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Scanning Probe Microscopy Controller and Data Visualization Software
...Based on several hardware options it supports a commercially available DSP hardware and provided also Open Source Code for all the low level signal processing tasks and instrument controls in a most flexible and adaptable manner.
All latest software is available via SVN only or Live Demo/Install CD: http://www.ventiotec.de/linux/GXSM-Linux.iso
Dodona is a molecular dynamics program which aims to treat nanostructures. It is provided with a basic interpretater language and can easily be extended with plugins. It supports basic matrix and vector manipulation in a Matlab/Octave-fashion way.
Vistools is a set of tools to easily visualize some scientific data, without need to learn difficult API, so you can see your 3d results very quickly. Also some sci tools for which we made it, including vector field tracing and simple optimization.