We propose a parameter-free algorithm for the identification of nearest neighbors. The algorithm is very easy to use and has a number of advantages over existing algorithms to identify nearest-neighbors. This solid-angle based nearest-neighbor algorithm (SANN) attributes to each possible neighbor a solid angle and determines the cutoff radius by the requirement that the sum of the solid angles is 4π. The algorithm can be used to analyze 3D images, both from experiments as well as theory, and as the algorithm has a low computational cost, it can also be used “on the fly” in simulations. In this paper, we describe the SANN algorithm, discuss its properties, and compare it to both a fixed-distance cutoff algorithm and to a Voronoi construction by analyzing its behavior in bulk phases of systems of carbon atoms, Lennard-Jones particles and hard spheres as well as in Lennard-Jones systems with liquid-crystal and liquid-vapor interfaces.
Skip Nav Destination
Article navigation
21 June 2012
Research Article|
June 20 2012
A parameter-free, solid-angle based, nearest-neighbor algorithm
Jacobus A. van Meel;
Jacobus A. van Meel
1
FOM Institute for Atomic and Molecular Physics
, Science Park 104, 1098 XG Amsterdam, The Netherlands
Search for other works by this author on:
Laura Filion;
Laura Filion
2Department of Chemistry,
University of Cambridge
, Lensfield Road, Cambridge CB2 1EW, United Kingdom
Search for other works by this author on:
Chantal Valeriani;
Chantal Valeriani
3SUPA, School of Physics and Astronomy,
University of Edinburgh
, Mayfield Road, Edinburgh, EH9 3JZ, Scotland
and Departamento de Quimica Fisica, Facultad de Quimica, Universidad Complutense de Madrid
, 28040 Madrid, Spain
Search for other works by this author on:
Daan Frenkel
Daan Frenkel
2Department of Chemistry,
University of Cambridge
, Lensfield Road, Cambridge CB2 1EW, United Kingdom
Search for other works by this author on:
J. Chem. Phys. 136, 234107 (2012)
Article history
Received:
March 02 2012
Accepted:
May 29 2012
Citation
Jacobus A. van Meel, Laura Filion, Chantal Valeriani, Daan Frenkel; A parameter-free, solid-angle based, nearest-neighbor algorithm. J. Chem. Phys. 21 June 2012; 136 (23): 234107. https://doi.org/10.1063/1.4729313
Download citation file:
Sign in
Don't already have an account? Register
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Pay-Per-View Access
$40.00
Citing articles via
A theory of pitch for the hydrodynamic properties of molecules, helices, and achiral swimmers at low Reynolds number
Anderson D. S. Duraes, J. Daniel Gezelter
DeePMD-kit v2: A software package for deep potential models
Jinzhe Zeng, Duo Zhang, et al.
Electronic structure simulations in the cloud computing environment
Eric J. Bylaska, Ajay Panyala, et al.
Related Content
Parameter-free coordination numbers for solutions and interfaces
J. Chem. Phys. (January 2020)
Simple and efficient methods for local structural analysis in polydisperse hard disk systems
J. Chem. Phys. (May 2024)
A transferable artificial neural network model for atomic forces in nanoparticles
J. Chem. Phys. (November 2018)
Locally adaptive method to define coordination shell
J. Chem. Phys. (August 2016)
Neutral nitrogen acceptors in ZnO: The 67Zn hyperfine interactions
J. Appl. Phys. (March 2014)