INJAVIS — INteractive JAva VISualization
The software package
Injavis (acronym for INteractive JAva VISualization) displays, analyzes, and manipulates particle simulation data. An emphasis lies on geometry and structural analysis as well as interactivity. The main input and output file format is .pos, which is a format developed specifically for Injavis and designed to be easily human readable and editable. The software is written in the Java programming language, which makes it transferable among operating systems without recompilation. Rendering and all analysis is performed using self-written code without external libraries. The software includes some newly developed analysis tools and algorithms.
Examples of application:
- analyze (many) simulation trajectories
- identify crystal structures of a self-assembly simulation
- perform interactive simulation by coupling Injavis to external MD or MC code
- educational / classroom use to teach MD and MC simulation
- generate high-quality images for publication
Injavis was involved in some form in many publications, including: PRL (2008), Nature (2009), ACS Nano (2012), Nature Chemistry (2013), Nano Letters (2013), Nature Materials (2015), Science (2017), Nature Communications (2018), PRL (2019), PNAS (2019). All cover images of the group were generated at least in part with Injavis.
Over the years, many features have been added. Injavis implements these features in modules. Some modules show as boxes on the screen, some are non-graphical. Each module corresponds to one menu item:
File: load and rapidly sample through configurations and trajectories
Edit: manipulate particles interactively
View: modify view parameters
Simulation: interactive simulation by connection to simulation codes
Objects: advanced rendering: anti-aliasing and ambient occlusion
Particles: various particle types spheres, (sphero)polyhedra, cylinders, etc.
Data: graphs of simulation observables
Box: extraction of unit cells from noisy simulation data*
RDF: radial distribution function
Bonds: bond orientational order diagram, including symmetry analysis*
Diffraction: diffraction images via FFT from arbitrary angles*
Network: network-based structural analysis
The features marked with * contain new or improved algorithms or methods that were, at least at the time of implementation and to the best of my knowledge, not found anywhere else.
History and Usage
Injavis has been developed since 2007 by me () with some additions and bug fixes by members of the Glotzer Group at the University of Michigan. Development started during my PhD thesis and later continued extensively while a postdoc funded by Deutsche Forschungsgemeinschaft and later Assistant Research Scientist at the University of Michigan. Development has always been geared towards my own research and usage interests in mind. However, over the years, colleagues and researchers from other labs found Injavis useful and repeatedly asked me to share the software for use in their research. This is the motivation for the present webpage: To make Injavis available as a tool to the community. Recently (since 2016), there has not been much development. But I believe the software can still be useful and continues to be used it in my own university lectures.
While the majority of the features should be intuitive together with the documentation provided below, some features are hidden or might not work perfectly. I never received any funding for the development, which means there is no time to implement new features or fix bugs, except if connected to my own work or serious. This being said, I am always interested to hear feedback and suggestions. Also, I am open for collaborations involving the use and further development of Injavis. Please contact me.
How to Cite
If the software helped your research and contributed to your publication or thesis, I would be grateful for a recognition of my development work by your acknowledgment of its use by the following citation:
INJAVIS — INteractive JAva VISualization
Zenodo, 4639570 (2021)
The Injavis software is provided free of charge and without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. The full license information (MIT license) is included in the software and can be accessed from the menu: (Objects → About).
Requirement: up-to-date Java Runtime Environment (JRE).
Run from the command line:
java -Xmx4096m -jar injavis.jar
A documentation can be found under the link above. Thanks to Rose Cersonsky!