AtomEye: an efficient atomistic configuration viewer

Abstract

AtomEye is free atomistic visualization software for all major UNIX platforms. It is based on a newly developed graphics core library of higher quality than the X-window standard, with area-weighted anti-aliasing. An order-N neighbourlist algorithm is used to compute the bond connectivity. The functionalities of AtomEye include: parallel and perspective projections with full three-dimensional navigation; customizable bond and coordination number calculation; colour-encoding of arbitrary user-defined quantities; local atomic strain invariant; coloured atom tiling and tracing; up to 16 cutting planes; periodic boundary condition translations; high-quality JPEG, PNG and EPS screenshots; and animation scripting. The program is efficient compared to OpenGL hardware acceleration by employing special algorithms to treat spheres (atoms) and cylinders (bonds), in which they are rendered as primitive objects rather than as composites of polygons. AtomEye can handle more than one million atoms on a PC with 1 GB memory. It is a robust, low-cost tool for surveying nanostructures and following their evolutions.

Comparison of the atomic level structure of the plastic crystalline and liquid phases of CBr2Cl2: neutron diffraction and reverse Monte Carlo modelling

“…The fcc structure remains, but the extent of the spots indicates that carbon atoms diverge from their original positions, due to large thermal movements. (Atomic configuration figures have been prepared by the ATOMEYE software [31]. Contour-plots have been made by the 'Confplot' software, which is part of the 'NFLP' program package.)…”

A new regime for mechanical annealing and strong sample-size strengthening in body centred cubic molybdenum

“…Large scale parallel molecular dynamics program LAMMPS 29 and visualization program AtomEye 30 were employed to perform the simulations and visualization. Finis-Sinclair potential 31 …”

How to identify dislocations in molecular dynamics simulations?

“…This measure has already been incorporated into the free visualization program AtomEye [35], using standard nearest neighbor cutoff distances for N i , which is the number of neighbors of atom i in the current configuration. This scheme works extremely well in practice [33] for directly visualizing microstructures, including point defects, dislocations, stacking faults, and their strain fields with color encoding.…”

“…Atoms with CN less than that of bulk crystal are defined as dislocation or defect cores. In practice, to clearly see the dislocation or defect cores, one needs to remove the perfectly coordinated atoms [35].…”