Glotzilla Overview

Typically, researchers in soft matter and condensed matter physics write their own codes or use standard simulation packages. While packaged codes are usually efficient and accurate, they are not typically flexible. While custom codes are flexible, they are typically not reusable. We take a unique approach to writing simulation and data analysis tools by introducing a generalized framework named Glotzilla. This allows the codes to be efficient, accurate, reusable and extendable. Glotzilla provides a C++ library for generating custom molecular simulation codes and Unix command line functions for visualization, data analysis, etc.

Glotzilla provides functionality in the following categories:

• Dynamics and Monte Carlo simulation library.
• Visualization library with particle visualizer binary (vis3d) and data plotter.
• Data manipulation (filters for preprocessing of data).
• Data analysis library and binaries (g(r), MSD, S(q), RYlm, etc).
• Image processing library for extracting particle information from confocal images.

The main idea behind Glotzilla is to extend typical unix functionality to molecular-simulation specific applications. Unix-like operating systems, such as linux and Mac OS X, are initially supplied with a minimal set of functions and libraries for performing basic tasks. Familiar examples include the "ls" terminal command or the C library. To become a part of the standard unix distribution, a function or library must be (1) freely available, (2) small and manageable, and (3) general and useful to a wide audience.

As the molecular simulation community represents only a small subset of the broader unix community, it is not surprising that most unix functions and libraries are not particularly useful for performing molecular simulations. Glotzilla aims to amend this problem by providing a complete set of freely-available molecular-simulation-specific add-on functions and libraries that can work within the unix framework. Currently, Glotzilla provides a C++ library for writing molecular simulations, data analysis codes, visualization tools, and for interfacing with other simulation packages. Glotzilla also provides a collection of simulation-specific unix executables. Since Glotzilla extends unix, it is inherently standardized. That is, anyone who understands unix understands Glotzilla.

The development page for Glotzilla--including source, documentation, tutorials and sample code--is hosted by MatForge as part of the Materials Digital Library Pathway (MatDL).

• Glotzilla Development Page: http://www.matforge.org/glotzer/
• A full overview of Glotzilla can be found here .