in this issue - december 2017 - nomad · api based on elasticsearch, the leading open ... a...

The NOMAD (Novel Materials Discovery) LaboratoryA European Centre of Excellence

©NOMAD, 2017

The Novel Materials Discovery (NOMAD) Laboratory Centre of Excellence (CoE) maintains the largest Repository of input and output files of all important computational materials science codes. From its open access data, it offers several Big-Data Services to advance materials science and engineering.

https://nomad-coe.eu/ @NoMaDCoE www.facebook.com/nomadCoE

What’s New on the NOMAD Website?We’ve added new virtual reality demos and more. Check it out! https://nomad-coe.eu/

NOMAD Advanced Graphics Page

IN THIS ISSUE - December 2017What’s New on the NOMAD Website? ................................. 1

Hands-on Workshop: DFT and Beyond ................................ 2

Big-Data-Driven Materials Science Workshop ..................... 2

NOMAD Summer ................................................................... 3

Update from the NOMAD Archive and Repository ............. 3

Update from the NOMAD Encyclopedia .............................. 4

Latest news from the Advanced Graphics Team ............... 4

Update from the NOMAD Analytics Toolkit ......................... 5

Selected NOMAD Publication ............................................. 5

New Tools Developed at the 2nd NOMAD Hackathon ...... 6

NOMAD Scientific Advisory Committee Meeting .................. 6

GTT Users’ Meeting ................................................................ 6

NOMAD Invited Talks........................................................... 7

Upcoming NOMAD Events .................................................. 7

©NOMAD, 2017

https://nomad-coe.eu/ @NoMaDCoE facebook.com/nomadCoE

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Hands-on Workshop: DFT and Beyond This year’s incarnation of the long-standing summer school on ‘Density-functional theory (DFT) and methods beyond’ was held in Berlin between 31 July - 11 August. Early-career scientists from all over the world gathered to attend lectures by internationally renowned experts in the field and to directly apply the concepts in practical computer sessions. The general theme of the school - Novel Materials Discovery by Learning from Electronic-Structure Theory - as well as the focus on accuracy and reproducibility are well in-tune with the spirit of the NOMAD Laboratory CoE.

The event was organized by the Theory Department of the Fritz Haber Institute with support from the solid-state theory group at HU Berlin and the AIMS group from Duke University, as well as generous support from the Volkswagen Foundation. A complete set of video lectures and materials on electronic structure theory-based materials science is now available as a supplementary resource on the workshop webpage for anyone not able to attend the event (https://th.fhi-berlin.mpg.de/meetings/dft-workshop-2017/).

Big-Data-Driven Materials Science WorkshopThe Big-Data-Driven Materials Science Workshop (https://th.fhi-berlin.mpg.de/meetings/BDMS2017/) was held 11 - 13 September at the CECAM Headquarters in Lausanne, Switzerland. Many, probably most, areas in the basic and applied sciences and engineering are increasingly facing the challenge of dealing with massive amounts of data. This Big-Data challenge is not only about storing and pro-cessing huge amounts of data, but also about developing new methodologies to handle, understand, and exploit this massive amount of information, thus opening up unprecedented and qualitatively new routes for doing research. This workshop facilitated contact between the community that de-velops models and methodologies for data analytics and a growing part of the materials science community that increasingly makes use of Big-Data models and methodologies to address relevant problems in their field. The purpose of this contact was two-fold: to expose materials scientists to novel, state-of-the-art analytics methods, and to stimulate the theoretical data-analytics and -manage-ment community with practical problems where solutions may require further advanc-es in their disciplines. Attendees of the Big-Data-Driven Materials Science Workshop

Attendees of the DFT and Beyond Workshop

©NOMAD, 2017


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Update from the NOMAD Archive and RepositoryToday, the Repository and Archive support 30 solid state physics, quantum chemistry and atomistic simulation codes and include 16.5 TB of compressed raw data, 5.6 TB of compressed extracted meta data, 44 million total-energy calculations, and more than 800 million parsed quantities. To enable users to fully exploit this ever-growing dataset, the Repository search functionality has started to use a new REST API based on ElasticSearch, the leading open source solution for querying large datasets. The speed of search and filtering operations has improved considerably (from 15 seconds on average to less than one second).

Further improvements are in the pipeline. Currently, the Repository and Archive team is:

• maintaining and upgrading the parser and normalizer infrastructure, • finalizing the development of fully automated data handling, from initial upload to final user

access, making the Repository and Archive more robust and ensuring uploaded data is quickly available for use,

• enriching the REST API to meet internal and external users’ requests for specific metadata, cal-culated quantities, etc.,

• migrating data to the parquet format in order to enable access via Apache Spark, which offers more flexible Big-Data queries and processing,

• planning for sustainable future usage and restructuring the internal architecture, making it more resilient to load and usage peaks, and

• creating an easily re-deployable package which will allow for replication of the Repository and Archive at different sites worldwide, as publicly accessible mirrors or as local stand-alone copies.

Time-evolution of total-energy calculations in the Archive.

NOMAD Summer 40 representatives from academia and industry enjoyed NOMAD Summer, a Hands-on Course on Tools for Novel Materials Discovery from 25 - 29 September 2017 in Berlin, Germany. This summer school demonstrated NOMAD‘s achievements, and taught novice and advanced researchers how to use the many tools newly developed by NOMAD. The topics covered spanned the data collections in the NOMAD Repository and Archive, as well as the NOMAD Encyclopedia, which provides a scientific overview of the available data, and the Analytics Toolkit, which provides data-analytics tools specifically designed to enable the materials science community to predict novel materials with tailored functions. Advanced visualization tools developed by NOMAD that make physical processes easier to understand were also showcased. Slides from the lectures are now available (https://www.nomad-coe.eu/the-project/outreach/nomad-summer).

Hands-on virtual-reality sessions (left), NOMAD Summer attendees (center), Encyclopedia hands-on session (right)

©NOMAD, 2017


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Latest news from the Advanced Graphics TeamA demonstration of the newly developed NOMAD vir-tual-reality tools took place during the 11th Triennial Congress of the World Association of Theoretical and Computational Chemists (WATOC 2017). These tools have seen increased usage by materials scientists out-side of NOMAD, with the Atomically Resolved Dynam-ics Department of the Max Planck Institute for the Structure and Dynamics of Matter, the Bio Application Lab of the Leibniz Supercomputing Centre (Munich) and the Shell IT Centre in Bangalore, all setting up HTC Vive installations.

At the NOMAD Summer school (Berlin, 25 - 29 Septem-ber 2017), a demonstrator for the NOMAD remote visualization service hosted multiple concurrent ses-sions and enabled remote access to the hardware, software, and data deployed at the Max Planck Com-puting and Data Facility for workshop participants us-ing just a standard web browser. This web-based ac-cess makes remote visualizations easier to access for a wide range of users. The NOMAD Advanced Graphics team guided the participants through a hands-on tu-torial about employing the open source tool VisIt for analyzing and visualizing data from ab initio molecular dynamics simulations.

NOMAD Summer remote visualization service session

Images of virtual-reality representations, WATOC 2017

Update from the NOMAD EncyclopediaSince the Encyclopedia’s launch in April 2017, we have seen a considerable increase in the number of users who are exploring our newly developed tools. Besides integrating the Encyclopedia into the central NOMAD user management and authorization system, we have been busy with preparing the Encyclopedia for its next large update, which will happen towards the end of the year. Our users can expect a wide variety of novel features and functionalities, including complex searches, the handling of more material classes, (such as 1D materials), new methodologies (such as electronic structures computed with the GW approach) and a system that will allow users to report issues with specific data or functionalities.

The presentation of the Encyclopedia GUI and API at NOMAD Summer was a big success. The Encyclopedia session included presentations by Georg Huhs and Claudia Draxl about the aims and implementation of the Encyclopedia, as well as a practical, hands-on session. Moreover, our user experience expert, Luz Calvo, explained how to design a GUI optimized to meet end-user needs. She also took the opportunity to collect further user feedback, in particular from industry representatives to inform future developments of the GUI.

Encyclopedia landing page

©NOMAD, 2017


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Selected NOMAD PublicationThe team at the Max Planck Institute for the Structure of Dynamics of Matter in Hamburg, Germany has recently published ‘Controlling heat and particle currents in nanodevices by quantum observation’ (Quantum Materials 2, 38 (2017)). They demonstrated that in a standard thermoelectric nanodevice, the current and heat flows are not only dictated by the temperature and potential gradient but also by the external action of a local quantum observer that controls the coherence of the device. Dynamical quantum measurement offers new possibilities for the control of quantum transport far beyond classical thermal reservoirs. Through the concept of local projections, they illustrated how to create and directionally control the injection of currents (electronic and heat) in nanodevices. This scheme provides novel strategies to construct quantum devices with application in thermoelectrics, spintronic injection, phononics, and sensing among others.

A list of NOMAD Publications is available at: https://www.nomad-coe.eu/outreach-publications

Structure map for the classification of octet binary semicon-ductors considering five different ground-state crystal struc-tures. Final result of the tutorial by Ahmetcik and Ziletti.

Update from the NOMAD Analytics ToolkitThanks to the second NOMAD Hackathon (Berlin, 03 - 05 July) and work preparing for NOMAD Summer, several new tutorials were developed and existing ones were updated (https://analytics-toolkit.no-mad-coe.eu). In particular, new extended tutorials in the form of full, interactive lectures presented in a web-based notebook were deployed. Emre Ahmetcik and Angelo Ziletti prepared a tutorial for intro-ducing compressed-sensing techniques, starting from linear regression and following with a step-by-step introduction to sparse regularization and thorough cross-validation analysis (https://analytics-toolkit.nomad-coe.eu/hands-on-cs). Gábor Csányi and James Kermode implement-ed a tutorial on the machine learning of forces for small molecules via the Gaussian Approxi-mation Potential, based on the Smooth Over-lap of Atomic Position local-order descriptor (https://analytics-toolkit.nomad-coe.eu/hands-on-learning-atomic-charges). Ádám Fekete et al. developed a tutorial for the automatic recogni-tion of grain boundaries in crystals, via the un-supervised machine-learning technique of clus-tering (https://analytics-toolkit.nomad-coe.eu/hands-on-grain-boundaries).

Particle and energy currents in the steady state

©NOMAD, 2017


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New Tools Developed at the 2nd NOMAD HackathonThe second NOMAD Hackathon, held 3 - 5 July 2017 at the Fritz Haber Institute, Berlin, was another great success! There were 25 attendees in total and there was an exciting, community-building atmosphere.

We focused on developing the following tools:• a GUI for Elastic-Search queries over the Archive,• a user-friendly browser of the json files resulting from a query over the Archive,• a framework for allowing users to submit a job from an Analytics Toolkit notebook on an HPC

cluster,• a tool to present default, flexible statistics to users as part of query results,• a framework for adding new metadata,• a tool for handling “cube” files, containing volumetric data (scalar fields),• an OpenKIM-Repository Interface for NOMAD, • a Kubernetes-only deployment of the Archive and Analytics infrastructure, in order to prepare for

transfer to cloud-like services, and• a tool/tutorial for the prediction of band-gaps of crystals.

Some of the tools that were developed at the Hackathon were presented at our second Scientific Advisory Committee Meeting in Copenhagen. Other tools will be presented at future meetings.

NOMAD Scientific Advisory Committee Meeting We met members of our Scientific Advisory Committee (SAC) at our recent Year 2 Meeting in Copenhagen (09 - 11 Oct 2017). Prof. Igor Abrikosov (Linköpings University, Sweden), Prof. Samuel Kaski (Aalto University, Finland) and Prof. Dr. Thomas Schulthess (ETH Zürich and Swiss National Supercomputing Centre, Switzerland) joined us to give their valuable feedback on our progress to date. Four young NOMAD researchers (Maria Troppenz, Angelo Ziletti, Mikkel Strange and Carl Poelking) presented their work and the NOMAD team showcased recent developments from the Repository, Archive, Encyclopedia, Analytics Toolkit and Advanced Graphics, including a demonstration of our virtual-reality tools. We also discussed our HPC services and infrastructure, including plans to establish additional NOMAD HPC sites. VR demo for SAC members

GTT Users’ Meeting Georg Huhs spoke recently at the annual GTT-Technologies Users’ Meeting (http://www.gtt-technologies.de/workshops). This meeting serves as a forum for users to share their experiences with GTT products, get new ideas for their work and make suggestions for further developments. His talk, The NOMAD Encyclopedia: Getting access to millions of calculated materials properties, was well received by attendees, which included users from both industry and academia.

Attendees of the GTT Users’ Meeting

Upcoming NOMAD EventsThird NOMAD Industry Meeting

05 - 06 Feb 2018, London, United KingdomWe will showcase NOMAD tools and services for novel materials discovery in industrial settings. Industry attendees will have the opportunity to give feedback to improve our tools and services, as well as influence future developments. To join us, contact: [email protected]

NOMAD Data WorkshopApril 2018, Munich, Germany

NOMAD virtual-reality tools will be showcased at our second Data Workshop. Visitors will have the opportunity to visit the LRZ CAVE-like installation to explore chemical simulations in the field of materials science. To join us, contact: [email protected].

Newsletter Editors: Risto Nieminen ([email protected]) and Kylie O’Brien ([email protected])

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 676580.The materials presented and views expressed here are the responsibility of the author(s) only. The EU Commission takes no responsibility for any use

made of the information set out.

©NOMAD, 2017


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NOMAD Invited Talks• NOMAD was represented at the 11th Triennial Congress of the World Association of

Theoretical and Computational Chemists in Munich, Germany, August/September 2017. Matthias Scheffler an gave an invited talk: Big data of the chemical physics of materials: discovering interpretable patterns, correlations and causality and Claudia Draxl gave an invited talk: From evaluation of methodology to error bars in computational materials science.

• Alessandro De Vita gave a keynote talk Accurate Molecular Dynamics of Complex Systems using Big Data and On-The-Fly Learning at the Symposium of Theoretical Chemistry, Basel, Switzerland, August 2017.

• NOMAD researchers presented at the Hands-on Workshop: Density-Functional Theory and Beyond in Berlin, Germany, August 2017. Invited talks were given by Matthias Scheffler (Big data of the chemical physics of materials: discovering interpretable patterns, correlations and causality) and Claudia Draxl (Linearized augmented planewave methods and Excited states by solving the Bethe-Salpeter equation). Lecture videos are available (https://www.youtube.com/playlist?list=PLbgFiRV2JFy-VQ3D6cJjn5jkXmAsjQPiT).

• NOMAD Summer, our hands-on course on tools for novel materials discovery, included a keynote talk by Dieter Kranzlmüller and invited talks from many NOMAD researchers. Slides of the talks are available (http://meetings.nomad-coe.eu/nomad-summer-2017/index.php?n=Meeting.Program).

• NOMAD was presented by Georg Huhs at the New Trends in Computational Chemistry For Industrial Application that took place in Barcelona in the framework of Expoquimia, the largest exhibition related to chemistry in Spain (http://www.expoquimia.com/es/side-events and http://www.xrqtc.com/workshop2017/program/).

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