Aten—An application for the creation, editing, and visualization of coordinates for glasses, liquids, crystals, and molecules

Abstract

Aten is a tool for Linux, Mac, and Windows platforms to ease the creation, editing, and visualization of coordinates for use in, for example, molecular dynamics simulations. The code handles gas-phase molecules in addition to crystals, surfaces, and liquids, providing standard tools to edit "by the atom" along with specific "by the box" methods suited to periodic systems, including full crystallographic spacegroup packing definitions. Visualization of systems encompasses the standard drawing styles and may be mixed with an arbitrary number of other basic objects, such as arrows and geometric objects allowing creation of scenes involving vector fields, coarse-grained particles, etc. Standard molecular mechanics forcefields can be read in, edited, applied to molecules using the built-in chemical typing language, and subsequently used to calculate energies and forces, minimize energies with respect to coordinates, decompose energies into contribution by molecule type, etc. Monte Carlo methods are available with which to generate random configurations of N-component systems, or solvate around molecules or in specific regions within existing configurations. Supported file formats are governed by user-defined "filters," which provide flexibility of input/output as well as the ability to define custom or extended formats of traditional files. Forcefield descriptions for loaded systems can be output and formatted for use as input to common codes. All features can be accessed by a comprehensive GUI and scripting language based on the C syntax.