Simulations of ultrafast x–ray laser experiments

Fortmann-Grote, Carsten; Andreev, Alexander A.; Appel, Karen; Branco, João; Briggs, R.J.; Bußmann, Michael; Buzmakov, A. V.; Garten, Marco; Grund, Alexander; Huebl, Axel; Jurek, Zoltán; Loh, N. Duane; Nakatsutsumi, M.; Samoylova, Liubov; Santra, Robin; Schneidmiller, E.A.; Sharma, Ashutosh; Steiniger, Klaus; Yakubov, S. D.; Yoon, Chun Hong; Yurkov, M.V.; Zastrau, U.; Ziaja, Beata; Mancuso, Adrian P.

doi:10.1117/12.2270552

Cited by 4 publications

(6 citation statements)

References 47 publications

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“…SIMEX platform [8,9] implements the openPMD standard [13] through HDF5 files and uses loose coupling to integrate "some of most advanced simulation tools […] to mimic an entire light source beamline". Similarly, Mayes et al [21] (LUME) integrates single simulation modules with openPMD into a file-based loosely coupled pipeline for unified particle accelerator and lightsource modeling.…”

Section: Related Workmentioning

confidence: 99%

Transitioning from File-Based HPC Workflows to Streaming Data Pipelines with openPMD and ADIOS2

Poeschel

Juncheng

Godoy

et al. 2022

Driving Scientific and Engineering Discoveries Through the Integration of Experiment, Big Data, and Modeling and Simulation

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This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome and flexibly extended for in situ analysis. The openPMD-api is a library for the description of scientific data according to the Open Standard for Particle-Mesh Data (openPMD). Its approach towards recent challenges posed by hardware heterogeneity lies in the decoupling of data description in domain sciences, such as plasma physics simulations, from concrete implementations in hardware and IO. The streaming backend is provided by the ADIOS2 framework, developed at Oak Ridge National Laboratory. This paper surveys two openPMD-based loosely coupled setups to demonstrate flexible applicability and to evaluate performance. In loose coupling, as opposed to tight coupling, two (or more) applications are executed separately, e.g. in individual MPI contexts, yet cooperate by exchanging data. This way, a streaming-based workflow allows for standalone codes instead of tightlycoupled plugins, using a unified streaming-aware API and leveraging high-speed communication infrastructure available in modern compute clusters for massive data exchange. We determine new challenges in resource allocation and in the need of strategies for a flexible data distribution, demonstrating their influence on efficiency and scaling on the Summit compute system. The presented setups show the potential for a more flexible use of compute resources brought by streaming IO as well as the ability to increase throughput by avoiding filesystem bottlenecks.

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Section: Related Workmentioning

confidence: 99%

Transitioning from File-Based HPC Workflows to Streaming Data Pipelines with openPMD and ADIOS2

Poeschel

Juncheng

Godoy

et al. 2022

Driving Scientific and Engineering Discoveries Through the Integration of Experiment, Big Data, and Modeling and Simulation

View full text Add to dashboard Cite

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“…The interactive simulation software for wave optics propagation [17] is fully integrated with FAST-XPD output. It has been used within strart-to-end frameworks [18,19] and for detailed analysis of XFEL beamlines [20,21].…”

Section: How To Access and Use Fel Datamentioning

confidence: 99%

“…Photon data base has been used intensively used for optimization of the photon beam transport and imaging experiment [22,23]. Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these experiments investigating ever more complex physical systems, e.g.…”

Section: Pioneer Users Of Xpdmentioning

confidence: 99%

“…the source spectrum, temporal structure and coherence properties of the photon beam, or the detector response. The authors of [22,23] implemented a platform for complete start-to-end simulations, following the radiation from the source, through the beam transport optics to the sample or target under investigation, its interaction with and scattering from the sample, and its registration in a photon detector, including a realistic model of the detector response to the radiation. Such an approach allows researchers to simulate their experiments and instruments in real life scenarios, identify promising and unattainable regions of the parameter space and ultimately make better use of valuable beamtime.…”

Section: -5mentioning

confidence: 99%

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FAST-XPD: XFEL photon pulses database for modeling XFEL experiments

Manetti¹,

Buzmakov²,

Samoylova³

et al. 2019

AIP Conference Proceedings

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Knowledge of different properties of the radiation from X-ray FEL is very important for planning experiments. An understanding of such properties can come from start-to-end simulations of experiments: modern FEL simulation allows to reliably predict the output radiation pulses from X-ray FEL. We present a web accessible XFEL photon pulses simulation database showing data calculated with the FAST simulation framework.

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“…We employ the start-to-end simulation framework simex platform [35][36][37] to simulate a SPI experiment at the European XFEL utilizing 4.96 keV photons in a 9 fs pulse focused to a spotsize of 100 nm. The XFEL pulses are queried from the XFEL X-ray Pulse Database 38 and propagated through the SASE1 beamline and focusing optics of the SPB-SFX scientific instrument.…”

Section: Start-to-end Simulationmentioning

confidence: 99%

Simulations of single-particle imaging of hydrated proteins with x-ray free-electron lasers

Fortmann-Grote

Bielecki

Jurek

et al. 2017

Advances in Computational Methods for X-Ray Optics IV

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We employ start-to-end simulations to model coherent diffractive imaging of single biomolecules using x-ray free electron lasers. This technique is expected to yield new structural information about biologically relevant macromolecules thanks to the ability to study the isolated sample in its natural environment as opposed to crystallized or cryogenic samples. The effect of the solvent on the diffraction pattern and interpretability of the data is an open question. We present first results of calculations where the solvent is taken into account explicitely. They were performed with a molecular dynamics scheme for a sample consisting of a protein and a hydration layer of varying thickness. Through R-factor analysis of the simulated diffraction patterns from hydrated samples, we show that the scattering background from realistic hydration layers of up to 3Å thickness presents no obstacle for the resolution of molecular structures at the sub-nm level.

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Simulations of ultrafast x–ray laser experiments

Cited by 4 publications

References 47 publications

Transitioning from File-Based HPC Workflows to Streaming Data Pipelines with openPMD and ADIOS2

Transitioning from File-Based HPC Workflows to Streaming Data Pipelines with openPMD and ADIOS2

FAST-XPD: XFEL photon pulses database for modeling XFEL experiments

Simulations of single-particle imaging of hydrated proteins with x-ray free-electron lasers

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