VΙ-SEEM NAT-GR LS+ : 2018 NWChem Workshop

10 Sep 2018, 09:00 → 11 Sep 2018, 14:00 Europe/Athens

National Hellenic Research Foundation (NHRF)

NWChem is a computational quantum chemistry package for the studies of electronic structure, geometry and properties of molecules and periodic systems.  It also includes classical and quantum (Carr-Parinello) molecular dynamics simulations. The package exhibits excellent parallel scaling and has been  shown to run on hundreds of thousands of cores on top Supercomputing systems.

NWChem is developed and maintained at EMSL, a US Department of Energy User Facility, located at Pacific Northwest National Laboratory.

This workshop is aimed at new and experienced users of NWChem. Basic knowledge of computational chemistry is desirable. A workshop will be a mix of morning lectures and afternoon hands-on tutorials where participants will have the opportunity to explore the various capabilities as well as interact with NWChem developers. Users and developers interested in developing and implementing new capabilities in NWChem are also welcome.

Organizers

• Theoretical & Physical Chemistry Institute / National Hellenic Research Foundation (D. Tzeli)
• VI-SEEM/GRNET (Z. Cournia, D. Dellis)
• Pacific Northwest National Laboratory, USA (E. Apra, K. Kowalski, S.S. Xantheas)
   

The maximum number of participants is 45.

Prerequisites

Bring your own laptop in order to be able to participate in the training hands on. Please have an ssh client installed in your laptop for the hands-on session. If you don’t have a laptop, you might work in pairs with a colleague or please let us know. Send an email at dtzeli@eie.gr and we will provide you with a tablet or laptop.

Course language is English.

About the instructors

Dr. Sotiris Xantheas is known in the chemical physics scientific community for his research in intermolecular interactions in aqueous ionic clusters and the use of ab-initio electronic structure calculations to elucidate their structural and spectral features. His research has ranged from the computation of potential energy surfaces for various chemical reactions using correlated wavefunctions to the elucidation of reaction paths governing carbene ring opening processes and the location and characterization of intersections of potential energy surfaces of the same symmetry in polyatomic systems. He has recently utilized the results of high-level electronic structure calculations to parametrize a family of ab-initio based interaction potentials for water and used those potentials to simulate the macroscopic properties of liquid water and ice.

Dr. Karol Kowalski received his Ph.D.  in theoretical physics in 1996 from Nicolaus Copernicus University of Torun, Poland. He leads the development of the parallel   implementations of high-accuracy Coupled Cluster (CC) methodologies in the NWChem modeling sofwtare.  He has published 150 peer-reviewed journal articles related to fundamental work on the renormalized CC methods and method of moments of CC equations, equation-of-motion CC formalism for excited electronic states, linear response CC theory for calculating molecular properties, and multi-reference CC methods for strongly correlated systems. He developed methods that have been applied to describe a wide spectrum of many-body systems ranging from nuclei and molecules, to the systems being at the cross-road between molecular- and nano-science.

Dr. Edoardo Apra' received his Ph.D.  in chemistry in 1993 from the University of Turin, Italy. He is the primary  contributor to the LCAO DFT module in the NWChem  chemistry code. He has published 90 peer-reviewed journal articles dealing with the applications of electronic structure methods to problems in catalysis, interfacial science, structural properties of molecules and materials. Another topic focus of his publications has been the implementation of high performance computational algorithms as part of the  software development of computational chemistry packages.

Dr. George Fanourgakis received his Ph.D. in theoretical chemistry in 1999 from the University of Crete.  Over the last few years, he has been interested in condensed phase dynamics and has performed simulations of liquid water and aqueous solutions. He has relied on a combination of techniques such as high-level ab initio calculations, development of a new generation of classical force-fields and  quantum path integral molecular dynamics (PIMD) simulations. He has developed several efficient and highly parallelized computer codes for molecular simulations, new approaches and theoretical extensions of existing methods to study a variety of structural, thermodynamic and dynamic properties of condensed phase systems. Currently, he also investigates the possibility of the application of Machine Learning techniques in the field of the theoretical physical chemistry. He has published 32 peer-reviewed journal articles.

Dr. Zoe Cournia is a Researcher – Assistant Professor level at the Biomedical Research Foundation, Academy of Athens, where she works on anticancer drug design, design of drug delivery systems and biomolecular modeling using computational techniques. She graduated from the Chemistry Department, University of Athens in 2001 and completed her PhD at the University of Heidelberg in Germany in 2006. She then worked as a postdoctoral researcher at the Chemistry Department, Yale University, USA, on computer-aided drug design and in 2009 she became a lecturer at Yale College. She has been awarded the American Association for Cancer Research Angiogenesis Fellowship (2008), the "Woman of Innovation 2009" Award from the Connecticut Technology Council, USA, the Marie Curie Fellowship from the European Union (2010), the "Outstanding Junior Faculty Award" from the American Chemical Society (2014) and the first "Ada Lovelace Award" from the "Partnership for Advanced Computing in Europe" (2016). She is currently teaching at the Master’s program “Information Technologies in Technology and Medicine” at the Department of Informatics and Telecommunications, National University of Athens.

ARIS - System Information

ARIS is the name of the Greek supercomputer, deployed and operated by GRNET (Greek Research and Technology Network) in Athens. ARIS consists of 532 computational nodes seperated in four “islands” as listed here:

•     426 thin nodes: Regular compute nodes without accelerator.
•     44 gpu nodes: “2 x NVIDIA Tesla k40m” accelerated nodes.
•     18 phi nodes: “2 x INTEL Xeon Phi 7120p” accelerated nodes.
•     44 fat nodes: Fat compute nodes have larger number of cores and memory per core than a thin node.

All the nodes are connected via Infiniband network and share 2PB GPFS storage.The infrastructure also has an IBM TS3500 library of maximum storage capacity of about 6 PB. Access to the system is provided by two login nodes.

System documentation is available at : http://doc.aris.grnet.gr/

 

Monday, 10 September

09:00 → 09:15 Welcome and logistics. Dr. D. Tzeli

09:15 → 10:00 Brief introduction to Computational Chemistry. Prof. S.S. Xantheas

10:00 → 10:45 Introduction of NWChem software, Dr. E. Apra / Dr. K. Kowalski

10:45 → 11:00 Cofee Break

11:00 → 11:45 Ground and excited states with DFT and TDDFT. Dr. E. Apra / Dr. K. Kowalski

11:45 → 12:30 Correlated methods for ground and excited states. Dr. K. Kowalski

12:30 → 14:00 Lunch Break

14:00 → 14:30 Industry 4.0: Materials Science in the Decision Take Process, Dr. Xenophon Krokidis, Managing Director, SCIENOMICS

14:30 → 14:50 Introduction to GRNET facilities. Dr. D. Dellis

14:50 → 17:30 Hands-On

Tuesday, 11 September

09:00 → 09:45 Calculation of intermolecular interactions. Prof. S. S. Xantheas

09:45 → 10:15 Classical molecular dynamics. Dr. Z. Cournia

10:15 → 10:45 Path integral nuclear quantum molecular dynamics. Dr. G. Fanourgakis

Convener: Dr G Fanourgakis

10:45 → 11:00 Cofee Break

11:00 → 13:30 Hands-On