Tutorial 5

Visualizing simulations from Archive and Analytics in virtual reality using NOMAD VR.

If you are using Google Cardboard, see also Tutorial 10.

Introduction

We use the NOMAD Analytics Toolkit tutorial Querying and visualizing the content of the NOMAD Archive to find the relevant datasets in the archive.

If you reached this page directly from the NOMAD Analytics Toolkit, please click here to have an overview of the virtual reality viewer developed by NOMAD (NOMAD VR). The viewer can take advantage of HTC Vive, Oculus Rift, Samsung GearVR, Google Cardboard for Android or iOS, or the CAVE-like environment at the Leibniz Supercomputing Centre. Please download the appropriate viewer for your device, or contact us if you'd like to use the LRZ facilities.

This tutorial explains how to obtain a VR-ready dataset from the Archive, which can be visualized within NOMAD VR. For each material, you will obtain a ZIP file containing both the dataset and an NCFG configuration file.

Your Beaker notebook may already support direct download of the ZIP file corresponding to each VR-ready material. If this is the case, you will see after each material a Nomad VR link (in addition to archive, calculation and section_run links). Decompress the ZIP file obtained by clicking on the Nomad VR link, and transfer the resulting directory to the computer or phone running NOMAD VR. Otherwise, this tutorial will show you how to obtain the ZIP file from a nmd:// url.

The phone-based NOMAD VR apps will request an NCFG on program start (a step-by-step example using NOMAD VR for Google Cardboard for Android is provided here). Please select the relevant NCFG from your material. The PC-based NOMAD VR takes the NCFG file as argument; either double-click on the NCFG, or drag & drop it into the EXE, depending on your system configuration. On the LRZ CAVE, you also should pass the NCFG as a parameter to the program.

 

Example

Accessing the tutorial within the analytics toolkit

In the tutorial, we enter the following query:

    atom_symbols = C

and click "Search"

The first result is:

Results About 3,178,000 results (0.29 seconds)

#1

nmd://N9_Y3hSMnDA2EjMR6tq8aAARjIvkH/CFpPH8JROWvod3RbnueeqbZNkybqL

Program Name:
Gaussian
Chemical Formula:
OC6H8
Atom Symbols:
["O", "C", "H"]
Basis Set Type:
gaussians
System Type:
Molecule / Cluster
XC Treatment:
hybrid
System Composition:
OC6H8
System Reweighted Composition:
O7C40H54

From the NOMAD url nmd://N9_Y3hSMnDA2EjMR6tq8aAARjIvkH/CFpPH8JROWvod3RbnueeqbZNkybqL we can request virtual reality datasets by:

http://nomad.srv.lrz.de/cgi-bin/NOMAD/materialAnalytics?N9_Y3hSMnDA2EjMR6tq8aAARjIvkH/CFpPH8JROWvod3RbnueeqbZNkybqL

The result is the file

N9_Y3hSMnDA2EjMR6tq8aAARjIvkH_CFpPH8JROWvod3RbnueeqbZNkybqL.zip

which contains a directory N9_Y3hSMnDA2EjMR6tq8aAARjIvkH_CFpPH8JROWvod3RbnueeqbZNkybqL with the following two files: OC6H8.ncfg, material.json

Use these files within NOMAD VR to visualize the different geometries in virtual reality (see detailed instructions for Google Cardboard for Android here).

Using the development version of the analytics toolkit

If you are using the new tutorial, VR-ready download links are already included. E.g. the query "atom_species = C" yields the following result:

Results
About 3,217,000 results (0.36 seconds)

#1
nmd://NwV8hYozPeklCwijei_Dez2q3F38_/C--03-lBsTgG7rndyKwsnGAv67Zz6

Program Name: FHI-aims
Chemical Formula: O3N3C8H15
Atom Symbols: ["H", "C", "N", "O"]
XC Functional Name: ["GGA_C_PBE", "GGA_X_PBE"]
Electronic Structure Method: DFT
Basis Set Type: numeric AOs
System Composition: O3N3C8H15
System Reweighted Composition: O11N11C28H51
Links:

Nomad VR archive calculation section_run

Where the NOMAD VR link sends the user the corresponding ZIP file.

Overview of the automatically generated NCFG

# Material N9_Y3hSMnDA2EjMR6tq8aAARjIvkH/CFpPH8JROWvod3RbnueeqbZNkybqL
background 0 0 0
atomscaling 0.5
analyticsjson material.json
displaybonds
displayunitcell
showcontrollers

The analyticsjson option indicates the path to the relevant dataset.

Specific Geometries

To restrict the json to a specific geometry, you can indicate the section_system you are interested in by using the standard notation, e.g.:

http://nomad.srv.lrz.de/cgi-bin/NOMAD/materialAnalytics?N9_Y3hSMnDA2EjMR6tq8aAARjIvkH/CFpPH8JROWvod3RbnueeqbZNkybqL/section_run/0c/section_system/1c

(section_system:1)

Datasets with lattice vectors

If lattice vectors are present, we can display the unit cell

In the tutorial, we enter the following query:

    atom_symbols = C

    and

    program_name = FHI-aims

    and

    lattice_vectors

and click "Search"

The first result is:

Results About 89,500 results (0.47 seconds)

#1

nmd://N4nt_VjeEO9ElydTIkQ_-m5QfWAMt/CLZMxrn8NtER2mEnuj9pXndRy5dVK
Program Name:
FHI-aims
Chemical Formula:
C6
Atom Symbols:
["C"]
Basis Set Type:
numeric AOs
Crystal System:
hexagonal
Spacegroup Nr:
191
System Type:
Bulk
XC Treatment:
LDA
System Composition:
C6
System Reweighted Composition:
C100

From the NOMAD url nmd://N4nt_VjeEO9ElydTIkQ_-m5QfWAMt/CLZMxrn8NtER2mEnuj9pXndRy5dVK we can request virtual reality datasets by:

http://nomad.srv.lrz.de/cgi-bin/NOMAD/materialAnalytics?N4nt_VjeEO9ElydTIkQ_-m5QfWAMt/CLZMxrn8NtER2mEnuj9pXndRy5dVK