Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

Summary

A new computational system featuring GPU-accelerated molecular dynamics simulation and 3D/VR visualization, analysis and manipulation of nanostructures has been implemented, representing a novel approach to advance materials research and promote innovative investigation and alternative methods to learn about material structures with dimensions invisible to the human eye.

Abstract

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

Introduction

Materials science is an interdisciplinary field that examines the structure-property relationships in matter for their application to many areas of science and engineering. As structure-property relationships are investigated through computer simulations in addition to experimentation, computational tools offer complementary features that can enhance research efforts. While nanomaterials are of interest to scientists and have redeeming value for their potential social impact, this size regime is fraught with many challenges found particularly in experimentation.

Computer simulations allow scientists and engineers to perform specialized test....

Protocol

1. Install 3D/VR Modeling Software on Modeling PC

1. Install LINUX base operating system on modeling PC (Ubuntu x86 / AMD64 depending on hardware).
2. Modify LINUX base operating system.
   1. Install libraries and add functionality as necessary.
3. Install VRUI and NCK 3D/VR modeling software on Modeling PC⁶.
   1. Check related websites^1,6 to obtain latest versions of all modeling software components.
   2. Compile, configure and test VRUI.
   3. Install and test NCK.

2. Set Up Tracking System¹

1. Mount IR Tracking Cam....

Results

This 3D/VR Visualization System presents new opportunities for conducting materials science studies. As this immersive environment operates in real time, in the form of 3D input and display, the researcher is presented with a fully interactive nanoscaled instrument². By following the protocol presented here, a silica helical nanoribbon was created in this step-by-step fashion. A snapshot of this structure produced from LAMMPS MD is shown in Figure 7. This structure was subjected to simulated t.......

Discussion

Critical elements in the successful installation and usage of the 3D/VR Visualization System are detailed in the Physical Environment and Design Considerations and Special Considerations in supplemental materials. Important installation considerations include 3D display height for comfortable long-term standing or seated usage, maximized tracking camera mounted height to create a large 3D working area, stable tracking camera and 3D display support to maintain configuration over time, and.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Samsung 61" 3D-capable high definition DLP TV	Samsung	http://www.samsung.com/us/video/tvs	See Protocol Section 3 (Step 3.2)  (Large format 3D-capable TV)
Alienware Area51 750i modeling computer	Alienware	http://www.alienware.com	See Protocol Section 1 (Step 1.1)  (Modeling computer)
HP EliteBook 8530w tracking computer	HP	http://www.hp.com	See Protocol Section 2 (Step 2.3)  (Tracking computer)
V100:R2 IR tracking cameras (3)	Naturalpoint	http://www.naturalpoint.com/optitrack/products/v100-r2/	See Protocol Section 2 (Step 2.1) and Reference [4]  (Tracking cameras)
OptiTrack Tracking Tools IR tracking software	Naturalpoint	http://www.naturalpoint.com/optitrack/software/	See Protocol Section 2 (Step 2.3) and Reference [4]  (Tracking software)
3D Goggles and 3D TV IR sync emitter	Ilixco	http://www.i-glassesstore.com/dlp3d-wireless-2set.html	See Protocol Section 3 (Step 3.2) and Reference [5]  (3D goggles)
Wiimote 3D controller	Nintendo	http://www.nintendo.com/wii	See Protocol Section 3 (Step 3.2)  (Wiimote)
VRUI, NCK and associated 3D/VR modeling software	Open source software	http://idav.ucdavis.edu/~okreylos/ResDev/NanoTech/index.html	See Protocol Section 1 (Step 1.3) and References [1,6]  (VRUI, NCK)
LAMMPS molecular dynamics software	Open source software	http://lammps.sandia.gov/	See Protocol Section 5 (Step 5.2) and Reference [12]  (LAMMPS)
NanospringCarver program code and files	UC Merced - open source	http://tinyurl.com/qame8dj	See Protocol Section 5 (Step 5.4) and References [16-17]  (NanospringCarver)
MATLAB GUI files	UC Merced - open source	http://tinyurl.com/qame8dj	See Protocol Section 5 (Step 5.4) and References [16-17]  (NanospringCarver)
Atomistic bulk glass input file	UC Merced - open source	http://tinyurl.com/qame8dj	See Protocol Section 5 (Step 5.4) and References [16-17]  (NanospringCarver)