CCP4 - Software for Macromolecular X-Ray Crystallography
CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. CCP4 aims to develop and support the development of cutting edge approaches to experimental determination and analysis of protein structure, and integrate these approaches into the suite. CCP4 is a community based resource that supports the widest possible researcher community, embracing academic, not for profit, and for profit research. CCP4 aims to play a key role in the education and training of scientists in experimental structural biology. It encourages the wide dissemination of new ideas, techniques and practice.
CCP5 - The Computer Simulation of Condensed Phases
Ilian Todorov
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Tom Keal |
John Purton
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Chin Yong
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Michael Seaton |
Vlad Sokhan |
Ivan Scivetti
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We
provide UK
scientists, engaged in developing, applying and exploiting computer simulation methods for condensed matter systems,
with collaborative research assistance via software and methodology development, training, networking and outreach. A distinctive feature of our CCP5 provision is our successful strategy of developing and disseminating new codes and methods for all kinds of materials problems. These include solid-state materials, polymers, colloidal solutions, liquids and mixtures, liquid crystals, surfaces and interfaces, homogeneous and heterogeneous catalysts, mineral, bio-mineral, organic and bio-molecular systems.
Our core
so
ftware support covers numerical energy minimisation, classical molecular dynamics and Monte Carlo simulation, ranging from atomistic to multi-scale molecular systems. An increasing effort is exerted to tackle major challenges in cutting edge parallel simulations, linking atomistic and higher level models with first principles (quantum), spanning longer time- and length-scales by means of coarse-graining and mesoscale modelling so as to provide reliable multi-scale simulation protocols.
CCP5 major software and methodology support includes five active projects which together account for over 4,000 active licence holders worldwide and over 500 google scholar citation in 2016. DL_POLY is a general purpose, classical, particle dynamics program. DL_MESO is a general purpose Dissipative Particle Dynamics program. DL_MONTE is a general
purpose particle Monte Carlo program. ChemShell is an advanced command line environment with tools and methods for modelling materials systems simultaneously in classical and quantum terms. DL_FIELD is a cheminformatics program for conversion of materials structures from XYZ/PDB description to structure and force-field model files suitable for input into DL_POLY, DL_MESO and DL_MONTE.
CCP9 - Electronic Structure of Solids
 Leon Petit
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Martin Lueders
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Barry Searle
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Jerome Jackson
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CCP9 is the Collaborative Computational Project for the Study of the Electronic Structure of Condensed Matter. The support from Daresbury laboratory involves the development of correlated electron methodologies and their application to transition metal, rare earth and nuclear materials in collaboration with colleagues at different Universities. For example, in an on-going collaboration with Julie Staunton at Warwick University and experimentalists at Ames Laboratory (US), we recently investigated the magneto-caloric properties of Gd-intermetallics, of relevance to environmentally friendly cooling. CCP9 also supports the community-wide validation and verification of electronic structure codes, which among others involves testing and comparing the performance of the full-potential LMTO based CCP9 flagship code, in collaboration with Mark van Schilfgaarde at King’s College London. The CCP9 staff at Daresbury Laboratory furthermore provides the UK-support to Psi-k, the international network on electronic structure calculations, and is in charge of the activities of the UK-STFC CECAM node activities.
CCP-Mag - Computational Multiscale Magnetism
Martin Lueders
| Barry Searle
|
One of the central themes of the CCP for computational magnetism is the multi-scale aspect, combining q
uantum-mechanical calculations of microscopic magnetic properties with atomistic models and continuum models, which can be used to study whole devices. To facilitate the interchange of data between these various models, the staff at Daresbury is developing a common data format, specifying how data shall be written to files, and a library which allows existing codes to easily read and write these files. Furthermore, the quality of ab-initio data will be investigated in order to assess the reliability of the multi-scale modelling chain.
CCP-NC - NMR Crystallography
Simone Sturniolo
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Albert Bartok-Partay
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Nuclear Magnetic Resonance (NMR) is a useful technique to determine chemical structure, especially in compounds of which it is hard to produce single crystals big enough for diffraction techniques, as commonly found in organic molecules. This class of materials includes many pharmaceutical compounds.
CCP-NC supports a multidisciplinary community of NMR spectroscopists, crystallographers, materials modellers and application scientists by developing and integrating software across the area of NMR crystallography. This is an emerging field, defined as the combined use of experimental NMR and computation to provide new insight, with atomic resolution, into structure, disorder and dynamics in the solid state.
CoSeC support for CCP-NC includes:
- The development of data processing and visualisation tools for the interpretation of NMR crystallography.
- Improvements to the theory and computational models used and their implementation in software.
- Ease-of-access tools to run state-of-the-art simulations on high-performance compute services.
- Provide user training and support for the above.
CCPQ - Quantum Dynamics in Atomic Molecular and Optical Physics
The overarching aim of 'Collaborative Computational Project in Quantum dynamics' (CCPQ) is to facilitate theoretical atomic, molecular and optical (AMO) physics in the UK by developing, curating and disseminating software for describing coherent quantum dynamics and interactions of particles.
CCPQ supports the development of community codes in a number of related areas: electron collisions, anti-matter, quantum information, attosecond physics, molecular wavepackets and ultra-cold molecules.
CoSeC support for CCPQ can be divided into three main types: detailed scientific and computational collaborative research and code development/optimization, more general best practice software engineering and ‘continuous integration’ support, and general administration including the CCPQ website. The first type is mainly provided by Martin Plummer and Andrew G Sunderland and is concentrated in the electron collisions, multiphoton interactions and antimatter areas.
CCP-Plasma / HEC-Plasma Physics
Joseph Parker
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CCP/HEC Plasma develops software to model plasma inside magnetic confinement fusion experiments, like JET and ITER. The equations for this are very computationally expensive, due to the wide range of scales in space and time which must be considered. Therefore, much of our work focuses on parallelizing and optimizing the software to allow users to fully exploit massively parallel HPC systems. There are also many physical effects which may be relevant for different plasma models, so we also focus on adding new functionality to the software.
CCPi - Tomographic Imaging
Sri Nagella
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Ron Fowler | 
Erica Yang
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Edoardo Pasca |
Non-destructive 3D X-ray, Neutron, PET and MR imaging are becoming increasingly important in many areas of science with application to Energy, Healthcare and Security. For example X-rays are having a dramatic impact on fields as diverse as security (e.g. baggage and body scanning at airports and screening of vehicles at ports), engineering (e.g. visualising stress corrosion cracking in nuclear plant and the degradation of fuel cells) and medicine (e.g. cancer treatment and artificial tissue engineering). The spatial and temporal resolutions are increasing dramatically. RC funded synchrotron sources are rapidly increasing the numbers of x-ray imaging instruments available (the European Synchrotron Radiation Facility (ESRF) now has 10 beamlines, and Diamond Light Source (DLS) is currently building 4 new imaging beamlines). Also laboratory x-ray imaging facilities are becoming increasingly widespread. This expansion is mirrored elsewhere with the global CT market now worth $150M (+ $5B in medical CT) both expanding at 10% per annum, while 30% of the data stored on the world's computers are now medical images. Unsurprisingly, papers on these tomography have also increased sharply this decade.
The CCPi was established in 2012 to support the emerging UK tomography community with a toolbox of algorithms to increase the quality and level of information
that can be extracted by computed tomography. There are four major parts: pre-processing techniques for image calibration and noise reduction, reconstruction techniques to create a 3D volume data set from projections and segmentation, quantification techniques that can extract relevant objective values from these 3D volumes, and software framework development to enable the exploitation of CCPi codes in a wide range of existing commercial and open source software.
The size of this community has grown over the last five years with many academic groups around the UK taking up tomographic imaging and purchasing new lab based x-ray CT scanners. The size of our community has arisen from ~250 in 2013 to over 330 in 2017, over 30% growth in the last five years. In 2012 there was an estimated 50,000 CT imaging sources around the world.
Our focus is aiming at bringing together the UK imaging community, specifically to maximising the return on investment in imaging software development through developing, maintaining, and prompting the CCPi core imaging toolbox. The staffing effort for CCPi core support is as follows: 0.2 FTE for maintaining network, website, running workshops and training course, benchmarking, licensing issues etc; 0.3 FTE enhancing frameworks, 0.3FTE for developing and maintaining the image reconstruction toolbox (including pre- and post- processing), and 0.3FTE for developing and maintaining the 3D image analysis pipeline.
CCP PET-MR - Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MR)
Evgueni Ovtchinnikov
| Edoardo Pasca
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Erica Yang
|
For medical imaging, the UK is a globally leading country. It has the highest number of Positron Emission Tomography and Magnetic Resonance (PET-MR) medical imaging machines in the world, evenly spread throughout the country. The CCP-PET-MR project established in 2015 aims at bringing together the best of the UK’s PET-MR imaging expertise to capitalise on the investment in this area.The main deliverable of the project is an open source PET-MR reconstruction software framework we named SIRF (Synergistic Image Reconstruction Framework). SIRF is designed be simple enough in use for educational and research purposes, thus reducing the “barrier for entry” for new contributors to PET-MR imaging research and development, and at the same time powerful enough to process real scanner data.
CCPBioSim - Biomecular Simulation at the Life Sciences Interface
Tom Keal
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Hannes Loeffler
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CCPBioSim is the Collaborative Computational Project in biomolecular simulation at the life sciences interface, bringing together chemists, physicists and chemical engineers as well as researchers from all branches of "molecule-oriented" biochemistry and biology. Simulations help to analyse how enzymes catalyse biochemical reactions, and how proteins adopt their functional structures e.g. within cell membranes. They contribute to the design of drugs and catalysts, and in understanding the molecular basis of disease. Our aim is to involve experimentalists and computational specialists in this work, sharing the belief that the best science can be done when theory and experiment are closely integrated. CCPBioSim engages with early career researchers and non-experts through the provision of tutorials and workshops enabling them to become proficient and productive users of biomolecular simulation techniques. We are also actively engaged in developing new advanced methods, which in future will be used by our community to deliver new and exciting science.
CCP-EM - Collaborative Computational Project for Electron cryo-Microscopy
The Collaborative Computational Project for electron cryo-microscopy (CCP-EM) supports users and developers in biological EM. The three principal aims are:
Build a UK community for computational aspects of cryo-EM. Provide a focus for the cryo-EM community to interact with CCP4/CCPN, and the broader international community.
Support the users of software for cryo-EM through dissemination of information on available software, and directed training.
Support for software developers including porting, testing, and distribution of software.
HEC MCC - Materials Chemistry Consortium
Leonardo Bernasconi |
Chin Yong | Ilian Todorov
| Tom Keal
| Barry Searle
|
The Materials Chemistry Consortium exploits high end computing in a broad programme of work modelling and predicting the structures, properties and reactivities of materials. The consortium is a broadly based but coherent grouping comprising 36 university groups, with the emphasis on modelling at the atomic and molecular level but with growing links to models at larger length and time scales. Founded in 1994, the current scientific programme is built around seven related themes: catalysis, energy storage and generation, surface and interfacial phenomena, nano- and defect structures, soft matter, biomaterials, environmental materials. The Consortium has an active programme of code development and optimisation, tapping into the ecosystem of UK based software development initiatives including CoSeC.
CoSeC supports the consortium across the range of techniques used by its members, embracing both force-field methods employing static and dynamical simulation methodologies and electronic structure methods with a strong emphasis in recent years on Density Functional Theory (DFT) techniques employing both periodic boundary conditions and embedded cluster implementations. The four main codes supported by CoSeC are: DL_POLY, DL_FIELD, CHEMSHELL, and CRYSTAL.
HECBioSim - High-End Computing for Biomolecular Simulation
James Gebbie |
HEC-BioSim exists to bring High-End Computing for biomolecular simulation to a wider community, including users from industry and experimental bioscientists, and to engage physical and computer scientists in biological applications. The Consortium works closely with CCP-BioSim.
HECBioSim core effort provides support for scientists applying for time on ARCHER, primarily through maintenance of the HECBioSim web portal. It includes help on preparation of applications e.g. with the HECtime resource calculator, and on reporting the outcomes of approved projects. The SLA post also works on a variety of codes for biomolecular simulation and analysis appropriate to High End Computing.
HEC UKCP Consortium - UK Car-Parrinello Consortium
Dominik Jochym
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The United Kingdom Car-Parrinello (UKCP) Consortium is a group of researchers across the UK who develop and use ’first principles’ materials modelling software. They apply these computer simulations of chemicals and materials to a wide variety of situations from novel battery technology to pharmaceutical compounds. The UKCP consortium is one of the longest-running High-End Computing Consortia in the UK, and has been funded almost continuously by EPSRC since the 1990s.
UKCP is supported by CoSeC to:
- Develop new scientific methods and software for the community.
- Maintain and distribute the simulation software CASTEP to UK academics.
- Provide training and technical support for CASTEP users.
UK-COMES - UK Consortium on Mesoscale Engineering Sciences
Michael Seaton
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Jianping Meng
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The United Kingdom Consortium On Mesoscale Engineering Sciences (UKCOMES) – founded in 2013 – is a group of researchers across the UK who develop and apply mesoscopic modelling techniques to explore systems of scientific and industrial interest at scales between atomistic and continuum-based levels. Several modelling techniques are applied in this consortium, but the most frequently used and studied is the Lattice Boltzmann Equation (LBE) method, a particle-based statistical technique capable of modelling fluid flows with complex geometries and interactions between multiple fluids and phases.
Core support is focused on developing DL_MESO, the consortium’s community code for LBE simulations, by adding new functionality and optimising for various computing architectures. Both activities allow for a wider range of systems to be modelled with available computing resources, including the UK’s national supercomputer ARCHER.
CCPEngSci - Software Developments to Support the Engineering Community
We provide theoretical, algorithmic, and software developments to support the engineering community in the use of local and national High Performance Computing (HPC). As we move into a post-petascale era of computing, the development, support, and role of the engineering communities and consortia have become critically important in enabling the successful delivery of increasingly ambitious and challenging research objectives on the national facilities. The formation of the engineering consortia followed the UK’s decision to embrace massively parallel computing and each consortium has enjoyed a considerable increase in membership. In addition to providing direct support to academic researchers and members of the consortia, CoSeC staff are also involved in algorithmic developments in its demonstrator software and in identifying strategic research themes with strong potential for building new engineering consortia.
Software Outlook
Luke Mason
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Sue Thorne
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Andrew Taylor
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Software Outlook focuses on software technologies that are vitally important to the development and optimisation of the world-leading scientific software produced by the CCPs. This includes evaluation of new programming techniques that are essential for the timely and cost-effective exploitation of current and near-future High Performance Computing systems, and demonstrating how specific software technologies can be applied to existing applications.
All activities of CoSeC are co-ordinated from the Project Office which is managed by Damian Jones.
The Project Office remit includes the collection and collation of data for the mid-term and annual CoSeC reports, monitoring of effort bookings and spend, monitoring of progress against project job plans and milestones, support for funded CCP and HEC conferences and workshops, monitoring of the SLA allocation on ARCHER, and advice to increase the impact and dissemination of the work completed using CoSeC funding through the Impact Manager Marion O'Sullivan. Ongoing support for the CoSeC project web sites is provided through the Project Office by the Research Infrastructure Group at Rutherford Appleton Laboratory.
