The NOMAD Advanced Graphics team has developed a number of virtual-reality (VR) examples that can be viewed with HTC Vive, which are presented below. Stereoscopic, 360° panoramic videos for outreach have also been developed from some of the post-processed datasets, in case you do not have access to an HTC Vive. 

We have developed three viewers:

Click here to learn more about how to use HTC Vive to experience our VR examples and for download links.

General viewer

The general viewer can be used to visualize datasets from the encyclopedia, or the result of user-created simulations. See here for download links for the software.

Visualization capabilities

Crystal structures, molecular dynamics (from xyz), electron density, Fermi surfaces and excitons can be visualized using the software. A collection of examples follow.

Crystal structures from NOMAD Encyclopedia

C10H14N8NiO2 - space group 12

Configuration file: 460225.ncfg (changed background colour, atom size, and added bonds and unit box)

Crystal structures from NOMAD Analytics

Bi5Rh

Configuration file: Bi5Rh.ncfg

Dataset: Analytics-Bi5Rh.json (this NOMAD Analytics result)

 

Molecular dynamics, from xyz files

Cytosine

Generated by thermal md at 300K, 241 timesteps.

Dataset provided by Raison Dsouza, Atomically Resolved Dynamics department, Max Planck Institute for the Structure and Dynamics of Matter.

Configuration file: cytosine.ncfg

Molecular dynamics simulation dataset: cytosine.xyz

Cracks in silicon

2880 atoms, 470 timesteps. Dataset provided by Prof Gábor Csanyi, Department of Engineering, University of Cambridge.

Relevant publication: Kermode et al, Nature, 2008

Configuration file: Si-csanyi.ncfg

Molecular dynamics simulation dataset (compressed, 22 MB): bulk_111_11b0_temp350.rar

IrO2 Nanoparticle

Nanostructures provided by Dr. Daniel Opalka and Jakob Timmermann - Chair of Theoretical Chemisty, Technical University of Munich, in the scope of the LRZ Summer of Simulation 2017

Configuration file: IrO2.ncfg

Molecular dynamics simulation dataset (compressed): 111_t1_4830.rar

Molecular dynamics with electron density

Adsorption of carbon dioxide on calcium oxide
Full densities
Molecular dynamics simulation dataset (1.8 GB)
Relative densities
Molecular dynamics simulation dataset (137 MB)

Excitons

Excitons in pyridine @ ZnO

Dataset provided by Olga Turkina, Solid-state theory group of the Physics Department of the Humboldt-Universität zu Berlin.

Data preparation by Dr Andris Gulans, Solid-state theory group of the Physics Department of the Humboldt-Universität zu Berlin, and Dr. Rubén García, Leibniz Supercomputing Centre of the Bavararian Academy of Sciences.

Please contact us if you are interested in this visualization.

Excitons in graphene-BN heterostructures

Dataset provided by Wahib Aggoune, Solid-state theory group of the Physics Department of the Humboldt-Universität Berlin.

This example was showcased at the Long Night of Sciences in Berlin (24 June 2017). You can also watch the video shown at the event.

Please contact us if you are interested in this visualization.

Fermi Surfaces

Silver

Dataset provided by Dr. Qiang Fu, Solid-state theory group of the Physics Department of the Humboldt-Universität zu Berlin.

Configuration file: AgFermi_Brillouin.ncfg

Surface: 1-Ag-brillouin.ply

Instructions to use the NOMAD Virtual Reality viewers for HTC Vive

General viewer

Download installer:

NOMADViveT-Setup.exe

For the configuration files and datasets:


-Download the files, and put them in one directory
-Decompress the zip or rar files if they exist.
-Double click on the .ncfg file and assign to the installed program NOMADViveT.exe

Control within the virtual reality environment:
-Trigger of controller 1 moves the user in the gaze direction
-Trigger of controller 2 moves the time forward (continuous)

-Side button of controller 1 moves the time backwards (discrete)
-Side button of controller 2 shows isosurfaces one-by-one, then atoms, then everything with transparency (but see caveat below).

-Menu (3 lines) button of controller 1 shows/hides atoms.
-Menu button of controller 2 starts/stops recording in c:/temp.

Caveats:
-At the beginning of the reaction, the relative densities may be zero (for example in the relative densities simulation of CO2@CaO), so nothing is shown if you press the isosurfaces button too early; if you press it by mistake, press it again until you see the atoms, then once more for the full system.
-Recording: SSD advised, affects tracking negativelly.
-A high-end graphics card is required.

Demos for specific chemical systems

Adsorption of carbon dioxide on calcium oxide

Shows the reaction of gaseous CO2 to CaO(001) surface.

Software and dataset

Since this is a 10 GB dataset, please contact us if you are interested in this visualization.

Excitons in lithium fluoride

Software and dataset

See here

 

Specific viewer for CO2@CaO

Since this is a 10 GB dataset, please contact us if you have interest in this visualization.

The control is similar to the general viewer, although the menu button functionality is not supported.

Specific viewer for LiF

Archive with standalone application (LiF-Vive.exe) and dataset here. (180 Mb)

The control is similar to the general viewer.

The left controller shows a vertical array of dots which correspond to the different isosurfaces. By pointing the controller up / down and pressing the trigger, the minimum (resp maximum) isosurface is removed. The side button selects in order among the available isosurfaces. The dot size corresponds to isosurface disabled (smallest), enabled but not shown currently (middle), and shown currently (large)

The right controller shows a cube with the 11x11x11 hole positions. Pointing the controller in a given direction will move the current hole position (shown with a larger dot) in that direction when the side button is pressed. The dots are colour-coded according to the maximum electron density at each hole position, from green for minimum among the hole positions to red for maximum.