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

The overall goal of this procedure is to visualize and analyze three dimensional real world nanostructure behavior. This is accomplished by first creating an interactive 3D visualization system with simulation capability. The second step is constructing and investigating 3D nano structures in the interactive environment.

Next, A 3D nano helical structure is prepared from a chosen bulk material and the system is used to conduct tensile or other simulations. The final step is visualizing and analyzing the resultant 3D real world atomistic behavior of the nano structure. Ultimately, the 3D visualization system in this work can be used for investigating realistic nano structures via molecular dynamics or MD simulations toward materials innovation research.

I had the idea about this method back in uc Davis when I was collaborating with Dr.Oliver k Craigo on the use of this technology for research and learning specifically in the field of material science. 3D visualization and interaction are important tools for the exploration and analysis of materials computationally. So we hope that this effort will help others to expand Further demonstrating this procedure will be Miguel Diaz, a graduate student from my laboratory.

To begin create a rigid camera suspension frame directly above the front edge of the 3D capable television near the ceiling for best coverage. Mount three, infrared or ir. Cameras on swivel mounts directly above the front corners and the front center of the 3D tv.

Ensure that the coverage angle of each camera just grazes the front surface of the tv. Next, assemble and configure the equipment and software for the 3D virtual reality or 3D VR visualization system as described in the text protocol, carefully place the controller where it can be reached easily from the modeling computer, taking care not to touch or move the spherical IR tracking markers attached to it. Also carefully place the 3D goggles on the TV stand, avoiding the reflective markers following additional setup.

As detailed in the text protocol, open a terminal window with several tabs on the modeling computer desktop on the tracking computer. Verify the ethernet adapter IP address by typing IP config in a command window on the modeling computer. Open a terminal window tab and check within the VR devices dot cfg file that the server name specifies the tracking computer ethernet adapter IP address on the tracking computer.

Allow the opti track rigid body tool software to open completely. Then click the large button near the top menu labeled load calibration result. Browse to and open the appropriate camera calibration file.

After the file is loaded, click the file menu and select load rigid body definitions. Browse to and open the appropriate rigid body definition file for the tracked controller and 3D goggles on the right most pane of the tracking software. Locate the section labeled streaming and expand the section under the VRPN streaming category.

Verify that the port number listed is 3 8 8 3, and check the broadcast frame data box inside the VRPN streaming engine category on the modeling computer. Bring up a tab in the terminal window created earlier in this session. Navigate to and initiate the VR device demon software.

Next, follow the prompt to press buttons one and two on the WiMo simultaneously. If the activity was successful, the window will now display VR device server waiting for client connection within the previously created modeling computer terminal window. Select the third tab to initiate the NCK software.

Navigate to the NCK installation directory and type the command shown here and also listed in the text protocol being very careful not to touch or loosen the attached tracking markers. Put on 3D goggles and pick up the controller. Adjust head goggle viewing position to ensure 3D goggles are receiving 3D TV IR emitter sync signal, allowing 3D VR viewing of TV display in order to have a tool set to add, move, and delete atoms.

Assign NCK command associations to buttons on the controller by first pressing and holding the wiimote home button, which brings up the main NCK onscreen menu. Navigate to and select the override tools menu item, and then release the home button. This allows assignment of commands to different buttons on the controller independently of one another.

To associate the WiMo trigger button with the action of manipulating atoms within NCK, press and hold the trigger button. Navigate the onscreen NCK menu to dragger and select six degree of freedom dragger before releasing the trigger. The trigger is now associated with the action of manipulating the atoms.

To assign the function of adding an atom to the plus button on the wiimote, bring the main menu up by pressing and holding the home button. Navigate to structural unit types and select triangle before releasing the home button. Next press and hold the plus button and select six DOF dragger as before.

Then release the plus button. The plus button is now associated with creating new atoms of the type selected in this case, carbon atoms represented by triangles. To assign the function of deleting an atom to the minus button on the wiimote, bring up the main menu by pressing and holding the home button.

Then navigate to structural unit types and select delete selected units. Before releasing the home button, press and hold the minus button and select six DOF dragger as before. Then release the minus button.

The minus button is now associated with deleting atoms. Follow a similar procedure to assign the functions of lock selected units to the one WiMo button and unlock selected units to the two controller button. Once the controller buttons have been configured, create a carbon nano tube using NCK by first using the plus button to add two three bond triangular carbon atoms to the NCK workspace.

Manipulate these using the trigger button until they join at a vertex. Then add four more carbon atoms to create a hexagonal star shape. Using the home menu, navigate to input output menus and then to save units, move the six pointed structure away from its current position.

Now use the home menu to again navigate to input output menus and then load units. Repeat the last two steps until a six by six sheet of hexagonal. Six atom rings has been created.

Using the one button lock, one atom in the top row and an opposing atom in the bottom row, the locked atoms will be marked with a pink color. Using the trigger button, carefully move one of the locked atoms in a circular arc until its free. Vertex approaches the free vertex of the opposing locked Adam.

Once successfully joined, unlock both of the atoms using the two button. Continue similarly locking, joining and unlocking opposing vertices in the carbon sheet. Effectively zipping the sheet into a final carbon nano tube.

Import an initial crystalline silicon dioxide cubicle model into the 3D VR NCK software and investigate the initial structure. Run a simulated melt quench procedure on this initial ordered structure to produce an amorphous silicon dioxide structure. Then import the resulting new disordered silicon dioxide model into the 3D VR NCK software and investigate the structure.

Create a silicon dioxide, nano springing or nano ribbon out of the new amorphous solid. Using the open source code, nano springing carver and associated instructional documentation. Use the lamps molecular dynamics package to perform tensile simulations on the nano or nano ribbon as reported elsewhere.

Finally, use the open source software tools, visualize molecular dynamics, image magic and FF m peg to create snapshots and animation of the helical nano structure throughout this simulation or presentation in the 3D VR visualization system. This protocol outlined here demonstrates how to create an integrated laboratory system for high performance atomistic simulation and interactive 3D visualization of nanostructures. Using the 3D VR visualization system, complex nano structures such as a carbon nano tube with real world atomic behavior can be constructed and investigated.

Silica helical nano ribbon has then been created and subjected to simulated tensile loads, and the results of the simulation have been visualized in three dimensions to investigate the structural transformation and failure of the nano structure under such tensile conditions. After watching this video, you should be able to analyze and visualize any nanostructure model behavior using a 3D visualization system like the one we have in the lab.