Efficient end-to-end simulation of time-dependent coherent X-ray scattering experiments.

Physical optics simulations for beamlines and experiments allow users to test experiment feasibility and optimize beamline settings ahead of beam time in order to optimize valuable beam time at synchrotron light sources like NSLS-II. Further, such simulations also help to develop and test experimental data processing methods and software in advance. The Synchrotron Radiation Workshop (SRW) software package supports such complex simulations. We demonstrate how recent developments in SRW significantly improve the efficiency of physical optics simulations, such as end-to-end simulations of time-dependent X-ray photon correlation spectroscopy experiments with partially coherent undulator radiation (UR). The molecular dynamics simulation code LAMMPS was chosen to model the sample: a solution of silica nanoparticles in water at room temperature. Real-space distributions of nanoparticles produced by LAMMPS were imported into SRW and used to simulate scattering patterns of partially coherent hard X-ray UR from such a sample at the detector. The partially coherent UR illuminating the sample can be represented by a set of orthogonal coherent modes obtained by simulation of emission and propagation of this radiation through the coherent hard X-ray (CHX) scattering beamline followed by a coherent-mode decomposition. GPU acceleration is added for several key functions of SRW used in propagation from sample to detector, further improving the speed of the calculations. The accuracy of this simulation is benchmarked by comparison with experimental data.

Physical optics simulations for synchrotron radiation sources.

We describe approaches to high-accuracy physical optics calculations used for the development of x-ray beamlines at synchrotron radiation sources, as well as simulation of experiments and processing of experimental data at some of these beamlines. We pay special attention to the treatment of the partial coherence of x rays, a topic of high practical importance for modern low-emittance high-brightness synchrotron radiation facilities. The approaches are based, to a large extent, on the works of Emil Wolf and co-authors, including the basic scalar diffraction theory and the coherent mode decomposition method. The presented simulation examples are related to the case of the novel Coherent Diffractive Imaging beamline that is currently under development at the National Synchrotron Light Source II at the Brookhaven National Laboratory.

AMX - the highly automated macromolecular crystallography (17-ID-1) beamline at the NSLS-II.

The highly automated macromolecular crystallography beamline AMX/17-ID-1 is an undulator-based high-intensity (>5 × 1012 photons s-1), micro-focus (7 µm × 5 µm), low-divergence (1 mrad × 0.35 mrad) energy-tunable (5-18 keV) beamline at the NSLS-II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17-ID with the FMX beamline, the frontier micro-focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro-focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17-ID-1 as well as some plans for the near future are presented.

Simulation of X-ray Hartmann wavefront sensing with the Synchrotron Radiation Workshop.

X-ray wavefront measurement is an important beam diagnostic tool, especially for the diffraction-limited X-ray beam. These in situ diagnostics give a better understanding of beam imperfections, and they enable feedback for possible corrections and/or optical alignment improvements. Hartmann wavefront sensing is one of the promising techniques to perform in situ X-ray wavefront measurements. In this work, a simulation tool of the X-ray Hartmann Wavefront Sensor (HWS) is developed under the Synchrotron Radiation Workshop (SRW) framework. Using this new simulation capability, one can take advantage of the full SRW package to simulate Hartmann wavefront sensing with the beam traveling from the X-ray source to the sample through different X-ray optical components. This SRW HWS simulation tool can help to optimize the wavefront sensor parameters for a specific X-ray energy range. It can also simulate an in situ wavefront measurement experiment with a particular beamline optical layout and predict the expected results of the wavefront measurement under different beamline configurations.

Memory and CPU efficient coherent mode decomposition of partially coherent synchrotron radiation with subtraction of common quadratic phase terms.

Application examples of a memory and CPU efficient coherent mode decomposition (CMD) method for wave-optics based simulation of the partially coherent undulator radiation propagation through a hard X-ray beamline in a 3rd generation synchrotron radiation source are presented. The high efficiency of the method is achieved thanks to the analytical treatment of the common quadratic phase terms that are developed in the phase of cross-spectral density (CSD) of partially coherent radiation at a distance from source. This treatment allows for a considerable, several orders of magnitude, reduction of the 4D CSD mesh density (and the memory occupied by the CSD) required for ensuring sufficient accuracies of wavefront propagation simulations with the modes produced by the CMD at a beamline entrance. This method, implemented in the "Synchrotron Radiation Workshop" open-source software, dramatically increases the feasibility of the CMD of 4D CSD for producing 2D coherent modes for a large variety of applications at storage rings and other types of radiation sources.

FMX - the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II.

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425, 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493, 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015, 1741, 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5-30 keV photon energy range and delivers a flux of 4.0 × 1012 photons s-1 at 1 Šinto a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 1012 photons s-1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods - serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25, 1362-1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ, 5, 238-246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5, 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

Memory and CPU efficient computation of the Fresnel free-space propagator in Fourier optics simulations.

We describe a version of the paraxial free-space Fourier optics propagator for numerical wave propagation simulations that eliminates the need for a dense sampling of an input electric field with phase dominated by quadratic terms developing at some distance from the source or from the radiation beam waist. This propagator requires considerably (two to three orders of magnitude as observed in routine simulations) less memory and CPU resources than the standard Fresnel free-space propagator while preserving its levels of accuracy and generality. This method has been successfully used in "Synchrotron Radiation Workshop" code for more than a decade. It has greatly contributed to the applicability of the code, and more generally the applicability of the Fourier optics methods, to wave-optics based simulations of radiation propagation through optical systems of beamlines at high-brightness and high-coherence synchrotron light sources.

Sirepo: an open-source cloud-based software interface for X-ray source and optics simulations.

Sirepo, a browser-based GUI for X-ray source and optics simulations, is presented. Such calculations can be performed using SRW (Synchrotron Radiation Workshop), which is a physical optics computer code, allowing simulation of entire experimental beamlines using the concept of a `virtual beamline' with accurate treatment of synchrotron radiation generation and propagation through the X-ray optical system. SRW is interfaced with Sirepo by means of a Python application programming interface. Sirepo supports most of the optical elements currently used at beamlines, including recent developments in SRW. In particular, support is provided for the simulation of state-of-the-art X-ray beamlines, exploiting the high coherence and brightness of modern light source facilities. New scientific visualization and reporting capabilities have been recently implemented within Sirepo, as well as automatic determination of electron beam and undulator parameters. Publicly available community databases can be dynamically queried for error-free access to material characteristics. These computational tools can be used for the development and commissioning of new X-ray beamlines and for testing feasibility and optimization of experiments. The same interface can guide simulation on a local computer, a remote server or a high-performance cluster. Sirepo is available online and also within the NSLS-II firewall, with a growing number of users at other light source facilities. Our open source code is available on GitHub.

WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulations.

This article describes the WavePropaGator (WPG) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop (SRW) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.

Ultra-high-resolution inelastic X-ray scattering at high-repetition-rate self-seeded X-ray free-electron lasers.

Inelastic X-ray scattering (IXS) is an important tool for studies of equilibrium dynamics in condensed matter. A new spectrometer recently proposed for ultra-high-resolution IXS (UHRIX) has achieved 0.6 meV and 0.25 nm(-1) spectral and momentum-transfer resolutions, respectively. However, further improvements down to 0.1 meV and 0.02 nm(-1) are required to close the gap in energy-momentum space between high- and low-frequency probes. It is shown that this goal can be achieved by further optimizing the X-ray optics and by increasing the spectral flux of the incident X-ray pulses. UHRIX performs best at energies from 5 to 10 keV, where a combination of self-seeding and undulator tapering at the SASE-2 beamline of the European XFEL promises up to a 100-fold increase in average spectral flux compared with nominal SASE pulses at saturation, or three orders of magnitude more than what is possible with storage-ring-based radiation sources. Wave-optics calculations show that about 7 × 10(12) photons s(-1) in a 90 µeV bandwidth can be achieved on the sample. This will provide unique new possibilities for dynamics studies by IXS.

Ultrahigh energy resolution focusing monochromator for inelastic x-ray scattering spectrometer.

A further development of a focusing monochromator concept for X-ray energy resolution of 0.1 meV and below is presented. Theoretical analysis of several optical layouts based on this concept was supported by numerical simulations performed in the "Synchrotron Radiation Workshop" software package using the physical-optics approach and careful modeling of partially-coherent synchrotron (undulator) radiation. Along with the energy resolution, the spectral shape of the energy resolution function was investigated. It was shown that under certain conditions the decay of the resolution function tails can be faster than that of the Gaussian function.

Partially coherent X-ray wavefront propagation simulations including grazing-incidence focusing optics.

X-ray beamlines in modern synchrotron radiation sources make extensive use of grazing-incidence reflective optics, in particular Kirkpatrick-Baez elliptical mirror systems. These systems can focus the incoming X-rays down to nanometer-scale spot sizes while maintaining relatively large acceptance apertures and high flux in the focused radiation spots. In low-emittance storage rings and in free-electron lasers such systems are used with partially or even nearly fully coherent X-ray beams and often target diffraction-limited resolution. Therefore, their accurate simulation and modeling has to be performed within the framework of wave optics. Here the implementation and benchmarking of a wave-optics method for the simulation of grazing-incidence mirrors based on the local stationary-phase approximation or, in other words, the local propagation of the radiation electric field along geometrical rays, is described. The proposed method is CPU-efficient and fully compatible with the numerical methods of Fourier optics. It has been implemented in the Synchrotron Radiation Workshop (SRW) computer code and extensively tested against the geometrical ray-tracing code SHADOW. The test simulations have been performed for cases without and with diffraction at mirror apertures, including cases where the grazing-incidence mirrors can be hardly approximated by ideal lenses. Good agreement between the SRW and SHADOW simulation results is observed in the cases without diffraction. The differences between the simulation results obtained by the two codes in diffraction-dominated cases for illumination with fully or partially coherent radiation are analyzed and interpreted. The application of the new method for the simulation of wavefront propagation through a high-resolution X-ray microspectroscopy beamline at the National Synchrotron Light Source II (Brookhaven National Laboratory, USA) is demonstrated.

DISCO: a low-energy multipurpose beamline at synchrotron SOLEIL.

DISCO, a novel low-energy beamline covering the spectrum range from the VUV to the visible, has received its first photons at the French synchrotron SOLEIL. In this article the DISCO design and concept of three experimental stations serving research communities in biology and chemistry are described. Emphasis has been put on high flux generation and preservation of polarization at variable energy resolutions. The three experiments include a completely new approach for microscopy and atmospheric pressure experiments as well as a ;classical' synchrotron radiation circular dichroism station. Preliminary tests of the optical design and technical concept have been made. Theoretical predictions of the beam have been compared with the first images produced by the first photons originating from the large-aperture bending-magnet source. Results are also reported concerning the cold finger used to absorb hard X-ray radiation in the central part of the synchrotron beam and to avoid heavy thermal load on the following optics. Wavelength selection using monochromators with different gratings for each experimental set-up as well as beam propagation and conditioning throughout the optical system are detailed. First photons comply very well with the theoretical calculations.