Supporting research communities with large-scale DFT in the next decade and beyond
Lead Research Organisation:
University of Southampton
Department Name: Sch of Chemistry
Abstract
First-principles quantum-mechanical simulations based on density-functional theory (DFT), are today used hand in hand with experiment to design new materials. Conventional DFT has a computational effort which increases with the cube of the number of atoms and this limits the practical size of calculations. ONETEP is a world-leading UK-developed software package which uses a linear-scaling framework to enable calculations on much larger scales, uniquely without loss of accuracy compared to traditional methods. Thus ONETEP offers unmatched capabilities for constructing and simulating more realistic models of materials and including their environment in multiscale simulations.
ONETEP has been developed from the beginning to take advantage of supercomputers. Due to its non-trivial formulation and wide-ranging functionality, it is a highly complex code consisting of around half a million lines of code.
ONETEP is an academic community code which emerged from CCP9, the Collaborative Computational Project for the electronic structure of condensed matter, bringing together academics across disciplines, and forming the UK branch of the European Psi-k Network. In 2016 ONETEP became the flagship project of CCP9 and free to UK academics. Industrial exposure to ONETEP has resulted from close collaboration with BIOVIA, which has enabled integration with their Materials Studio user interface. This has led to considerable commercial impact and new industrial collaborations. Beyond the UK, ONETEP is gaining in popularity with developers in Ireland and China and users in many countries in Europe as well as the USA, China, Mexico and South Africa.
As with all software, ONETEP needs to be continuously evolved and updated in order to stay at the cutting edge. This is particularly challenging for a large collaborative academic project that has evolved over two decades. Furthermore, a range of developments, such as excited states, electrochemistry, embedding and wavefunction methods, have required pervasive changes. Since they affect the core algorithms of the code, these changes have inevitably led to increased complexity. Thus the code now needs to adopt a new structure to ensure its continued growth. At the same time it is important to maintain and further widen the community of users and developers to fulfill its primary objective to cater for the needs of the scientific community.
This project is targeted towards these two interconnected aims. It will re-engineer the code in its entirety, rationalising internal structure to allow further development and enhance the interoperability of existing functionality. Modern software engineering principles will be followed throughout, in close collaboration with the computational physics and chemistry groups of STFC SCD and research software engineers in Southampton, Warwick and Imperial. At the same time developments of new functionality to enable large-scale calculations of crystalline and semicrystalline materials will satisfy a demand in this area by many researchers, such as in the CCP9 and the solid state microscopy and spectroscopy communities at STFC Facilities. Workflow tools and coupling with the ChemShell QM/MM code will be developed to allow adoption of the code by the biomolecular simulations community. The code will also be ported to emerging supercomputing architectures with GPU accelerators.
Thus the project will support the rapidly-expanding communities within solid-state materials and biochemistry that deploy first-principles quantum simulations based on DFT. The project will deliver significant communication, engagement, and expert training and mentoring of new users to overcome initial barriers to access and enable them to use the code to make impact in their diverse research areas. Training events for both users and developers of the code will be embedded within each community.
ONETEP has been developed from the beginning to take advantage of supercomputers. Due to its non-trivial formulation and wide-ranging functionality, it is a highly complex code consisting of around half a million lines of code.
ONETEP is an academic community code which emerged from CCP9, the Collaborative Computational Project for the electronic structure of condensed matter, bringing together academics across disciplines, and forming the UK branch of the European Psi-k Network. In 2016 ONETEP became the flagship project of CCP9 and free to UK academics. Industrial exposure to ONETEP has resulted from close collaboration with BIOVIA, which has enabled integration with their Materials Studio user interface. This has led to considerable commercial impact and new industrial collaborations. Beyond the UK, ONETEP is gaining in popularity with developers in Ireland and China and users in many countries in Europe as well as the USA, China, Mexico and South Africa.
As with all software, ONETEP needs to be continuously evolved and updated in order to stay at the cutting edge. This is particularly challenging for a large collaborative academic project that has evolved over two decades. Furthermore, a range of developments, such as excited states, electrochemistry, embedding and wavefunction methods, have required pervasive changes. Since they affect the core algorithms of the code, these changes have inevitably led to increased complexity. Thus the code now needs to adopt a new structure to ensure its continued growth. At the same time it is important to maintain and further widen the community of users and developers to fulfill its primary objective to cater for the needs of the scientific community.
This project is targeted towards these two interconnected aims. It will re-engineer the code in its entirety, rationalising internal structure to allow further development and enhance the interoperability of existing functionality. Modern software engineering principles will be followed throughout, in close collaboration with the computational physics and chemistry groups of STFC SCD and research software engineers in Southampton, Warwick and Imperial. At the same time developments of new functionality to enable large-scale calculations of crystalline and semicrystalline materials will satisfy a demand in this area by many researchers, such as in the CCP9 and the solid state microscopy and spectroscopy communities at STFC Facilities. Workflow tools and coupling with the ChemShell QM/MM code will be developed to allow adoption of the code by the biomolecular simulations community. The code will also be ported to emerging supercomputing architectures with GPU accelerators.
Thus the project will support the rapidly-expanding communities within solid-state materials and biochemistry that deploy first-principles quantum simulations based on DFT. The project will deliver significant communication, engagement, and expert training and mentoring of new users to overcome initial barriers to access and enable them to use the code to make impact in their diverse research areas. Training events for both users and developers of the code will be embedded within each community.
Organisations
- University of Southampton (Lead Research Organisation)
- Rosalind Franklin Institute (Project Partner)
- Diamond Light Source (Project Partner)
- CCP-Biosim (Project Partner)
- Collaborative Computational Project ccp9 (Project Partner)
- CCP5 (Project Partner)
- Science and Technology Facilities Council (Project Partner)
- nVIDIA (Project Partner)
- University of Leeds (Project Partner)
People |
ORCID iD |
| Chris-Kriton Skylaris (Principal Investigator) |
Publications
Anwar N
(2024)
Large-scale density functional theory simulations of defects and hydrogen incorporation in PuO 2
in Physical Review B
Bhandari A
(2024)
Mechanisms of Li deposition on graphite anodes: surface coverage and cluster growth
in Journal of Materials Chemistry A
Bhandari A
(2022)
Li nucleation on the graphite anode under potential control in Li-ion batteries
in Journal of Materials Chemistry A
Bramley GA
(2022)
Understanding Adsorption of Organics on Pt(111) in the Aqueous Phase: Insights from DFT Based Implicit Solvent and Statistical Thermodynamics Models.
in Journal of chemical theory and computation
| Description | As the project approaches its end, all its main objectives have been completed or are close to completion. They are interrelated and are all of equal priority: We have widened the user and developer base of ONETEP to support the rapidly-expanding communities within Materials Science and Life Sciences via training School and coding retreats that we have run in the last 3 years. We have re-engineer the entire ONETEP code, to allow future growth. This included implementing new data structures for major parts of the calculation, redesign key parallel algorithms and enhance the performance of the code. We have ported a significant part of the code to GPUs and emerging hybrid GPU-CPU architectures which are becoming available in many High Performance Computing (HPC) platforms. We have developed k-point Brillouin zone sampling and spin-orbit coupling to enable calculations of large-scale crystalline and semi crystalline materials to support the needs of the solid state communities. We developed an interface with QM/MM simulations to support the needs of the life sciences communities. We performed extensive maintenance of the entire code that will include refactoring to ensure interoperability of all functionalities, robust platform-independent checkpointing for any calculation sequence, complete online documentation, automatic quality assurance testing. |
| Exploitation Route | This project is a truly national effort, and our developments and training have been tailored to benefit as widely as possible our project partners and related stakeholders. CCP9 will derive significant benefits from our development of k-points sampling and spin-orbit coupling as a large proportion (~half) of its members work on crystalline systems with periodicity in one or more dimensions. Our developments and training address the high demand within the CCP9 community for such a method as the cost of including vacuum spacing in supercells for periodic models of surfaces (slabs) and nanowires can be prohibitive in standard DFT. CCPBioSim, who represent much of the UK biochemistry and biophysics computational simulations practitioners, benefit by using ONETEP as large-scale DFT has the ability to describe entire biomolecular entities as used in drug design and enzymatic processes, and the advantage of DFT is its high accuracy and transferability compared to the force fields that are typically used for such simulations. This is enabled by our interfacing ONETEP with ChemShell, one of the main tools for biomolecular hybrid QM/MM simulations and workflows. CCP5 also benefit using large-scale DFT for their applications to mitigate the limitations of force fields. Furthermore, large-scale DFT calculations with ONETEP can serve as a reliable reference for training the emerging machine-learning force fields such as MACE-MP-0 which promise DFT-level accuracy with orders of magnitude smaller computational effort. |
| Sectors | Chemicals Electronics Energy Environment Pharmaceuticals and Medical Biotechnology |
| URL | http://onetep.org |
| Description | The significant performance improvements (more than 10 times faster) that have been done to the ONETEP code as part of this work have dramatically speeded up the time to solution for most applications of the code, enabling users to perform faster simulations. There developments have also found their way into the commercial version of the code which is marketed to companies via BIOVIA/DS. The code is free for academics worldwide. |
| First Year Of Impact | 2024 |
| Sector | Chemicals,Electronics,Energy,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Description | ONETEP Masterclass 2023 |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Increased uptake and confident use of the EPSRC-supported ONETEP code across different UK and international (e.g. EU, Africa) simulation-based projects. |
| URL | https://onetep.org/news/onetep-masterclass-2023/ |
| Description | ONETEP Rutherford Appleton Laboratory training 2023 |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Increased uptake of the ONETEP code across STFC facilities and ensuing use in different follow-up research activities funded by STFC (e.g. STFC's Ada Lovelace Centre) |
| URL | https://onetep.org/news/onetep-training-at-ral-on-13-1-2023/ |
| Title | Multiscale coupling of atomistic simulations with higher scale models for batteries |
| Description | We are developing appropriate parametrisations and workflows to link large length and time-scale atomistic DFTB simulations with the ONETEP program to DFN simulation models for batteries such as in the PyBAMM program. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | The model is currently under development and we are focusing on predicting diffusion coefficients from atomistic simulations to be used in PyBAMM simulations. A unique strength of this approach is that it can be applied to virtually any material overcoming the lack of experimentally available parameters. |
| Title | New website for the ONETEP linear-scaling DFT software |
| Description | The old website of the code (www.onetep.org) was outdated. A modern, more presentable and functional website has been developed. The website is focused on displaying the code capabilities and has sections with content and examples specific to the different user and developer communities that are interested in large-scale DFT. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | We have seen an increase in the number of academic ONETEP licenses and comments on the ONETEP mailing list since the new website became active. |
| Title | ONETEP within Materials Studio 2024 |
| Description | An updated version of ONETEP within Dassault Systemes BIOVIA's Materials Studio 2024 release. |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Impact | Through this release the most recent developments in ONETEP have been made available to the many industrial customers of Dassault Systemes BIOVIA. It is also worth noting that ONETEP is also available to academics free of charge. |
| URL | https://www.3ds.com/assets/invest/2024-02/whatsnew-biovia-materials-studio-2024.pdf |
| Description | ONETEP calculations on metallic nanoparticles: applications in catalysis |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | This was an invited seminar by BIOVIA / Dassault Systemes to showcase to industrial researchers cutting edge simulations in catalysis with the ONETEP linear-scaling DFT code we develop. There was much interest in questions after the talk the feedback was very positive. |
| Year(s) Of Engagement Activity | 2023 |
| Description | ONETEP coding retreat (20-22 Sept 2022) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This 3-day workshop took place between 20 and 22 September 2022 at STFC RAL, in Harwell. The participants were developers, from all levels of experience, which were trained how to develop code in ONETEP through achieving pre-set development goals. The event was supported by CCP9. |
| Year(s) Of Engagement Activity | 2022 |
| Description | ONETEP user training (13 January 2023) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This one-day ONETEP training event took place at the Rutherford Appleton Laboratory (RAL) for members of the DIAMOND light source, the ISIS neutron and muon source and the Rosalind Franklin Institute (RFI). After some introduction to the code the participants set up simple ONETEP calculations, with the help of the tutors, on their scientific problems. The event was supported by CCP9. |
| Year(s) Of Engagement Activity | 2023 |