exFock – cluster for experimentalists

exFock – cluster for experimentalists

exFock is the latest iteration of the Fock Cluster. This has been in use by the NRC theory group for several years, and recently superseded. As of early 2023, some nodes have been passed on to the experimental groups for general computational use. (For a general introduction to computational clusters, try this overview or the wikipaedia page.)

exFock is a 14+1 node linux cluster for CPU-compute, each with dual Intel Xeon E5-2660 v4 @ 2.00GHz CPU, 128Gb ECC RAM and ~700Gb fast scratch space, running Ubuntu 16LTS. The cluster is managed by a head node with ~8Tb shared storage, with a gigabit Ethernet backbone. (Limited GPU-compute is also available, via NVidia Quadro K2200 cards – one per node, CUDA compute capability 3.0, 640 CUDA cores, 4Gb RAM per card.)

Computational jobs can be dispatched via Slurm or Docker. The former was in use by the theory group (mainly for electronic structure and molecular dynamics codes, running from local shared installations); the latter has just been added to exFock and is suggested for ongoing general use to avoid issues with OS-specific applications and compilation, as well as general sandboxing and as an easy way to enable local user development and testing capabilities (since the Docker containers are fully portable). Note that initial users may need some basic background knowledge whilst exFock is in the setup/trial stage, although the barrier to entry will gradually drop over time. A global installation of Jupyter (Hub) is also planned in the near future, for general data analysis tasks, and will offer a lower barrier to entry for users interested in data analysis tasks.

If you’re interested in using exFock, please use the registration form below (or via the google form page). For more on our heterogeneous compute projects, see here.

Multivariate Discrimination in Quantum Target Detection

Multivariate Discrimination in Quantum Target Detection

Update July 2020: now published as Appl. Phys. Lett. 117, 044001 (2020); https://doi.org/10.1063/5.0012429

[Submitted on 1 May 2020]

Peter Svihra, Yingwen Zhang, Paul Hockett, Steven Ferrante, Benjamin Sussman, Duncan England, Andrei Nomerotski

We describe a simple multivariate technique of likelihood ratios for improved discrimination of signal and background in multi-dimensional quantum target detection. The technique combines two independent variables, time difference and summed energy, of a photon pair from the spontaneous parametric down-conversion source into an optimal discriminant. The discriminant performance was studied in experimental data and in Monte-Carlo modelling with clear improvement shown compared to previous techniques. As novel detectors become available, we expect this type of multivariate analysis to become increasingly important in multi-dimensional quantum optics.


Fibre VUV generation & applications

Fibre VUV generation & applications

Over the last few months (summer 2018) a new project has been shaping up, in collaboration with colleagues from the PCF division (Russell research group) at MPL.  The aim is to develop new ultrafast experiments based on their hollow-core PCFs, which can be used to provide tuneable UV and VUV. This work is part of our larger source development project, and will develop towards applications in photoelectron metrology and quantum optics (amongst others!).

More details to follow, but for now here are a few images of the work in progress…

Direct Ion Detection Summary (March 2018)

Direct Ion Detection Summary (March 2018)

Our Direct Ion Detection Technology Project is wrapping up in its current form, with a plan to reemerge – bigger and better – next year. See this PDF for a summary of the project to date, and plans for future work. Further details can also be found on the project webpages.

Heterogeneous & GPU compute

Heterogeneous & GPU compute

Heterogeneous computing, holds many opportunities for simulation and data analysis applications in the physical sciences. On the desktop, massively parallel calculations are now possible with the use of GPUs. We are currently exploring the capabilities of Nvidia’s CUDA platform on multi-GPU machines, and application to new and existing applications. This project is closely related to our AR/VR project.

The image above shows AntonJr, a dual-CPU (Xeon E5-2680), triple-GPU (GeForce 1080Ti), water-cooled machine.

Reading today…

Reading today…

Linac Coherent Light Source: The first five years

Christoph Bostedt, Sébastien Boutet, David M. Fritz, Zhirong Huang, Hae Ja Lee, Henrik T. Lemke, Aymeric Robert, William F. Schlotter, Joshua J. Turner, and Garth J. Williams

Rev. Mod. Phys. 88, 015007 – Published 9 March 2016

A new scientific frontier opened in 2009 with the start of operations of the world’s first x-ray free-electron laser (FEL), the Linac Coherent Light Source (LCLS), at SLAC National Accelerator Laboratory. LCLS provides femtosecond pulses of x rays (270 eV to 11.2 keV) with very high peak brightness to access new domains of ultrafast x-ray science. This article presents the fundamental FEL physics and outlines the LCLS source characteristics along with the experimental challenges, strategies, and instrumentation that accompany this novel type of x-ray source. The main part of the article reviews the scientific achievements since the inception of LCLS in the five primary areas it serves: atomic, molecular, and optical physics; condensed matter physics; matter in extreme conditions; chemistry and soft matter, and biology.

DOI: 10.1103/RevModPhys.88.015007 

Direct Ion Detection & Detector Technology Development

Direct Ion Detection & Detector Technology Development

Our VIRP chamber (for rapid vacuum instrument prototyping), is designed to perform experiments with new detector technologies, and provide a route to optimising the methodologies and technologies. Early work has been based around novel scintillators recently developed in Oxford [1,2], and also involved trialling the PImMS camera (for 3D ion imaging) for ultrafast pump-probe experiments [3] – see our blog for further information. New project work will continue to build in these directions.

[1] A new detector for mass spectrometry: Direct detection of low energy ions using a multi-pixel photon counter
Edward S. Wilman, Sara H. Gardiner, Andrei Nomerotski, Renato Turchetta, Mark Brouard and Claire Vallance
Rev. Sci. Instrum. 83, 013304 (2012).

[2] Improved direct detection of low-energy ions using a multipixel photon counter coupled with a novel scintillator
Winter, King, Brouard & Vallance
International Journal of Mass Spectrometry, 397–398, 27–31 (2016)

[3] Time-resolved multi-mass ion imaging: femtosecond UV-VUV pump-probe spectroscopy with the PImMS camera
Ruaridh ForbesVarun MakhijaKévin VeyrinasAlbert StolowJason W. L. LeeMichael BurtMark BrouardClaire VallanceIain WilkinsonRune LaustenPaul Hockett
arXiv 1702.00744 (2017)The Journal of Chemical Physics 147, 013911 (2017), DOI: http://dx.doi.org/10.1063/1.4978923



Augmented and Virtual Reality for Data Visualization & Research Applications

Augmented and Virtual Reality for Data Visualization & Research Applications

Recent developments in AR & VR hardware have resulted in a range of nascent commercial products, e.g. the Microsoft Hololens and DAQRI smart helmet (augmented reality), Occulus Rift and HTC Vive (virtual reality).  Laboratory use is an obvious application of current tether-free AR technology, which could enable new experimental methodologies as well as offer basic procedural, efficiency, training and health and safety benefits.  VR technology, which typically requires tethering to a high-performance PC, provides a complementary platform, more suited to fully immersive computational uses such as multi-dimensional data visualization and big data applications.

Early work with the Hololens, investigating 3D visualization and basic lab usage, has already begun in the group; this project would further work to explore and develop these capabilities. See also the related project on heterogenous computing.

Press Release: The Inner Lives of Molecules

Press Release: The Inner Lives of Molecules

Our latest work with the PImMS camera, femtosecond VUV pulses, and velocity-map imaging, has been picked up for a press release by AIP.

The Inner Lives of Molecules

New method takes 3-D images of molecules in action

WASHINGTON, D.C., April 4, 2017 — Quantum mechanics rules. It dictates how particles and forces interact, and thus how atoms and molecules work — for example, what happens when a molecule goes from a higher-energy state to a lower-energy one. But beyond the simplest molecules, the details become very complex.

“Quantum mechanics describes how all this stuff works,” said Paul Hockett of the National Research Council of Canada. “But as soon as you go beyond the two-body problem, you can’t solve the equations.” So, physicists must rely on computer simulations and experiments.

Now, he and an international team of researchers from Canada, the U.K. and Germany have developed a new experimental technique to take 3-D images of molecules in action. This tool, he said, can help scientists better understand the quantum mechanics underlying bigger and more complex molecules.

The new method, described in The Journal of Chemical Physics, from AIP Publishing, combines two technologies. The first is a camera developed at Oxford University, called the Pixel-Imaging Mass Spectrometry (PImMS) camera. The second is a femtosecond vacuum ultraviolet light source built at the NRC femtolabs in Ottawa.

Mass spectrometry is a method used to identify unknown compounds and to probe the structure of molecules. In most types of mass spectrometry, a molecule is fragmented into atoms and smaller molecules that are then separated by molecular weight. In time-of-flight mass spectrometry, for example, an electric field accelerates the fragmented molecule. The speed of those fragments depends on their mass and charge, so to weigh them, you measure how long it takes for them to hit the detector.

Most conventional imaging detectors, however, can’t discern exactly when one particular particle hits. To measure timing, researchers must use methods that effectively act as shutters, which let particles through over a short time period. Knowing when the shutter is open gives the time-of-flight information. But this method can only measure particles of the same mass, corresponding to the short time the shutter is open.

The PImMS camera, on the other hand, can measure particles of multiple masses all at once. Each pixel of the camera’s detector can time when a particle strikes it. That timing information produces a three-dimensional map of the particles’ velocities, providing a detailed 3-D image of the fragmentation pattern of the molecule.

To probe molecules, the researchers used this camera with a femtosecond vacuum ultraviolet laser. A laser pulse excites the molecule into a higher-energy state, and just as the molecule starts its quantum mechanical evolution — after a few dozen femtoseconds –another pulse is fired. The molecule absorbs a single photon, a process that causes it to fall apart. The PImMS camera then snaps a 3-D picture of the molecular debris.

By firing a laser pulse at later and later times at excited molecules, the researchers can use the PImMS camera to take snapshots of molecules at various stages while they fall into lower energy states. The result is a series of 3-D blow-by-blow images of a molecule changing states.

The researchers tested their approach on a molecule called C2F3I. Although a relatively small molecule, it fragmented into five different products in their experiments. The data and analysis software is available online as part of an open science initiative, and although the results are preliminary, Hockett said, the experiments demonstrate the power of this technique.

“It’s effectively an enabling technology to actually do these types of experiments at all,” Hockett said. It only takes a few hours to collect the kind of data that would take a few days using conventional methods, allowing for experiments with larger molecules that were previously impossible.

Then researchers can better answer questions like: How does quantum mechanics work in larger, more complex systems? How do excited molecules behave and how do they evolve?

“People have been trying to understand these things since the 1920s,” Hockett said. “It’s still a very open field of investigation, research, and debate because molecules are really complicated. We have to keep trying to understand them.”

Text reproduced from AIP.

The article, Time-resolved multi-mass ion imaging: femtosecond UV-VUV pump-probe spectroscopy with the PImMS camera, is now published in the Journal of Chemical Physics, and also available via the arXiv 1702.00744 and Authorea (original text), DOI: 10.22541/au.149030711.19068540.

The full dataset and analysis scripts are available via OSF, DOI: 10.17605/OSF.IO/RRFK3.