N8 HPC Network Event- New Approaches to Atomistic/Quantum Simulation of Materials

Are you active in, or interested in, the computational modelling/simulation of materials? Are you aware of what can (and cannot) be currently achieved using quantum mechanical or atomistic simulations? With the development of new algorithms, the ever growing rise in available computer power, and the availability of general purpose modelling codes, the answers might be different to what you think! In this 1-day meeting you will meet with leading researchers working with quantum / atomistic simulations from across the North of England.


This free event will consist of invited and contributed talks, and a poster session. This event will be relevant for beginners and experts alike.

Confirmed invited speakers:
· Professor Jamshed Anwar, Lancaster University
· Dr Colin Freeman, University of Sheffield
· Professor Roy Chantrell, University of York
· Professor Patrick Briddon, Newcastle University
· Dr Neil Drummond, Lancaster University
· Professor Mark Wilson, Durham University



10:00 – 10:20 Coffee & put up posters
10:20 – 10:30 Welcome / intro
10:30 – 11:00 Prof Roy Chantrell, University of York – Multiscale approaches to magnetic materials simulation
11:00 – 11:20 Dr Matthew Dyer, University of Liverpool – Computer Aided Discovery of Magnetic and Polar Oxides
11:20 – 11:40 Dr Chris Handley, University of Sheffield – Neural Networks for Chemical Simulation
11:40 – 12:10 Dr Colin Freeman, University of Sheffield – Computational advances in modelling inorganic-organic interfaces and biomineralisation
12:10 – 12:30 Dr Pierre Fayona, Lancaster University – Generating periodic amorphous models for micro-porous networks
12:30 – 13:00 Prof Jamshed Anwar, Lancaster University – Calculation of free energy from molecular simulation
13:00 – 14:00 Lunch + posters
14:00 – 14:30 Dr Neil Drummond, Lancaster University – High-Pressure Phase Diagram of Solid Molecular Hydrogen
14:30 – 14:50 Dr Phil Hasnip, University of York – Advanced Brillouin Zone Sampling Methods
14:50 – 15:10 Mr Marcin Szyniszewski, Lancaster University – Diffusion Monte Carlo Study of Charge Carrier Complexes in Two-Dimensional Semiconductors
15:10 – 15:30 Dr Benjamin Irving, Czech Technical University in Prague – Designing Ultralow Friction Surfaces
15:30 – 15:45 Coffee & take down posters
15:45 – 16:15 Prof Patrick Briddon, Newcastle University – Title TBA
16:15 – 16:45 Prof Mark Wilson, Durham University – Simulation studies of chromonics liquid crystal phases using a multiscale modelling approach
16:45 Close & final comments


Abstract Submission

Attendees are invited  to submit an abstract of no more than 200 words detailing a topic for a contributed talk or poster. Abstracts can be submitted during the registration process.  Please note that you do not have to submit an abstract to register for the event.


Thanks to the generous sponsorship of CCP5 and UKCP, registration for the event is free but is required.  Registration is now closed.

Key Dates:

Closing date for registration and abstract submission: Friday 11 December

Meeting date: 10.30am – 4.30pm, Friday 8 January


The Bar Convent, situated in central York, is just a five minute walk from the train station and a public Pay and Display car park is also located nearby. Coffee will be available from 10am and a free buffet lunch will be provided at 1pm.

Please pass this information on to any colleagues who may be interested in attending. If you have any further questions please do not hesitate to contact enquiries@n8hpc.org.uk

Local Organiser: Dr Matt Probert (Department of Physics, University of York).

The event is supported by N8 HPC, CCP5 and UKCP.

N8 HPC Network Event- Multiscale Computational Mechanics


This one day networking event on the 30th Oct at the University of Sheffield will bring together members of the N8 community who share a common interest in the topic of ‘Multiscale Computational Mechanics’ with a focus on structural continuum computational methods. The greatest challenges that we have to face are often of multiscale nature. The material behaviour must commonly be described at the microscopic, mesoscopic and macroscopic levels in order to understand the overall behaviour of the material.

Multiscale methods need to be developed across scales in order to design and manufacture safer, more reliable and more effective products. However, in order to tackle the great complexity associated to such multiscale approach, efficient computational approach must be developed and often High Performance Computing (HPC) systems must be harnessed to perform large calculations. Such complex multiscale nature is true for any discipline such as bioengineering, structural civil engineering, aerospace, automotive industry, material science, tribology, etc.

Therefore, this event will aim to draw academic and industrial researchers across disciplines together to mutually inform each other on the latest multiscale approach in their own field. We wish to promote inter-breeding across sectors and promote the establishment of new collaborations within the N8 HPC consortium as a result of the discussions within this event.

We hope to see longevity from the event with the ambition to develop it in to an annual networking day – informed by the best available experience and expertise.

Further information on topics to be covered during the day and information on key note speakers can be found in the event brochure.

Attendees are welcome to submit abstracts (max. 500 words)  through the event registration form.  The closing date for abstract submission is 5pm on the 20th of September 2015. Normal registration will remain open until 5pm on 19th October 2015.

Local organiser: Prof. Damien Lacroix, University of Sheffield

9:30 Registration & Welcome Refreshments
10:00 Opening Prof Mike Hounslow
Pro-Vice-Chancellor, University of Sheffield
10:10 Computational modelling of the mechanics of metallic biodegradable stents Prof Peter McHugh
National University of Ireland Galway
10:40 A bottom-up approach to describe protein-protein interactions in a continuum mechanics biomolecular model Dr Albert Solernou
University of Leeds
11:00 Morning Refreshment Break
11:30 Multiscale modelling of the musculoskeletal system Dr Pinaki Battacharya

University of Sheffield

11:50 Multi scale analysis of large composite structures Prof Silvestre Pinho
Imperial College London
12:20 Lunch
13:20 Civil engineering design using the Exascale desktop Dr Lee Margetts
University of Manchester
13:50 Multiscale modelling of material failure Dr Karl Travis
University of Sheffield
14:10 Microscopic modelling of fibre reinforced composite – a DEM approach Prof Jianqiao Ye
Lancaster University
14:30 Multiscale modelling of moisture diffusion coupled with stress distribution in CFRP composites Mr Maozhou Meng
Plymouth University
14:50 Afternoon Refreshment Break
15:15 Debate: HPC opportunities in multiscale computational mechanics  Chaired by Professor Damien Lacroix
University of Sheffield
15:45 N8 HPC Presentation Dr Robin Pinning


15:55 Closing Prof Damien Lacroix
University of Sheffield
16:00 END


Prof. Peter McHugh. 
Presentation title- “Computational Modelling of the Mechanics of Metallic Biodegradable Stents”. Guest Speakers:


Stents have revolutionised the treatment of arterial disease. Acting as a supporting scaffold, these small mesh devices are now routinely inserted into arteries where the blood flow has become dangerously restricted. In relation to coronary stents, one of the most fertile technological growth areas is biodegradable stents; here there is the possibility to generate stents that will break down in the body once the initial necessary scaffolding period is past (6-12 months) and when the artery has remodelled (including the formation of neo-intima). This brings advantages including the possibly of reduced risk of in-stent restenosis and late stent thrombosis, and the restoration of vasomotion potential. This is a very exciting technology and stents based on both metal and polymer platforms are emerging.

In this presentation a method to simulate the degradation of metal stents (magnesium alloy) is summarised, and implications for stent scaffolding performance presented. A stent angioplasty computational test-bed has been developed by the authors, based on the Abaqus software (DS-SIMULIA, USA), capable of simulating stent tracking, balloon expansion, recoil and in-vivo loading, in an atherosclerotic artery model. Additionally, a surface corrosion model has been developed and calibrated against experimental corrosion data for Magnesium alloy AZ31, and implemented in Abaqus/Explicit. This model takes two forms, a Uniform Corrosion model and a Pitting Corrosion model, and in both cases, material removal through corrosion is simulated by individual element removal from the finite element mesh. The model (in both forms) is implemented in the computation test-bed and used for stent analysis and design simulations. Recommendations are made on future stent design in relation to fundamental material properties and the optimization of stent geometry to maximize stent scaffolding support.

Prof. Silvestre Pinho. Presentation title- “Multi scale analysis of large composite structures”.


For the efficient structural design of large composite components, the numerical analysis of their mechanical response often requires different parts of the structure to be modelled at multiple length- and time-scales, eventually even using different physics. To this purpose, it is crucial to develop (i) suitable techniques for coupling areas of the structure discretized using different finite element types and (ii) numerical methods to efficiently compute equivalent homogenized properties to be used in both 2D FE models and in the coarse-scale subdomains of multiscale FE models of large composite components.

Regarding the first point, a novel Mesh Superposition Technique (MST) for the progressive transition between differently-discretized subdomains will be presented. The MST is applied to the multiple length/time-scale analysis of a low-velocity impact on a composite plate. Unlike using a sudden discretization-transition approach, the use of the MST avoids the undesirable stress disturbances and wave reflections at the interfaces between differently-discretized subdomains; therefore, it correctly captures the impact- induced damage pattern at a lower computational cost.

To address the second point, a novel set of PBCs named Multiscale Periodic Boundary Conditions (MPBCs), that represents the first set of PBCs that apply to reduced Unit cells (rUCs) and enable the direct two-scale (solid-to-shell) numerical homogenization of periodic structures, including their bending and twisting response, will be presented. Therefore, the MPBCs enable the use of rUCs to obtain the full ABD matrix needed in the coarse-scale subdomains of the MST models, with a significant computational cost reduction compared to the use of standard Unit Cells (UCs).

The results of these analyses demonstrate the relevance of the proposed approaches for an efficient multiple length/time-scale simulation of large composite structures.

Dr. Lee Margetts. Presentation title- “Civil engineering design using the Exascale desktop”.


One of the many challenges in multiscale modelling is dealing with increased computational complexity and computational cost for realistic simulations which involve different time and length scales. Exascale computing is expected to be with us in a couple of years and this new capability will be a game changer for multiscale modelling. But how long will it take these technologies to benefit industry? A recent survey from NAFEMS has shown that the majority of engineers in industry prefer to use their own workstation for engineering analysis, with little use of commercial software on HPC systems. This presentation will give an overview of the challenges of developing multiscale modelling software for Exascale systems. In particular, it will set out how open source academic software could form the basis of a new generation of modelling tools for the Exascale desktop of 2030. The talk will focus on examples of multiscale modelling in the field of civil engineering.



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N8 HPC Network Event- HPC for Quantum Materials Simulation

Over 50 participants including PhD students and professors from N8 institutions came together for N8 HPC’s first network event “HPC for Quantum Materials Simulation”, held at The University of York. The event was designed to facilitate informal discussions between various groups of people active or interested in computational modelling and simulation of materials.


The day consisted of key presentations from Dr Gilberto Teobaldi of The University of Liverpool and Professor Stewart Clark of Durham University, and presentations and posters from PhD students and staff at Manchester, Leeds, Lancaster, Newcastle and York universities.

The day also included two breakout discussions which allowed groups to explore possible scenarios such as what they’d do with 10,000 times their current amount of computing resource.

In 12 months’ time N8 HPC will be holding a follow up meeting, focusing on the broader area of atomistic simulation of materials. This will allow us to see what new collaborations have been made as a result of the event and what else has been accomplished since the event. If you are interested in hosting an N8 HPC Network event at your institution, please get in touch.

HPC for Quantum Materials Simulation- Friday 9th January 2015 at The Bar Convent, York

Are you active in, or interested in, the computational modelling / simulation of materials? Are you aware of what can (and cannot) be currently achieved using quantum mechanics based techniques? With the ever growing rise in available computer power, and the development of general purpose modelling codes, the answers might be different to what you think! In this 1-day meeting you will meet other researchers working with quantum materials simulation from across the N8 Universities to discuss your current research and ideas for the future. This event will be relevant for beginners and experts alike.




This event will run from 10am-5pm and will consist of

  • Invited presentations by Prof Stewart Clark of Durham University and Dr Gilberto Teobaldi of the University of Liverpool
  • Contributed talks (see below for more details)
  • Two group discussion sessions
  • Presentation on N8 HPC facility and how to access Polaris

Full agenda:

10:00 –10:20 Coffee
10:20 –10:30 Welcome / Intro
10:30 –11:00 Invited Presentation – Dr Gilberto Teobaldi, University of Liverpool – HPC Screening of One-Dimensional Inorganic Materials for Photocatalytic Applications.
11:00 –12:00 Contributed Talks:
11:00-11:20 Keith McKenna (York)-  Grain Boundaries in PV Materials
11:20-11:40 Elaheh Mostaani (Lancaster)- VDW and Bi-Layer Graphene with QMC
11:40-12:00 Stephen Stackhouse (Leeds)- Thermal Conductivity of Planetary Core Materials. Slides coming soon.
12:00 –12:45 Discussion Topic 1
12:45 –14:00 Lunch + Posters
14:00 –14:30 Invited Presentation- Prof Stewart Clark, University of Durham – First  principles DFT methods for the solid state. Slides coming soon.
14:30-15:10 Contributed Talks:
14:30-14:50 Trevor Hardcastle (Leeds)- EELS of Graphene with Plasmons
14:50-15:10 Oras Al-ani (Newcastle)- Atomistic Modelling of Segregation of Iron at Twist Grain Boundary
15:10-15:30 Joydeep Pal (Manchester)- Piezoelectric Nanostructures
15:30 – 15:45 Coffee
15:45 – 16:30 Discussion 2
16:30 – 16:45 How to Access Polaris
16:45 Meeting Close


Invited Presentations

Professor Stewart Clark, Professor of Computational Physics, University of Durham.

Professor Clark’s work lies in developing theoretical methods and computational tools for electronic structure calculations. He is also an author of the CASTEP code.

Presentation Title: First principles DFT methods for the solid state

With recent theoretical and computational advances we have been able to calculate the properties of condensed matter systems from first principles. That one can even hope to do this is down to the accuracy of quantum mechanics in describing the chemical bond. Dirac’s apocryphal quip that after the discovery of quantum mechanics “the rest is chemistry” sums it up: if one can solve the Schrodinger equation for something – an atom, a molecule, assemblies of atoms in solids or liquids – one can predict every physical property.  Dirac’s statement doesn’t quite show how difficult doing “the rest” is, and it has taken great effort and ingenuity to take us to the point of calculating some of the properties of materials with reasonable accuracy. The impact of simulations on our thinking about condensed matter problems is immense. Here I shall concentrate on just a few elements of what is a very large subject. I shall discuss how to ‘simulate experimental measurements’ focusing on one of the most successful approaches, the application of density-functional perturbation approach and consider why this method turned out to be so important. To illustrate the usefulness of some of the methods I shall present highlights of a number of simulations to indicate the wide applicability of the method.

Dr Gilberto Teobaldi, University of Liverpool

Bio: Gilberto Teobaldi (GT) holds a Lectureship and an EPSRC Career Acceleration Fellowship at the Stephenson Institute for Renewable Energy, Department of Chemistry, the University of Liverpool. GT received his PhD in Chemistry from Bologna University (Italy) in 2005, and then worked as a research associate at the Surface Science Research Centre (University of Liverpool, UK: 2005-2009), and at the Institute for Scientific and Industrial Research (Osaka University, Japan: 2009-2010) in collaboration with the Department of Physics and Astronomy of University College London (UK). GT’s scientific interests are at the interface between Chemistry, Computational Materials Science and Surface Science.

Presentation Title: HPC Screening of One-Dimensional Inorganic Materials for Photocatalytic Applications

In the pursuit of a more sustainable energy-economy, growing efforts are devoted to the development of cost-effective photocatalytic systems capable of converting sunlight into industrially viable forms such as electrical power or fuels. Atomic-scale understanding of the different materials and interfaces constituting such systems is crucial for rational, cost-effective progress. This, in turn, requires access to the atomic-scale parameters that govern the thermodynamics and kinetics of charge (energy) transfer processes at photo catalytic interfaces. The experimental challenges in time- and atom-resolved characterization of these interfaces, together with the improving accuracy-compromises of Density Functional Theory (DFT) simulations, have made High Performance Computing (HPC) an important component in fundamental research in photocatalysis. This is because HPC DFT-simulations can relatively inexpensively access (most of) the atomic and electronic factors underpinning the (mal-)functioning of a given photocatalytic interface. Furthermore, as presented and discussed here, DFT-simulations can be also used to identify elements hardly accessible to experimental analysis, which could be used to develop novel strategies and solutions. Along these lines, I will present recent findings on the intriguing local redox properties of Imogolite nanotubes, which suggest potentially rewarding application of this class of one-dimensional materials in photocatalysis.


Contributed Presentations and Registration

The event is free and tickets must be booked online by 5pm Monday 22nd December. All attendees should submit an abstract of no more than 200 words detailing a topic for a contributed talk or poster. Given the breadth of potential topics and the limited time available, we ask that the topic should NOT be soft condensed matter or biophysics/biochemistry based – there may be a subsequent meeting with these materials as its focus. Abstracts can be submitted in the text box at the bottom of the registration form on the above link.

Key Dates:

Closing date for registration: Monday 22 December

Meeting date: Friday 9 January



The Bar Convent, situated in central York, is just a five minute walk from the train station and a public Pay and Display car park is also located nearby. Coffee will be available from 10am and a free buffet lunch will be provided at 1pm.

Please note that if you are travelling by car, the road to the car park on Nunnery Lane is shut due to road works in one direction, however  Nunnery Lane WILL be open from Micklegate Bar (near the train station) going towards the Bishopthorpe Road. Alternatively, there is both short and long stay car parking available at the train station (postcode YO24 1AB).

Any questions?

If you have any further questions please do not hesitate to contact enquiries@n8hpc.org.uk

Local organiser: Dr Matt Probert, Department of Physics, University of York.


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