moleculardynamics simulation has become a powerful tool to deepen the understanding of the radiation damage mechanism of nuclear materials. Extracting point defects, analyzing their diffusion, and visualizing the def...
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moleculardynamics simulation has become a powerful tool to deepen the understanding of the radiation damage mechanism of nuclear materials. Extracting point defects, analyzing their diffusion, and visualizing the defect dynamics in atomic simulation data are important, but challenging tasks to understand irradiation behavior. In the past, irradiation defects have been detected using the so-called Wigner-Seitz cell method and analyzed by the statistics of Frenkel pairs. However, traditional analysis modes blur the fine details of defect dynamics. In this paper, we present a visual analysis pipeline for domain scientists to comfortably explore radiation damage simulation data. We couple defect identification, defect clustering, molecule visualization, and tracking graph to form an integrated visual exploration approach. We describe the application of our approach in practice to study defect clustering in Ni-Fe alloy. With our proposed pipeline, defects can be extracted in a robust way, clusters can be visualized with a favorable representation, in-depth data analysis can be setup, and defect dynamics can be demonstrated in greater detail than previously possible. Graphic Abstract
The winners of the 2012 IEEE visualization Contest combined methods from molecular, flow, and scalar data visualization to reveal the characteristics and processes in the contest data. Because the simulated material d...
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The winners of the 2012 IEEE visualization Contest combined methods from molecular, flow, and scalar data visualization to reveal the characteristics and processes in the contest data. Because the simulated material didn't behave according to theory from textbooks, one challenge was to find meaningful visualizations to facilitate exploratory analysis. The contest winners created an interactive visual-analysis application based on MegaMol, their visualization framework. The tailored visualizations revealed data characteristics such as thermal vibrations and the spatial distribution of polarization domains. Domain expert knowledge verified the results. This video at http://***/RXnNKekY7VE shows the dataset used and the development of vector clusters over time. [ABSTRACT FROM AUTHOR]
VMD (Visual moleculardynamics) is a molecularvisualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assem-blies, etc. This unit will serve as an introductor...
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A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the form...
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A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented.
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures ...
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VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more ''representations,'' in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate moleculardynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design;the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
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