Virtual Reality and Ray Tracing for Computational Materials Science Data Visualization

Sean Lin(Student), Jinlin Xu(Student)

Professor Andre Schleife(Mentor)
Abstract
Computational materials science research produces large amounts of static and time-
dependent data that is rich in information. Extracting relevant information from these data to
determine underlying processes and mechanisms constitutes a significant scientific challenge.
Through this project, we have used and developed stereoscopic rendering techniques to visualize
the structure of existing and novel materials for solar-energy harvesting and optoelectronic
applications. We have developed codes based on the open-source ray-tracer Blender to produce
image files. We have visualized stereoscopic images by using virtual reality viewer Google
Daydream View headset.
Background
Materials science research generates large sets of data about properties, structures, and
chemical bondings of materials. Analyzing the mechanism behind the data and determining the
process which generates the data make materials modeling possible and provide scientists with a
visual representation of the data. Scientists will also be able to take a closer look at atomic level
behaviors of materials molecules through immersive images. This project aims to develop an
application that is intended to be shown at the Engineering Open House, which allows high
school students to come to the campus and enjoy featured exhibits created by engineering
students. This application visualizes complicated molecular structures in a comprehensive way
and allows users to interact with molecules by moving atoms around, viewing molecular
structures in different modes, and seeing detailed atomic structures. It helps student visitors have
a better understanding of the structures of various molecules they have learned in class.
Summary of Main Achievements
We have converted the data about molecular structures into space-filling and polyhedral
modes. We have added atomic structures like ionic bonds and electron density to molecules. We
have also implemented a list of functions we got from our targeted users, like switching between
different modes, displaying names of molecules and atoms, and moving around and changing
the size of molecules. Finally, we have improved the user experience by changing visual and
interaction design, and we made the application more user-friendly.
Methodology
For the data visualization part, we visualized atoms and added atomic structures like
electron density via VESTA. We referred to VESTA: a Three-Dimensional Visualization System
for Electronic and Structural Analysis for adding isosurfaces and file format converting. We then
used Blender as a format converter to convert .vesta files to .fbx files. We then imported the file
into Unity for application development.
For the application development part, we heard from high school students who
participated in outreach events held by the Department of Materials Science. We learned
what they want to see in the application. We then made a list of functions for our application
and implemented those functions in Unity. We also showed the application to our peers and
potential users after implementation and improved it based on the feedback we got.
Literature Review
Preliminary implementation of this project already exists and is done by student intern
Pei Liu, Sujay Shah, Siddharth Ahuja, and Zekun Wei. They developed functions like displaying
the main menu, downloading data files from a web server, and visualizing molecules.
Results
We have finished the following functions for the application:
1. Visualization of molecules in space-filling and polyhedral modes. The space-filling mode
only shows atoms, while in the polyhedral mode, atoms have ionic bonds and planes connected
between them.

Figure 1 Polyhedral mode Figure 2 Space-filling mode

2. Visualization of atoms with electron densities as isosurfaces.

Figure 3 Electron densities are shown as isosurfaces

3. Display the name of the molecule. In the main page, users are able to see the names of
all molecules, and in each molecule's subpage, users are able to see the name of the
corresponding molecule.
4. Switch between space-filling mode, polyhedral mode, and mode with electron densities.
5. Display the name of the atom when the user clicks on it.
6. Minify/Magnify molecules via controller touchpad.
7. Move and rotate molecules. By clicking buttons in the app and then moving the controller,
users are able to move molecules around and rotate them.
8. When the user clicks an atom, all other atoms that are the same element as the clicked atom
will be highlighted.

Figure 4 Main menu

Figure 5 Subpage for Aluminum in the polyhedral mode

 Figure 6 Subpage for K3Fe(CN)6 in the space-filling mode

Discussion
Our research results could be potentially beneficial for the following area:
1. Scientific research. Most of the data generated by materials science research are at an
atomic scale, and it is hard to analyze the data without a deep understanding of the behaviors
and properties of a material. By visualizing the data about materials, scientists will be able to
clearly see relative atomic positions, electronic structures, and other important information
about a material and have a better understanding of its properties. This project aims to
develop an application that visualizes data about different molecules in the virtual reality view,
which provides a more vivid view of molecular structures compared to the traditional 2D view.
The research results may potentially be used for research on solar-energy harvesting and
optoelectronic applications. 

2. Educational outreach. Students usually are not exposed to materials science until they are in
college since materials science is not in the curriculum in most high schools. By developing
this application, which will be shown at the Engineering Open House, we hope to garner interests
among high school students attending and help them have a better understanding of
fundamental concepts in materials science and chemistry. By using the application, high
school students will have the opportunity to get to know names of different materials, have a
detailed view of their atomic structures, and play around with materials molecules, which
provides a more interactive way to learn about different materials than looking at 2D images
in the textbook. This application will help high school students be exposed to basic ideas in
materials science and potentially become interested in the field. 

Further Work
There are three possible future development aspects of the application:
1. We hope to hear more from high school students at outreach events and make changes to our
application accordingly. We will improve the user interface of the application based on
 feedback from users. We will also perform user and task analysis by examining what facts
about materials high school students might be interested in and add those to the application.
Finally, we will improve the graphical user interface to enhance the efficiency and ease of
use and make the application look more aesthetically pleasing.
2. We plan to turn this application into an open-source application and publish it to Google
Play. Additionally, we would like to extend the platform the application is hosted at. Right
now, the application can only be used on Android phones, and we would like to make it
available on laptops. We will modify our code and make it be compatible with Windows PC
and Microsoft Mixed Reality Headset.
3. We plan to turn the application into a data visualization helper application for people who
don't have much coding background. Detailed implementation has not been specified yet, but
the general idea is to allow people to visualize their data via the applications by following
the instructions we provide.
Conclusion
By using VESTA and Blender, we have visualized most of the data about molecular
structures and imported them into the application. In Unity, we have implemented all functions
that we aimed to have at the beginning of the program. The results of this project are potentially
beneficial for scientific research and high school educational outreach. There are three possible
further development aspects of the application, and we hope to work on them in the future.