo Calligari, Konrad Hinsen, and Gerald R Kneller. Nmoldyn-interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. École thématique de la Société Française de la Neutronique, 12:201–232, 2011.

FB09

Christopher L. Farrow and Simon J. L. Billinge. Relationship between the atomic pair distribution function and small-angle scattering: implications for modeling of nanoparticles. Acta Crystallographica Section A, 65(3):232–239, 2009. URL: https://doi.org/10.1107/S0108767309009714, doi:10.1107/S0108767309009714.

FHND10

L. Filion, M. Hermes, R. Ni, and M. Dijkstra. Crystal nucleation of hard spheres using molecular dynamics, umbrella sampling, and forward flux sampling: a comparison of simulation techniques. The Journal of Chemical Physics, 133(24):244115, Dec 2010. URL: http://dx.doi.org/10.1063/1.3506838, doi:10.1063/1.3506838.

FSEW21

Erik Fransson, Mattias Slabanja, Paul Erhart, and Göran Wahnström. Dynasor—a tool for extracting dynamical structure factors and current correlation functions from molecular dynamics simulations. Advanced Theory and Simulations, 4(2):2000240, 2021. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/adts.202000240, doi:https://doi.org/10.1002/adts.202000240.

HAG15

Amir Haji-Akbari and Sharon C Glotzer. Strong orientational coordinates and orientational order parameters for symmetric objects. Journal of Physics A: Mathematical and Theoretical, 48(48):485201, Oct 2015. URL: http://dx.doi.org/10.1088/1751-8113/48/48/485201, doi:10.1088/1751-8113/48/48/485201.

HH16

Jonathan Higham and Richard H. Henchman. Locally adaptive method to define coordination shell. The Journal of Chemical Physics, 145(8):084108, 2016. URL: https://doi.org/10.1063/1.4961439, doi:10.1063/1.4961439.

HAN+16

Michael P. Howard, Joshua A. Anderson, Arash Nikoubashman, Sharon C. Glotzer, and Athanassios Z. Panagiotopoulos. Efficient neighbor list calculation for molecular simulation of colloidal systems using graphics processing units. Computer Physics Communications, 203:45–52, June 2016. doi:10.1016/j.cpc.2016.02.003.

JJ17

Matthew L. Jones and Eric Jankowski. Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology. Molecular Simulation, 43(10-11):756–773, 2017. URL: https://doi.org/10.1080/08927022.2017.1296958, doi:10.1080/08927022.2017.1296958.

KDvAG19

Andrew S. Karas, Julia Dshemuchadse, Greg van Anders, and Sharon C. Glotzer. Phase behavior and design rules for plastic colloidal crystals of hard polyhedra via consideration of directional entropic forces. Soft Matter, 15:5380–5389, 2019. doi:10.1039/C8SM02643B.

LD08

Wolfgang Lechner and Christoph Dellago. Accurate determination of crystal structures based on averaged local bond order parameters. The Journal of Chemical Physics, 129(11):114707, Sep 2008. URL: http://dx.doi.org/10.1063/1.2977970, doi:10.1063/1.2977970.

LP16

Hongjun Liu and Stephen J. Paddison. Direct calculation of the x-ray structure factor of ionic liquids. Phys. Chem. Chem. Phys., 18:11000–11007, 2016. URL: https://dx.doi.org/10.1039/C5CP06199G, doi:10.1039/C5CP06199G.

MKSTM13

Walter Mickel, Sebastian C. Kapfer, Gerd E. Schröder-Turk, and Klaus Mecke. Shortcomings of the bond orientational order parameters for the analysis of disordered particulate matter. The Journal of Chemical Physics, 138(4):044501, 2013. URL: https://doi.org/10.1063/1.4774084, arXiv:arXiv:1209.6180, doi:10.1063/1.4774084.

Ryc09

Chris Rycroft. Voro++: a three-dimensional voronoi cell library in c++. Technical Report, Lawrence Berkeley National Lab, 1 2009. doi:10.2172/946741.

Ste83

Paul J. Steinhardt. Bond-orientational order in liquids and glasses. Physical Review B, 28(2):784–805, 1983. doi:10.1103/PhysRevB.28.784.

TvAG19

Erin G. Teich, Greg van Anders, and Sharon C. Glotzer. Identity crisis in alchemical space drives the entropic colloidal glass transition. Nature Communications, 10:1–10, 12 2019. URL: https://doi.org/10.1038/s41467-018-07977-2, doi:10.1038/s41467-018-07977-2.

tW95

Pieter Rein ten Wolde. Numerical evidence for bcc ordering at the surface of a critical fcc nucleus. Physical Review Letters, 75(14):2714–2717, 1995. doi:10.1103/PhysRevLett.75.2714.

vAAS+13

Greg van Anders, N. Khalid Ahmed, Ross Smith, Michael Engel, and Sharon C. Glotzer. Entropically patchy particles: engineering valence through shape entropy. ACS Nano, 8(1):931–940, Dec 2013. URL: http://dx.doi.org/10.1021/nn4057353, doi:10.1021/nn4057353.

vAKA+14

Greg van Anders, Daphne Klotsa, N. Khalid Ahmed, Michael Engel, and Sharon C. Glotzer. Understanding shape entropy through local dense packing. PNAS; Proceedings of the National Academy of Sciences, 111(45):E4812–E4821, 2014.

vMFVF12

Jacobus A. van Meel, Laura Filion, Chantal Valeriani, and Daan Frenkel. A parameter-free, solid-angle based, nearest-neighbor algorithm. The Journal of Chemical Physics, 136(23):234107, 2012. URL: https://doi.org/10.1063/1.4729313, doi:10.1063/1.4729313.

VymvetalVondravsek11

Jiří Vymětal and Jiří Vondrášek. Gyration- and inertia-tensor-based collective coordinates for metadynamics. application on the conformational behavior of polyalanine peptides and trp-cage folding. Journal of Physical Chemistry A, 115(41):11455–11465, 2011. URL: https://pubs.acs.org/doi/full/10.1021/jp2065612, doi:https://doi.org/10.1021/jp2065612.

Wie12

Thomas Wieder. The debye scattering formula in n dimensions. Journal of Mathematical and Computational Sciences, 2:1086–1090, 2012. URL: https://www.scik.org/index.php/jmcs/article/viewFile/263/120.