Abstract
The study of molecular dynamics simulations is largely facilitated by analysis and visualization toolsets. However, these toolsets are often designed for specific use cases and those only, while scripting extensions to such toolsets is often exceedingly complicated. To overcome this problem, we designed a software application called AViS which focuses on the extensibility of analysis. By utilizing the dataflow programming (DFP) paradigm, algorithms can be defined by execution graphs, and arbitrary data can be transferred between nodes using visual connectors. Extension nodes can be implemented in either Python, C++, and Fortran, and combined in the same algorithm. AViS offers a comprehensive collection of nodes for sophisticated visualization state modifications, thus greatly simplifying the rules for writing extensions. Input files can also be read from the server automatically, and data is fetched automatically to improve memory usage. In addition, the visualization system of AViS uses physically-based rendering techniques, improving the 3D perception of molecular structures for interactive visualization. By performing two case studies on complex molecular systems, we show that the DFP workflow offers a much higher level of flexibility and extensibility when compared to legacy workflows. The software source code and binaries for Windows, MacOS, and Linux are freely available at https://avis-md.github.io/.
Highlights
The study of molecular behaviour through analysis and visualization of Molecular Dynamics (MD) simulations is becoming more widely adopted with the increasing processing power of modern computers
Dataflow programming for the analysis of molecular dynamics with the AViS software application software offer very extensive analysis capabilities, and they allow complex modifications and extensions to the framework, a deep knowledge of their respective scripting interfaces are required, and hard constraints applied to valid scripts are a hurdle for novice users, even those well versed in bare-bone analysis programming
We have introduced Dataflow Programming for the analysis of MD data by creating AViS and demonstrated its flexibility in two complex case studies
Summary
The study of molecular behaviour through analysis and visualization of Molecular Dynamics (MD) simulations is becoming more widely adopted with the increasing processing power of modern computers. Dataflow programming for the analysis of molecular dynamics with the AViS software application software offer very extensive analysis capabilities, and they allow complex modifications and extensions to the framework, a deep knowledge of their respective scripting interfaces are required, and hard constraints applied to valid scripts are a hurdle for novice users, even those well versed in bare-bone analysis programming. Common analysis methods such as hydrogen bonds or Common Neighbor Analysis are often provided in most applications and new algorithms are seldom implemented for integration with the software, except for advanced users. Other software such as OVITO [9] uses a combined visual workflow of analysis and visualization, and enabling complicated techniques to be separated and applied in steps. By using AViS, we are able to simplify and accelerate various analysis and visualization tasks, as described in the sections that follow
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