Embedded CSE (eCSE) support

Through a series of regular calls, Embedded CSE (eCSE) support provides funding to the ARCHER user community to develop software in a sustainable manner to run on ARCHER.

Details of any current eCSE calls and their remit can be found on the eCSE calls page

Details of any current Early Career eCSE Panel Observers calls and their remit can be found on the Early Career eCSE Panel Observers calls page. There are currently no calls open.

Watch our recent Webinar on applying for eCSE funding!

Useful Links

The eCSE programme provides tangible software enhancements to the communities exploiting software on ARCHER. This in turn has led to significant scientific advancements and both economic and social benefits to society.

Reports from completed eCSE projects


Fast and Massively Distributed Electromagnetic Solver for Advanced HPC Studies of 3D Photonic Nanostructures

The work performed in this project built upon our recent development of the OPTIMET code, a project funded by the University dCSE Programme. OPTIMET is based on the multiple scattering matrix (MSM) method, a method widely used in computational electromagnetism. The main computational work in the MSM method consists of computing the system scattering matrix, S and solving a linear system of equations, Sa=b. Once a is known, the electromagnetic field can be computed at any point, as well as the corresponding cross-sections. As part of the eCSE project, the efficiency and functionality of the code were greatly enhanced.



libcfd2lcs: A general purpose library for computation of Lagrangian coherent structures during CFD simulation<

In this eCSE project, a new computational library, libcfd2lcs, was developed, that provides the ability to extract LCS on-the-fly during a computational fluid dynamics (CFD) simulation with only modest additional overhead. Users of the library create "LCS diagnostics" through a simple but flexible API, and the library updates the diagnostics in the background as the user's CFD simulation evolves. By harnessing the large-scale parallelism of platforms like ARCHER, this enables CFD practitioners to make LCS a standard analysis tool, even for large scale three-dimensional simulations. Moreover, libcfd2lcs provides access to the time evolution of LCS with unprecedented detail, giving researchers a powerful new tool to study unsteady flow structures. Read more...


Adding Multiscale Models of DNA to the LAMMPS Molecular Dynamics code

DNA modelling has been an important field in biophysics for decades. In this project, the oxDNA coarse-grained model for DNA and RNA was ported into the popular and powerful LAMMPS molecular dynamics code. This makes oxDNA widely accessible to the global community of LAMMPS users, whereas previously it was only available as bespoke and standalone software. Through the efficient parallelisation of LAMMPS it is now also possible to run oxDNA in parallel on multi-core, multi-processor and distributed memory architectures, extending its capabilities to unprecedented time and length scales. Read more...

polarising optical microscopy image

Introducing Thread and Instruction Level Parallelism into Ludwig Code for Modelling Complex Fluids

The Ludwig code is used to simulate a wide variety of soft matter substances, including liquid crystals. Liquid crystals are widespread in technology (including displays and other optical devices), but much is yet to be understood about the range of possible configurations. Simulations are vital in paving the way to improved knowledge. This project applied a new custom-made programming model, targetDP, to Ludwig to allow it to perform as well as possible not only on ARCHER but across a range of emerging hardware platforms, thereby exploiting the more complex hierarchical parallelism which is becoming typical. Read more...

Instantaneous concentration isocontours from point source dispersion with the source located within the urban
canopy layer

Large-Eddy Simulation Code for Air Quality Modelling in City-Scale Environments

The ELMM large-eddy simulation software is used for simulating wind flow in the atmospheric boundary layer, and the transport and dispersion of pollutants in areas with complex geometry, primarily cities. This project aimed to enhance the code to enable simulations of whole cities, i.e. areas with a horizontal dimension of 10 km or more, while maintaining high resolution in the areas of interest. The work has enabled much larger simulations to be carried out in areas of great interest such as urban air quality, including modelling of the dispersion of dangerous pollutants in cities and of the effects of the urban heat island. Read more...

Sound of Islay Large Eddy Simulation (LES) model

Developing Fluidity for high-fidelity coastal modelling

Fluidity is an open source finite-element computational fluid dynamics code. This project aimed to improve the performance of Fluidity and improve its ease of use. The improvements made to the code allow fluids problems to be studied in greater detail, and open up Fluidity to tidal modellers, with particular applications in the field of marine renewable energy. Research in areas such as aerodynamics, wind energy, marine energy, and environmental/pollution modelling will also benefit from the improvements to the code. Read more...

Power spectral density of lift coefficent for the flow around a circular cylinder

Implementation of a highly scalable aeroacoustic module in Code_Saturne Computational Fluid Dynamics software

This project aimed to expand the capabilities of the open-source CFD software Code_Saturne to directly perform noise predictions by means of an acoustic analogy. Noise prediction is key for many engineering applications ranging from aerospace to combustion, but traditional methods of simulating noise are very computationally demanding. This project aimed to implement an acoustic module within Code_Saturne while maintaining the code's excellent scalability. Read more...

CRYSTAL software logo

Removing pseudo-linear dependence in Gaussian basis set calculations on crystalline systems with CRYSTAL

CRYSTAL is a world-leading electronic structure program for the ab initio quantum mechanical simulation of crystals, nano-structures, surfaces and molecules. Its uses include research into new materials in areas such as photovoltaics. This project implemented automatic screening of the matrices affected by linear dependence issues when using high-quality molecular basis sets in CRYSTAL. By reducing the effort associated with the calculation set-up and with convergence checks for large basis sets, the results enable a wider community of users to perform faster calculations and achieve higher levels of accuracy in the calculated properties. Read more...

Molecular model

Implementation of Dual Resolution Simulation Methodology in LAMMPS, leading to improved studies of biological processes

Classical Molecular Dynamics simulations are widely used to understand the behaviour of biological systems. Calculations at the atomistic level are very computationally demanding, but coarse-grain (CG) models provide less accuracy. Hybrid models allow the most critical parts of the system to be represented at the atomistic level, with the remainder done by CG. This project updated and optimised the LAMMPS simulation software, enabling the use of hybrid simulations for the study of larger systems over longer timescales. This will not only improve our understanding of important fundamental biological processes, but also has the potential to assist with the development of new drug therapies. Read more...

MPI Cartesian Virtual Topology

Full parallelism of optimal flow control calculations with industrial applications

This project aimed to fully parallelize SEMTEX, a well-established open-source quadrilateral spectral element Direct Numerical Simulation (DNS) code which previously only had a limited parallel implementation. The improvements to the code will accelerate research in developing disruptive technologies in flow control, which is recognised as the leading edge of fluid dynamics research. The code has applications in the oil, aviation and wind energy industries. Read more...

Benchmark of running fitGlyR4 on one ARCHER node, showing the number of 
likelihood function evaluations per second

Enabling high performance computing for tools for the analysis of single molecule ion channel currents: probing the energy landscape of channel activation to understand the protein's structure-function relation

Ion channels mediate excitability and information processing in all living organisms and are the target of many therapeutic drugs. Recent technical advances have enabled the recording of the tiny (picoampere) electric current flowing through a single ion channel. Uniquely for a protein, tens of thousands of channel openings and closings with a temporal resolution of around 10 microseconds can be recorded in a single experiment. HJCFIT is a library for the maximum likelihood fitting of kinetic mechanisms to these sequences of open and shut time intervals. This project has enabled HJCFIT for ARCHER, significantly shortening the analysis time, potentially allowing more complex questions to be addressed and enabling a new community of researchers who have not previously exploited HPC facilites for the efficient use of HJCFIT. Read more...

Angularly resolved photoelectron spectra

POpSiCLE: A photoelectron spectrum library for laser-matter interactions

Molecules driven out of equilibrium by intense, ultrashort laser pulses are of central importance in many areas of science and technology. In such a non-equilibrium situation, charge and energy transfer can be induced across the molecule on a femtosecond timescale. Understanding and controlling these transfer processes is fundamental to many chemical processes and key to future ultrafast technologies: e.g. the design of electronic devices, probes and sensors, biological repair and signalling processes, and development of optically driven ultrafast electronics. This project developed a portable parallel library that implements three methods for calculating photoelectron spectra. Read more...

EMPIRE data assimilation code - communication model

Improving the EMPIRE data assimilation code for weather forecasting and other geosciences applications

Data assimilation is an essential part of any prediction system, such as weather forecasting. It combines a numerical model with all observations available to generate the best starting point for the forecast. The EMPIRE data assimilation system is a community system used by increasing numbers of researchers across the UK from all branches of geosciences. This project improved the efficiency of the EMPIRE software. The improved code will be available to all EMPIRE users on ARCHER and future UK national HPC systems. Read more...

Glaciology simulation image

Enabling high-performance oceanographic and cryospheric computation on ARCHER via new adjoint modelling tools

The study of the ocean and cryosphere is crucially dependent on computationally-intensive, large-scale numerical models that must be run on HPC systems. In recent years, the use of adjoint models has led to unique insights in this area. However, the uptake of adjoint modelling has been hindered due to poor access to efficient, cost-effective tools. This project aimed to bolster the ARCHER community's access to oceanic and cryospheric adjoint modelling through the development of model test suites. Read more...

Simulation of water droplet

Optimising Essential Particle Dynamics Codes for Multi-Scale Engineering Flow Simulation

This project aimed to further develop a software application built upon the Computational Fluid Dynamics (CFD) framework OpenFOAM, which uses the framework to run molecular dynamics (MD) simulations of nanoscale and multi-scale flow problems. The output software of this project has had a substantial impact in generating scientific insight for future micro/nano flow technologies with many practical applications, e.g. water impedance in carbon nanotube membranes for water purification; slip flows over nanostructured surfaces for marine drag-reduction, and control of deposit patterns using electro-wetting of nano-droplets for 3D printing. Read more...

Image courtesy of Micro & Nano Flows for Engineering

Schematic diagram showing dual direct-gap/indirect-gap nature of MAPI, an efficient, inexpensive solar cell material

QuasiParticle Self-Consistent GW electronic structure calculations of many-atom systems

Quasiparticle Self-Consistent GW approximation (QSGW) is a novel method for electronic structure calculations, which addresses many shortcomings of the standard method, density functional theory (DFT). An example of its use is for studies of photovoltaic materials and their efficiencies. QSGW is applied successfully to small systems. This project aimed to enable QSGW calculations for larger system sizes, by parallelising the code and adapting it to large multi-core HPC systems. Read more...

1,3-dimethylimidazolium chloride

Improving DL_POLY_4 molecular dynamics package performance and scalability using multiple time stepping

DL_POLY is a general purpose classical molecular dynamics (MD) simulation software package, which is used by the materials science, solid state chemistry, biological simulation and soft condensed-matter communities. In this project, researchers at STFC and the University of Oxford have implemented a multiple time stepping scheme, RESPA, for less frequent calculations of expensive operations. This has been shown to consistently bring about a 15-25% improvement in performance at fixed process count, and noticeably improves the scaling of the code. Read more...

Visualisation of numerical simulation of flooding following a dam breach

High performance multi-physics simulations with FEniCS/DOLFIN

The FEniCS Project is a collection of free, open-source, software compnents with the common goal of enabling automated solution of differential equations. DOLFIN is a C++/Python library which functions as the main problem-solving environment and user interface. Researchers at the University of Cambridge have enhanced the FEniCS/DOLFIN library to extend its functionality for multi-physics / multi-field simulations on parallel computers. The new functionality has enabled simulations of partially molten magma and analysis of CO2 subsurface sequestration to be carried out. Future projects which will benefit from the the improvements include brain simulations and simulation of float glass processing. Read more...

Visualisation of numerical simulation of flooding following a dam breach

Delivering a step-change in the performance and functionality of the Fluidity shallow water solver

Fluidity is an open source, computational fluid dynamics (CFD) framework used to solve large-scale geophysical/oceanographic problems, such as marine renewable energy, tsunami simulation and inundation, and palaeo-tidal simulations for hydrocarbon exploration. Researchers from Imperial College London have significantly enhanced Fluidity's shallow water model, and prepared the code for running on state-of-the-art HPC systems without the need for model developers to re-write any of their existing code. Preliminary work on tidal turbine modelling was performed during this project and the improved code has also been used in an undergraduate project to study the potential impact of tsunamis to the UK. Read more...

Image of meshes used in example

Parallel supermeshing for multimesh modelling

Models which use multiple non-matching unstructured meshes typically need to solve a computational geometry problem, and construct intersection meshes in a process known as supermeshing. An implementation of the algorithm for solving this problem exists in the unstructured finite element model Fluidity, but this implementation has, until now, been deeply embedded within the code and unavailable for widespread use. In this project, researchers from the University of Edinburgh and University of Oxford created a standalone general-purpose numerical library, named libsupermesh, which can easily be integrated into new and existing numerical models. Read more...

Red fox skull

VOX-FE for biomechanical modelling - new functionality for new communities

Understanding the mechanics of biological structures such as bones is very challenging, and experimental measurements can be extremely difficult. Computational modelling offers an alternative approach for studying the biomechanics of living and extinct animals, from insects to dinosaurs. In this project, researchers at the Universities of Hull and Edinburgh have significantly extended the VOX-FE modelling software, which can be used in predictive biology and virtual experimentation to reduce animal experiments. Potential applications include high resolution modelling of whole bones to understand normal and pathological bone biomechanics (e.g. in osteoporosis), and in silico design and testing of new dental and orthopaedic implants. Read more...

Illustration of Hilbert space-filling curve

Optimisation of the EPOCH laser-plasma simulation code

The EPOCH laser-plasma simulation code is a mature community code with a large international user base. The code uses particle-in-cell (PIC) techniques. The purpose of this project was to both improve the performance of EPOCH and futureproof the code for next generation multi-core architectures. As a result of the improvements made to the code, a speed-up of up to 3.58 has been achieved, and EPOCH can now be used for a wider variety of simulations that feature non-uniform particle distributions. Read more...

Image: Illustration of Hilbert space-filling curves for 3D spaces: William Gilbert, University of Waterloo

Ocean simulation

NEMO Regional Configuration Toolbox for ocean modelling

NEMO is a state-of-the-art ocean modelling framework used by the Met Office, NERC and many other UKHEIs to simulate the ocean from the global scale down to that of estuaries. This project has developed a unique set of tools - the NEMO Regional Configuration Toolbox (NRCT) - to aid users to set up lateral boundary conditions for near real-time regional ocean simulations within the NEMO environment. The NRCT provides access to remote datasets, and the tool effectively translates data from a parent model source into a format suitable to run a regional NEMO ocean simulation. A GUI is also provided to allow the user to define the regional ocean model domain. Read more...

Illustrative heterogeneous electrical activation over the surface of a diseased human left atrium

Improving the performance of Nektar++ using communication and I/O masking

Nektar++ is an open-source spectral/hp element framework for numerical solution of partial differential equations in complex geometries using high-order discretisations. As a result of the work done in this project, the code now makes more efficient use of computational resources and scales to higher core counts, allowing simulations to run in a shorter period of time. This benefits a wide range of application areas including transient aerodynamics simulation (F1, aircraft design and analysis), aero-acoustic simulation (aircraft engines), modelling of patient-specific cardiac electrophysiology (atrial fibrillation) and biological flow simulations for understanding disease formation and development (atherosclerosis). Read more...

Contour plot of the relative free energy density (summed enthalpy and entropy) for hydration of the cucurbit[7]uril system.

Algorithmic Enhancements to the Solvaware Package for the Analysis of Hydration

The Solvaware package is a workflow that runs and analyses molecular dynamics (MD) trajectories to estimate hydration free energies by computing the contribution of different subvolumes around a solute. The accurate calculation of hydration free energies is a vital goal in computational modelling of biological and engineered aqueous systems. This project has enhanced the Solvaware package by improving the efficiency of key algorithms in the workflow, increasing its functionality, and widening its impact by making it available to the ARCHER community. Read more...

Shape of a GS2 flux tube in MAST

Optimising GS2 plasma physics simulation code used by fusion energy researchers

This project improved the performance at high core counts of the GS2 plasma physics simulation code. With a speed-up of up to 5 times (for short simulations) or up to 2 times (for longer simulations), this will allow plasma simulations to be carried out in much more detail, leading to a better understanding of the turbulence features in the plasma. Understanding, and controlling, turbulence in plasma is one of the key requirements for building a usable fusion reactor, and codes like GS2 can help in the design and understanding of such reactors. Fusion energy has the potential to provide a clean source of electricity for future generations. Read more...

3D Domain Decomposition

Developing highly scalable 3-D Incompressible Smoothed Particle Hydrodynamics

Smoothed Particle Hydrodynamics (SPH) is a novel computational technique that is fast becoming a popular methodology to tackle industrial problems with violent flows. Recently, accurate incompressible SPH (ISPH) codes have become more popular now that the numerical stability can be ensured, particularly for free-surface flows. In this eCSE project, researchers from the University of Manchester and STFC Daresbury Laboratory have developed a scalable, 3-D ISPH engineering toolkit. Read more...

strand of DNA

Efficient computation of two-electron integrals in a mixed Gaussian/B-spline basis

The aim of this project was to develop efficient parallel routines to calculate two-particle integrals in a mixed basis of Gaussian Type Orbitals (GTOs) and B-spline orbitals. The object-oriented library developed in the project has contributed to a significant improvement in the capability of the UKRmol+ suite of codes, designed to study electron and positron collisions with molecules. This will allow the study of electron interaction with bigger molecules than ever before, which could lead, for example, to a better understanding of how radiation damages cell constituents, in particular DNA. Read more...

Image: DNA ©iStock.com/nechaev-kon


Optimising van der Waals simulations with CASTEP code

CASTEP is a general purpose code for the quantum simulation of properties of materials. Researchers have improved the performance of the van der Waals (vdW) interactions as implemented by CASTEP by replacing the previous simple sum method with a modified Ewald scheme. The code has also been parallelised using MPI. As a result of these two changes, for large calculations on ARCHER the code now runs many times faster. Read more...

reconstructed three-dimensional luminal surface ready to be used for HemeLB simulation

Microvasculature blood flow simulation using HemeLB

The work done in this project by researchers at UCL represents a substantial leap forward for the simulation of blood flow in microvasculature and enables for the first time the theoretical study of advanced aspects of haemorheology, oxygen transport, and cell trafficking in realistic vascular networks, and of the collective dynamics of dense red blood cell suspensions in complex vessel geometries. Read more...

Zacros software package logo

Pushing the Frontiers of Kinetic Monte Carlo Simulation in Catalysis - Zacros Software Package Development

The importance of heterogeneous catalysis in applications that enhance the quality of life cannot be overstated. Iron-based catalysts for the production of ammonia by the Haber process is a notable example, the importance of which is shown by the fact that fertilisers generated from ammonia produced in this way are responsible for sustaining one third of the Earth's population. Scientists at UCL have employed kinetic Monte Carlo methodology and their own software package, Zacros, to contribute to the unravelling of complex phenomena on catalytic surfaces. This knowledge can be used to improve existing catalysts or design novel materials with optimal activity and selectivity for bespoke applications. Read more...

Visualisation of convergence for Poisson mother problem

Scalable automated parallel PDE-constrained optimisation for dolfin-adjoint

The dolfin-adjoint package enables the automated optimisation of problems constrained by partial differential equations (PDEs). These problems are ubiquitous in engineering, eg the design of wings to maximise lift, or the cheapest bridge that will support the required load. Prior to this project, dolfin-adjoint was limited to serial optimisation libraries with no concept of parallel linear algebra. The work done in this project has eliminated the performance penalty associated with gathering the data and lifted the upper bound on the size of problems which can be considered. Read more...

Section of Crambin unit cell

Hybrid OpenMP and MPI within the CASTEP code

First-principles simulations of materials have had a profound and pervasive impact on science and technology, from physics, chemistry and materials science to diverse areas such as electronics, geology and medicine. CASTEP is a widely-used, UK-developed program for the quantum mechanical modelling of materials. This project has added a new level of parallelism to CASTEP, laying the foundations for a version of the code that will work well on future exascale supercomputers. The net result is a new science capability, allowing the study of larger and more complex systems than before, in less time. Read more...

test systems modelled by the software

Tuning FHI-Aims for complex simulations on Cray HPC platforms

The main objective of this project was to tune FHI-aims, a quantum mechanical electronic structure code, for optimal efficiency on ARCHER's hardware, for the benefit of members of the Materials Chemistry Consortium (MCC) and other users. The overarching target of this work by scientists at University College London was to improve scalability for a wide range of applications to enable new science, using current and emerging UK computer facilities, in a wide range of fields including materials and life sciences, chemistry, physics, and engineering. Read more...

image of alizarin in implicit solvent

Calculating Excited States of Extended Systems in LR-TDDFT

Electronic structure theory is a hugely important contributor to understanding properties of materials. Large-scale Density Functional Theory (DFT) codes such as ONETEP allow us to predict ground-state properties for large systems such as complex biomolecules. In this project, scientists at the University of Cambridge aimed to enhance, extend and improve the implementation in ONETEP of Linear Response Time-Dependent Density-Functional Theory (LR-TDDFT), the method of choice for computing optical properties of large systems. Read more...

Climate simulation image

Porting and enabling use of the Community Earth System Model (CESM) climate model on ARCHER

The Community Earth System Model (CESM) is a state-of-the-art coupled climate model for simulating the earth's climate system. Composed of four separate sub-models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, CESM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Scientists at the University of Edinburgh have ported to ARCHER and optimised two versions of CESM, and these are now both readily usable by the UK climate research community. This is expected to generate a further growth in interest in the model. Read more...

image of solvent cavity for the T4 lysozyme protein L99A/M102Q (2600 atoms) as produced by the ONETEP solvation model

A pinch of salt in ONETEP's solvent model

Chemical reactions, drug-protein interactions, and many chemical and physical processes on surfaces are examples of technologically important processes that happen in the presence of solvents. The inclusion of electrolytes (salt) in solvents such as water is crucial for biomolecular simulations, as most processes (e.g. protein-protein or protein-drug interactions or DNA mutations) take place in saline solutions. This project aimed to develop the capability to model electrolyte-containing solvents in quantum-mechanical simulations of materials from first principles. Using a linear-scaling code such as ONETEP enables simulations to be performed on entire biomolecules or catalysts that typically involve hundreds or thousands of atoms. Read more...

Visualisation of wavefunction density at the end of an RMT calculation

Performance enhancement in RMT codes in preparation for application to circular polarised light fields

One of the grand challenges in physics and chemistry is to understand what actually happens during a chemical reaction. The nuclei in molecules move on the femtosecond (10-15 s) timescale, but the electrons in the molecules move on the attosecond (10-18 s) timescale. The R-matrix with time dependence (RMT) code is a leading code for the description of ultra-fast processes in general atoms and molecules. Scientists at Queen's University Belfast have been working on the RMT code, increasing its speed by up to a factor of 5 and reducing the amount of memory required by one or more orders of magnitude. Read more...

Cross-section of the proximal end of a human femur

Understanding how bones develop and respond to disease and the use of implants

Scientists at the University of Hull have developed their simulation software to utilise ARCHER to model complete bones or large sections of bones. This offers the exciting opportunity to model skeletal development and adaptation. The potential benefits are enormous, ranging from a better understanding of both the fundamental biomechanics of bone and the cause and effects of musculoskeletal conditions, to better implant design. Read more...

Gas pipelines on the sea floor

TPLS: Optimised Parallel I/O and Visualisation

TPLS (Two Phase Level Set) is a powerful 3D Direct Numerical Simulation (DNS) solver that is able to simulate multi-phase flows at unprecedented detail, speed and accuracy with applications in energy (oil/gas pipeline flows, microelectronic cooling via phase-change), environment (carbon capture and cleaning) and health (flows in retinal capillaries). Scientists at the University of Edinburgh have been working on the code, converting the previously serial I/O to a scalable parallel implementation. This results in a halving of the time taken for each simulation from set-up to complete analysis. Read more...

Topological connectivity diagram

Scalable and interoperable I/O for Fluidity

At Imperial College London, scientists have been working with the Fluidity CFD code to improve file I/O and the performance and scalability of the underlying PETSc library. The resulting performance increase is then utilised to improve the mesh initialisation performance of the Fluidity CFD code through run-time distribution and more efficient data migration. In addition to performance improvements the capabilities of PETSc's DMPlexDistribute interface have been extended to include load-balancing and re-distribution of parallel meshes, as well as the ability to generate multiple levels of partition overlap. Furthermore, support for additional mesh file formats has been added to DMPlex and Fluidity, including binary Gmsh, Fluent-Case. Read more...