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Software solutions to the challenges of materials modelling

08 - 09 June 2022 07:55 - 15:30

Satellite meeting organised by Professor Scott Woodley, Professor Sir Richard Catlow FRS, Professor Nora H de Leeuw and Professor Angelos Michaelides FRS.

In the Discussion meeting the aim was to discuss the challenges and achievements in materials modelling that will and have been enabled by High End Computer (HEC) resources. The Satellite meeting moved on to the software solutions recently developed and still required in order to effectively exploit HEC to address the scientific challenges identified during the Discussion meeting.

The schedule of talks and speaker biographies can be found below. Speaker abstracts can also be found below. 

Attending this event

This meeting has taken place.

Enquiries: contact the Scientific Programmes team.

Organisers

  • Professor Scott Woodley, University College London, UK

    Scott Woodley is a Professor of Computational Chemistry and Physics with University College London, London, UK. He is the PI of two Design and Development Working Groups of the Excalibur Project - Materials and Molecular Modelling DDWG (EPSRC grant EP/V001507) and Particles At the eXascale on HPC (EP/W026775) - and co-I on two Excalibur crosscutting projects (EP/W00772X, EP/W007711). He leads UK's HEC Materials Chemistry Consortium (EP/R029431), and he is the Director of the Materials and Molecular Modelling Hub (one of UK's Tier-2 HPC centres; EP/L000202 and EP/T022213). He also led three EPSRC software development projects for materials modelling and structure prediction (EP/0022235, EP/K038958, EP/I03014X) and the lead creator of two web-based databases and tools, one for modelling nanoclusters and another for modelling surfaces.

  • Sir Richard Catlow FRS, Cardiff University and University College London, UK

    Richard Catlow is developing and applying computer models to solid state and materials chemistry: areas of chemistry that investigate the synthesis, structure and properties of materials in the solid phase. By combining his powerful computational methods with experiments, Richard has made considerable contributions to areas as diverse as catalysis and mineralogy. His approach has also advanced our understanding of how defects (missing or extra atoms) in the structure of solids can result in non-stoichiometric compounds. Such compounds have special electrical or chemical properties since their contributing elements are present in slightly different proportions to those predicted by chemical formula. Richard’s work has offered insight into mechanisms of industrial catalysts, especially involving microporous materials and metal oxides. In structural chemistry and mineralogy. Simulation methods are now routinely used to predict the structures of complex solids and silicates, respectively, thanks to Richard’s demonstrations of their power. Richard was Foreign Secretary of the Royal Society from 2016 until 2021. He has for many years been involved in the exploitation of High Performance Computing in Modelling Materials.

  • Professor Nora H de Leeuw, University of Leeds, UK

    Nora de Leeuw is Professor of Computational Chemistry at the University of Leeds, UK, and she also holds a Chair position in Theoretical Geochemistry and Mineralogy at Utrecht University in the Netherlands. Her research is focused on the atomic-level understanding of composite materials and complex processes in biomedical applications and materials for sustainable energy applications, including novel catalysts for CO2 conversion to synthetic fuels, and materials relevant for nuclear energy, fuel cell and battery applications. Nora has held a number of independent research fellowships, including an EPSRC Advanced Research Fellowship (2002), Royal Society Wolfson Research Merit Award (2009), Royal Society Industry Fellowship (2012) and AWE William Penney Fellowship (2014). She is a Fellow of the Royal Society of Chemistry, elected Fellow of the Learned Society of Wales and elected Member of Academia Europaea.

  • Professor Angelos Michaelides FRS, University of Cambridge, UK

    Angelos Michaelides obtained a PhD in Theoretical Chemistry in 2000 from The Queen's University of Belfast. Following this, he worked as a Post-doctoral Research Associate and Junior Research Fellow at the University of Cambridge and then at the Fritz Haber Institute, Berlin as an Alexander von Humboldt Research Fellow and subsequently Research Group Leader. Between 2006 and 2020 he was at University College London where he was Director and Co-Director of the Thomas Young Centre: The London Centre for the Theory and Simulation of Materials and the founding Director of the Materials and Molecular Modelling Hub. Since 2020 he has been the 1968 Professor of Chemistry at the University of Cambridge.

Schedule

Chair

Professor J Christian Schoen, Max-Planck-Institute for Solid State Research, Germany

07:55 - 08:00 Welcome
08:00 - 08:30 The NOMAD Artificial-Intelligence toolkit: turning materials-science data into knowledge and understanding

The talk describes recent glass-box (in contrast to black box) AI developments for learning rules for materials properties and functions by artificial intelligence and for identifying materials genes.1,2

Then Professor Scheffler will present the Novel-Materials-Discovery (NOMAD) Artificial-Intelligence (AI) Toolkit3, a web-based infrastructure for the interactive AI-based analysis of the material-science. The present implementation is linked to the NOMAD Archive, the largest database of computational materials-science data worldwide4, 5. However, the NOMAD Oasis, a local, standalone server can be used as well. Users of the NOMAD AI toolkit can modify the offered Jupyter notebooks towards their own research work.

1C Draxl and M Scheffler, Big-Data-Driven Materials Science and its FAIR Data Infrastructure. Plenary Chapter in Handbook of Materials Modeling (eds. S. Yip and W. Andreoni), Springer (2020). Reprint: doi.org/10.1007/978-3-319-44677-6_104

2M Boley and M Scheffler, Learning Rules for Materials Properties and Functions. Roadmap for Machine Learning in Electronic Structure Theory, ed. by S. Botti and M. Marques; Preprint: https://arxiv.org/abs/2104.01352

3The NOMAD AI Toolkit: https://nomad-lab.eu/aitoolkit

4C Draxl and M Scheffler, The NOMAD Laboratory: From Data Sharing to Artificial Intelligence. J. Phys. Mater. 2, 036001 (2019). Reprint DOI: 10.1088/2515-7639/ab13bb

5The NOMAD Data Base: https://nomad-lab.eu/prod/v1/staging/gui/about/information

Professor Matthias Scheffler, The NOMAD Laboratory at the FHI of the Max Planck Society, Germany

08:30 - 09:00 Protocols for fitting first principles force fields using machine learning

Abstract not available at time of publication.

Professor Gábor Csányi, University of Cambridge, UK

09:00 - 09:30 Predicting material properties with the help of machine learning

A central goal of computational physics and chemistry is to predict material properties using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as chemical potential, heat capacity and thermal conductivity. In this talk, Dr Cheng will first discuss how to enable such predictions by combining advanced statistical mechanics with data-driven machine learning interatomic potentials. As an example, the researchers computed the phase diagram of water from density functional theory at the hybrid level, accounting for thermal fluctuations, proton disordering and nuclear quantum effects. As applications in high-pressure physics, they simulated the high-pressure hydrogen system and found supercritical behaviour above the melting line and mapped the phase diagram of superionic water. Besides thermodynamic properties, Dr Cheng will talk about how to compute the heat conductivities of liquids just from equilibrium molecular dynamics trajectories. During the second part of the talk, Dr Cheng will rationalise why machine learning potentials work at all, and in particular, the locality argument. Dr Cheng will show that a machine learning potential trained on liquid water alone can predict the properties of diverse ice phases, because all the local environments characterising the ice phases are found in liquid water.

Dr Bingqing Cheng, Institute of Science and Technology, Austria

09:30 - 10:00 Coffee
10:00 - 10:20 Contributed talk: A universal and modern approach towards molecular modelling at first principles accuracy, Venkat Kapil, University of Cambridge, UK

Progress in the atomic-scale modelling of matter over the past decade has been tremendous, primarily due to improvements in techniques that compute or approximate the Born-Oppenheimer (BO) potential energy landscape (PES) and methods that describe the motion of atoms on the BO PES. Consequently, it is now possible to identify (meta)stable states, sample configurations consistent with the appropriate thermodynamic ensemble, and estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic structure and empirical-potential codes. To address this problem, Venkat Kapil presents a new version of the i-PI software. This release extends the scope of the software, originally on path integral methods, towards a general and easily extensible framework that implements advanced algorithms for ‘moving’ atoms and ‘communicates’ with codes that compute the PES seamlessly through a server-client connection. The agnosticism of i-PI with the calculation of the PES allows a facile combination of advanced sampling methods with the latest developments in electronic structure methods and machine learning potentials. This leads to a universal and modern approach toward first-principles level materials modelling, as showcased by studies of complex systems such as porous materials for gas separation, pharmaceutically active molecular crystals, and monolayer water confined in graphene nanochannel.

10:20 - 10:40 Contributed talk: Efficient computation of optical properties of large-scale heterogeneous systems, Joseph Prentice, University of Oxford, UK

The optical properties of large-scale (>1000 atoms) heterogeneous systems are of interest in several fields, from photovoltaics to biological systems. Computing such properties accurately from first principles, however, is challenging; even if only a small region is optically active, quantum mechanical environmental effects must often be included, and the cost of applying a quantitatively accurate level of theory is prohibitive. The work presented here demonstrates how such calculations can be performed efficiently from first principles via two methods: an extension of the spectral warping method of Ge et al, and a novel combination of quantum embedding (specifically embedded mean-field theory) and linear-scaling (time-dependent) density functional theory. The accuracy and utility of these methods is demonstrated by applying them to systems including the molecular crystal ROY, chromophores in solution, and pentacene-doped p-terphenyl. The results pave the way for quantitatively accurate calculations to be performed on previously inaccessible large-scale systems.The optical properties of large-scale (>1000 atoms) heterogeneous systems are of interest in several fields, from photovoltaics to biological systems. Computing such properties accurately from first principles, however, is challenging; even if only a small region is optically active, quantum mechanical environmental effects must often be included, and the cost of applying a quantitatively accurate level of theory is prohibitive. The work presented here demonstrates how such calculations can be performed efficiently from first principles via two methods: an extension of the spectral warping method of Ge et al, and a novel combination of quantum embedding (specifically embedded mean-field theory) and linear-scaling (time-dependent) density functional theory. The accuracy and utility of these methods is demonstrated by applying them to systems including the molecular crystal ROY, chromophores in solution, and pentacene-doped p-terphenyl. The results pave the way for quantitatively accurate calculations to be performed on previously inaccessible large-scale systems.

10:40 - 11:30 Discussion

Chair

Dr Kalpana Katti, North Dakota State University, USA

12:30 - 13:00 Recent developments and applications of the quantum Monte Carlo method

The quantum Monte Carlo (QMC) technique is often referred to as a beyond density functional theory (DFT) method, because of its generally higher accuracy. It is becoming increasingly popular in computational material science, mainly thanks to the staggering increase and wide availablity of high performance computing, and to algorithmic developments.  Because of its statistical foundations, the method is well suited to run effectively on massively parallel computers. Here Professor Alfè will briefly introduce the method, and outline recent developments that have improved its accuracy and efficiency. Professor Alfè will then present some selected systems that highlight the need for a post-DFT method, showing that QMC is indeed capable of providing the required additional accuracy.

Professor Dario Alfè, University College London, UK and and University of Naples Federico II, Italy

13:00 - 13:30 Bringing quantum mechanics for electrons and nuclei to larger scales

Abstract not available at time of publication.

Dr Mariana Rossi, Max Planck Institute for the Structure and Dynamics of Matter, Germany

13:30 - 14:00 Precise, accessible all-electron theory for real, complex materials: organic, inorganic, organic-inorganic hybrids

Abstract not available at time of publication.

Dr Volker Blum, Duke University, USA

14:00 - 14:30 Tea
14:30 - 15:00 Billy McGregor, UKRI, UK
15:00 - 15:20 Contributed talk: Quantifying the breakdown of electronic friction theory during molecular scattering of NO from Au(111), Connor Box, University of Warwick, UK

The Born-Oppenheimer approximation fails to capture the extent of multiquantum vibrational energy loss recorded during molecular scattering from metallic surfaces. Vibrational state-to-state scattering of NO on Au(111) has been one of the most studied examples in this regard, providing a testing ground for developing various nonadiabatic theories. The exact failings compared to experiment and their origin from theory are not established for any system, particularly since dynamic properties are affected by many compounding simulation errors, of which the quality of nonadiabatic treatment is just one. The authors use a high-dimensional machine learning representation of the energy and electronic friction tensor to minimise errors that arise from quantum chemistry. This allows us to perform a comprehensive quantitative analysis of the performance of molecular dynamics with electronic friction in describing state-to-state scattering. They find that electronic friction theory accurately predicts elastic and single-quantum energy loss, but underestimates multi-quantum energy loss and overestimates molecular trapping at high vibrational excitation. This analysis reveals potential remedies to these issues.

15:20 - 16:00 Discussion
16:00 - 17:30 Poster session

Chair

Professor Leeor Kronik, Weizmann Institute of Science, Israel

08:00 - 08:30 Modelling ultralong organic phosphorescence in molecular crystals of carbazole and derivatives

Ultralong Organic Phosphorescence (UOP) has generated significant interest because of its applications in several areas such as photovoltaic cells, bioimaging and anticounterfeiting.1 The molecule of carbazole (Cz) is commonly used as a building block in organic materials for optoelectronic applications, acting as a light-absorbing, electron donor and emitting moiety. Cz and its derivatives display UOP at room temperature.  While the processes behind UOP have been associated with the stabilisation of H-aggregates, recent experimental studies indicate the presence of impurities drives the mechanism keeping the excited states alive for a long time.2  In this talk, Dr Crespo Otero will discuss the mechanism behind light-induced processes in crystalline and impure Cz and some derivatives using embedding methods developed in our group.3,4 Dr Crespo Otero will revisit the role of aggregation and isomeric impurities on the excited state pathways and analyse the mechanisms for exciton, Dexter energy transfer and electron transport considering Marcus and Marcus–Levich–Jortner theories.5 The researchers' excited state mechanisms provide a plausible interpretation of the experimental results and support the formation of charge-separated states at the defect/host interface. They believe these results contribute to a better understanding of the factors that enhance the excited-state lifetimes in organic materials and the role of doping with organic molecules. 
 

References

1 Kenry, C. Chen and B. Liu, Nat. Commun., 2019, 10, 2111. 

2 C. Chen, Z. Chi, K. C. Chong, A. S. Batsanov, Z. Yang, Z. Mao, Z. Yang and B. Liu, Nat. Mater., 2021, 20, 175–180. 

3 M. Rivera, M. Dommett, A. Sidat, W. Rahim and R. Crespo‐Otero, J. Comput. Chem., 2020, 41, 1045–1058. 

4 M. Rivera, M. Dommett and R. Crespo-Otero, J. Chem. Theory Comput., 2019, 15, 2504–2516. 

5 F. J. Hernández and R. Crespo-Otero, J. Mater. Chem. C, 2021, 9, 11882–11892. 

 

Dr Rachel Crespo Otero, Queen Mary, University of London, UK

08:30 - 09:00 QM/MM simulations of materials chemistry with ChemShell

ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. The use of QM/MM embedded cluster calculations for studying materials systems will be highlighted with recent results on copper-containing zeolites, where selective catalytic reduction with ammonia can reduce the emission of environmentally harmful nitrogen oxides. Insights from QM/MM calculations on the influence of solvent on the SCR mechanism will be discussed. The recent major redevelopment of ChemShell as an open source, python-based package will also be presented, including implementation of new QM/MM schemes for materials modelling and the use of multi-level parallelisation frameworks on high performance computing platforms.

Dr Thomas Keal, STFC Daresbury Laboratory, UK

09:00 - 09:30 Next-generation kinetic Monte Carlo approaches for understanding catalytic kinetics at unprecedented spatial and temporal scales

Kinetic Monte-Carlo (KMC) simulations have been instrumental in multiscale catalysis studies, enabling the elucidation of the complex dynamics of heterogeneous catalysts and the prediction of macroscopic performance metrics, such as activity and selectivity. However, the accessible length- and time-scales are still limited, and handling lattices containing millions of sites with 'traditional' sequential KMC implementations becomes prohibitive due to large memory requirements and long simulation times. Domain decomposition approaches could address these limitations, but they are challenging to implement in KMC simulation due to the inherently sequential nature thereof, by which one reactive event is causally linked to future (and past) events. These causal relations and the random time advancements of KMC steps, necessitate sophisticated protocols for conflict resolution at the boundaries between subdomains. Jefferson’s Time-Warp algorithm overcomes these challenges using local operations: sending and receiving messages/anti-messages, saving simulation state snapshots, and rolling-back in time to reinstate a previous state. Thus, any causality violations, arising transiently during simulation, are corrected, and the exact dynamics of the underlying stochastic model (the master equation) are finally reproduced. In this work, the researchers have coupled the Time-Warp algorithm with the Graph-Theoretical KMC framework enabling the handling of complex adsorbate lateral interactions and reaction events within large lattices. This approach has been implemented in Zacros, their general-purpose KMC software, and has been validated and benchmarked for efficiency in model systems as well as realistic chemistries. This work makes Zacros the first-of-its-kind general-purpose KMC code with distributed parallelisation capability to study heterogeneous catalysts.

Dr Michail Stamatakis, University College London, UK

09:30 - 10:00 Coffee
10:00 - 10:30 Advanced software, machine learning, powerful computers: enough for materials modelling?

Modeling has two main objectives, the rationalisation of existing results and the prediction of new systems and new phenomena. The field has made tremendous progress, and the availability of powerful computers, sophisticated software solutions, and machine learning algorithms are contributing to the discovery of new materials. However, the widespread use of modeling tools can also lead to inaccurate or useless predictions with potentially negative effects on the credibility of the field. In this talk Professor Pacchioni will briefly illustrate this emerging problem using materials for catalysis as an example. A large number of variables determine the performance of a heterogeneous catalyst, posing a challenge for quantum chemical modeling. The complexity of the problem has been significantly reduced with the advent of single atom catalysts (SACs) and, in particular, graphene-based SACs. In this context we are witnessing an increasing tendency to screen large number of materials based on density functional theory (DFT) and to propose universal descriptors to provide a guide for the synthesis of new catalysts. Professor Pacchioni will critically analyse some of the current problems associated with this activity: accuracy of calculations, neglect of important contributions in the models used, physical meaning of the proposed descriptors, imprecise data sets used to train machine learning algorithms, not to mention a few serious data reproducibility problems. The final message is that in an era where computing power has grown enormously, perhaps the time has come to shift the focus from the quantity to the quality of the data produced, to be of real help to the experimentalist in the design of new catalytic 1

1G. Di Liberto, Luis A. Cipriano, G. Pacchioni, “Universal principles for the rational design of single atom electrocatalysts? Handle with care”, ACS Catalysis, 12, 5846-5856 (2022).

Professor Gianfranco Pacchioni, Università di Milano-Bicocca, Italy

10:30 - 10:50 Contributed talk: Using cluster expansions to predict the structure and properties of PdZn bimetallic catalysts, Lara Kabalan, Cardiff University, UK

Metals alloys are known to improve the performance of heterogenous catalysts for many different reactions, such as CO2 hydrogenation1,2. Predicting an effective and novel catalyst, by computing combinations of elements and compositions using Density Functional Theory (DFT), is expensive and highly time-consuming. To accelerate the discovery process, one can couple DFT with cluster expansion (CE), which the authors demonstrate here in the identification of an effective and novel catalyst for CO2 hydrogenation. The authors focus on the PdZn (101) and (110) facets, which are most stable for binary alloys, and CE models for both of facets were tested in the concentration range where the body-centred tetragonal (BCT) phase exists, which is from 40 to 50% Zn concentration. These results show that higher Pd concentrations are predicted for both facets in the sub-surface while the top layers remain chemically ordered in a 1:1 alloy; the behaviour changes outside the stable BCT range, where segregation of Zn on the top surface is predicted for Zn concentrations above 50%. The outcomes highlight the critical importance of CE approach for determining structure−property relationships and accelerating the discovery and design of surfaces and nanostructured materials.

1GA Olah, Angew. Chem., Int. Ed. (2005), 44, 2636.
2F Brix et al, The Journal of Physical Chemistry Letters 2020 11 (18), 7672-7678

10:50 - 11:30 Discussion

Chair

Professor Julian Gale, Curtin University, Australia

12:30 - 13:00 Molecular crystal structure prediction for guiding materials discovery Abstract not available at time of publication

Professor Graeme Day

13:00 - 13:20 Contributed talk: DMC-ICE13: ambient and high pressure polymorphs of ice from Diffusion Monte Carlo and Density Functional Theory, F Della Pia, University of Cambridge, UK

Ice is one of the most interesting molecular crystals for a wide range of scientific fields, including physics, chemistry, biology, as well as space and material science. Its electronic properties are determined by complex topologies of hydrogen bonds as well as non-local dispersion interactions, providing a stern set to test electronic structure theory methods and get general insights both on molecular crystals and liquid water, where high accuracy simulations are hindered by prohibitive computational cost. Moreover, the recent discoveries of new ice phases have renewed the interest and increased the already extreme complexity of the water phase diagram, calling for a new analysis on the performance of electronic structure methods on the stability of the known polymorphs. The DMC-ICE13 dataset was constructed by computing reference lattice energies of thirteen ice polymorphs with sub-chemical accuracy using Diffusion Monte Carlo and conducting an extensive benchmark of several Density Functional Theory functionals. The obtained results suggest that a single functional achieving reliable performances for all phases is still missing, and that care is needed in the selection of the most appropriate functional for the desired application.

13:20 - 13:40 Contributed talk: Crumbling crystals, Niamh O'Neill, University of Cambridge, UK

Dissolution is a ubiquitous phenomenon, and important biological and physical processes rely on dissolution of ionic salts in water. Simulations lend themselves conveniently to studying dissolution, providing the spatio-temporal resolution that can be difficult or impossible to obtain experimentally. Nevertheless, it's a complex process, requiring ab initio level of treatment and long time simulations, typically hindered by computational expense. The authors use advances in machine learning potential methodology to resolve the entire dissolution mechanism of NaCl in water under multiple conditions with an ab initio equivalent accuracy. A general overall mechanism pervades whereby a steady ion-wise unwrapping of the crystal precedes its rapid disintegration. This disintegration is characterised by the crystal reaching a point of maximum instability, where destabilising ion-water interactions dominate over the cohesive ion-ion interactions of the crystal. From high to low concentrations, dissolution times can be categorised as highly stochastic to almost completely deterministic respectively. They show the stochastic extent of the overall mechanism can be reasoned by simple arguments with respect to microscopic sub-events during the dissolution. This study provides important insight into a long-standing fundamental scientific problem. Moreover, this has important implications on our general understanding of dissolution in other crystals, as well as crystal nucleation.

13:40 - 14:10 Tea
14:10 - 15:00 Panel discussion/Overview (future directions)