Excitations in Complex Environments: Multiphysics embedding for large scale electronic structure

Lead Research Organisation: University of Warwick
Department Name: Physics


Quantum mechanical simulations from first principles are today used hand in hand with experiments to guide the design of new materials or biomolecules as they provide a very accurate description of the electrons that determine all the observable properties of the materials. With the advent of first principles quantum methods where the computational effort increases linearly with the number of atoms we have the capability to simulate complex materials at the forefront of research such as nanostructures (e.g. in fuel cell catalysts or electronic devices) and entire biomolecules (as needed in drug design or studies of components of the living cell). The UK-developed ONETEP program is the leading linear-scaling first principles quantum code, due to its new generation of theory that retains the full level of accuracy of conventional cubic-scaling first principles quantum methods. ONETEP has a wide and growing international user base not just within academia, but within industry (via the commercial version of the code distributed by BIOVIA). The code was developed from the beginning using modern software engineering principles with the aim of portability and high scalability to modern supercomputing platforms and user-friendly interactive input and output.

The present project aims to develop in ONETEP the capabilities for a whole new level of simulation. It will expand the regime of applicability of the code from the ground state to excited states; it will provide much more accurate approximations for the electrons (hybrid and range-separated exchange correlation functionals) and finally it will dispense with the monolithic single-theory description of the entire system by allowing to seamlessly combine different levels of theory that match the different parts of complex materials systems. A multitude of grand-challenge problems will become accessible to accurate simulation with these developments: examples include light energy harvesting in biomolecules such as chlorophyl, new materials for flexible and cheap organic photovoltaics, new types of lasers/masers. In all these problems there are different levels of complexity as the photoactive site and its environment are clearly distinct, thus the multilevel description will be indispensable.

This project is the flagship project of the CCP9 materials simulation community and has received overwhelming support with several members of the CCP9 consortium offering to be early adopters of our developments. The ONETEP code will become freely available to all UK academics (via free membership of CCP9, which is open to the whole UK academic community) and as a result it is expected to be accessible to all the materials, chemistry and biomolecular simulation communities. We will further promote the dissemination of the code via a dedicated masterclass (open to both academic and industrial users), and a European CECAM/Psi-k workshop. The new developments will also be disseminated to industry through their exposure within the BIOVIA Materials Studio graphical user interface via which the ONETEP code is marketed to industrial customers.

Planned Impact

ONETEP has both a growing base of academic users and is a code that is commercially licensed to industry by Dassault Systèmes BIOVIA, a company that is committed to enhancing innovation and accelerating product development through scientific research and development. It has over 2,000 customers including 30 of the top 35 pharma & biotech companies, 7 of the top 10 chemicals companies and the top 5 aerospace companies. In particular, it has an established position in the field of materials modelling and simulation currently based around their Materials Studio package. The potential integration of ONETEP into their Discovery Studio package for life-sciences simulation is a particularly exciting development that will lead to greater impact of the code in pharma and biotech sector. The developments within this project will be made available to users across industrial and government sectors through BIOVIA. As the importance of theory and simulation of materials grows within industry, so the development of new methodologies with expanded capabilities will contribute to the UK economy through the creation of jobs and improved products.

One of the principal goals in developing ONETEP has been to maximise its economic impact by expanding the scale and scope of the simulations that are possible: for example, its capability to model much larger systems than traditional methods has made first-principles methods applicable to problems in nanotechnology and biology, such as modelling entire nanocrystals and proteins. In this proposal, we plan to further extend its capabilities to the simulation of electronically-excited states of large systems in complex environments. This will provide a simulation tool that the electronic structure community has identified as a priority to tackle high-impact research challenges including functional organic devices (photovoltaics and MASERs) and photoprotective molecules.

The existing strong links to industry, through collaborations and through BIOVIA, mean that the simulations enabled will accelerate the development of more competitive technologies and thus drive economic growth. Both emerging technologies, such as organic photovoltaics and MASERs, and established ones, such as dyes and sun-cream, stand to benefit from improved fundamental understanding of atomistic mechanisms of light-matter interaction. Understanding and improving upon light-harvesting in biological systems could lead to more productive crops via genetic modification, while understanding photodegradation and photoprotective mechanisms in organic compounds could lead to longer-lasting, higher-quality pharmaceutical products.

The team has a strong track record in training researchers to find successful strategies for simulating complex systems. In recent years, we have developed a training event in which the majority of the time is not spent giving lectures and running toy tutorial problems. Instead, "Masterclasses" are held in which a small number of attendees are invited to work for a week with experienced ONETEP developers and users on their own research problem. This event is open both to academic users (from theoretical and experimental groups) and to industrial partners (identified through our partner BIOVIA). Training events are complemented by online support and documentation on the ONETEP wiki (www.onetep.org) and ONETEP email forums. Members of the team will also give webinars on the latest developments for BIOVIA users and talks at BIOVIA International User Meetings.

Finally, Training PDRAs and PhD students in advanced electronic structure methods and high-quality software engineering prepares them well for R&D jobs in industry, in which there is an identified skills gap. Many former members of our groups are now working in software/HPC, including two for MathWorks, one for Materials Design, one for QuantumWise, one at the Argonne Leadership Computing Facility, and one at the A*STAR Institute of HPC.


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Charlton R (2018) Implicit and explicit host effects on excitons in pentacene derivatives in The Journal of Chemical Physics

Description In the final year of the project we completed almost all of the goals of the project successfully.

Work Package 1: Embedding methods

The final version of the embedding framework has been committed to the repository for the ONETEP code and validation tests and benchmarks completed. The formalism has been published in J. Chem. Phys.

Work Package 2: Hybrid & Range-Separated Functionals

The WP on enabling exact exchange for conduction NGWF optimisation, was completed successfully in 2018/19 and committed to the repository. In 2019/20, the second part, dramatically accelerating exact exchange calculations and enabling them for use in TDDFT calculations was completed. This is being published in two forthcoming publications by the Skylaris group.

Work Package 3: Excited State Forces and Geometries

A version of excited state forces, with certain caveats, was been completed and has been fairly extensively tested. This work was presented at the ACS conference in Spring 2019 and was committed to the ONETEP repository in summer 2020. A paper on this topic is still planned, but is not expected to be a high-impact publication.

Work Package 4: Validation, Demonstration and Dissemination

Several papers have been written on excitations in complex environments by the investigators, contributing to dissemination of the methods. Crucially, a new flagship review paper by the whole ONETEP team was published in JCP in 2020.
Exploitation Route The main goal of this project is developing the capabilities of the ONETEP LS-DFT software. Therefore all improvements to this widely-used package are intended to be used by others elsewhere as well as our own groups: there are over 500 individual, group and commercial licenses issued to use the code.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Chemicals,Electronics,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL http://www.onetep.org
Description BIOVIA, part of Dassault Systèmes (formerly Accelrys) is a leading scientific research and development software and service company. It has 1,300 customers including 29 of the top 30 pharma/biotech companies, 4 of the top 5 chemicals companies and the top 5 aerospace companies. In particular, it has an established position in the field of materials modelling and simulation currently based around the Materials Studio application. This provides a graphical interface to a wide variety of simulation methods, including ONETEP.
First Year Of Impact 2004
Sector Aerospace, Defence and Marine,Chemicals,Digital/Communication/Information Technologies (including Software),Electronics,Energy,Transport
Impact Types Economic

Description ESTEEM is a python package designed to interface with the Atomic Simulation Environment, and with several advanced Electronic Structure and Molecular Dynamics codes (specifically NWChem, ONETEP, Amber and AMP), which automate and formalise the process of calculating excitations of complex systems and the modelling of potential energy surfaces by Machine Learning. It makes it relatively "black-box" to perform explicit solvent calculations, which otherwise require a high level of expertise. 
Type Of Material Improvements to research infrastructure 
Year Produced 2020 
Provided To Others? Yes  
Impact This toolkit has already been used in one paper (the secondary species determination paper), and will soon be used in at least two more. It has been publically released at the end of the project. 
URL https://bitbucket.org/ndmhine/esteem
Description Dassault Systemes BIOVIA 
Organisation Dassault Systemes UK Ltd
Country United Kingdom 
Sector Private 
PI Contribution The ONETEP Developers Group work closely with our partners at Dassault Systemes BIOVIA to make sure the latest research developments in the software are exposed to the industrial, government lab and academic users of the commercial code, in order to maximise the impact of these developments.
Collaborator Contribution Accelrys provides the resources required to ensure a continued support of the new developments into commercial quality software environments. In particular, Accelrys committed to devoting the equivalent of roughly one full time person to the integration, bug fixing, quality control, scientific support and marketing of ONETEP over the duration of this award at a value in the region of £100,000 per year. Accelrys also provided each member of the ONETEP Developers Group with the whole of the Materials Studio(TM) software suite.
Impact ONETEP integration in Materials Studio. Total commercial revenue from ONETEP via this route to date exceeds £3M from over 200 organisations worldwide.
Title ONETEP linear-scaling DFT code 
Description Linear-scaling density-functional theory code for understanding and predicting the properties of materials from first-principles quantum mechanics. 
Type Of Technology Software 
Year Produced 2020 
Impact ONETEP is continually developed and new, updated versions are released on an annual basis. The developments associated with this grant were released during the period of the grant, between 2017 and 2020. It is one of the leading codes of its kind in the world and unique in being sold commercially: in 2004 it was adopted by Accelrys (now Dassault Systemes BIOVIA), a leading scientific software company, and has been one of the flagship products within the Materials Studio suite of software since 2008. An inexpensive academic license is also available worldwide direct from Cambridge Enterprise Ltd. Total revenue from ONETEP to date exceeds £3M from over 200 organisations worldwide. The current project has added extensive new functionality in the area of theoretical spectroscopy, leading to the ability to describe uv/vis absorption from first principles in unprecedentedly large systems, such as whole proteins. 
URL http://www.onetep.org