High-Performance Multi-Mode Ptychography Reconstruction on Distributed GPUs

Ptychography is an emerging imaging technique that is able to provide wavelength-limited spatial resolution from specimen with extended lateral dimensions. As a scanning microscopy method, a typical two-dimensional image requires a number of data frames. As a diffraction-based imaging technique, the real-space image has to be recovered through iterative reconstruction algorithms. Due to these two inherent aspects, a ptychographic reconstruction is generally a computation-intensive and time-consuming process, which limits the throughput of this method. We report an accelerated version of the multi-mode difference map algorithm for ptychography reconstruction using multiple distributed GPUs. This approach leverages available scientific computing packages in Python, including mpi4py and PyCUDA, with the core computation functions implemented in CUDA C. We find that interestingly even with MPI collective communications, the weak scaling in the number of GPU nodes can still remain nearly constant. Most importantly, for realistic diffraction measurements, we observe a speedup ranging from a factor of $10$ to $10^3$ depending on the data size, which reduces the reconstruction time remarkably from hours to typically about 1 minute and is thus critical for real-time data processing and visualization.Comment: work presented in NYSDS 201

Takagi-Taupin Description of X-ray Dynamical Diffraction from Diffractive Optics with Large Numerical Aperture

We present a formalism of x-ray dynamical diffraction from volume diffractive optics with large numerical aperture and high aspect ratio, in an analogy to the Takagi-Taupin equations for strained single crystals. We derive a set of basic equations for dynamical diffraction from volume diffractive optics, which enable us to study the focusing property of these optics with various grating profiles. We study volume diffractive optics that satisfy the Bragg condition to various degrees, namely flat, tilted and wedged geometries, and derive the curved geometries required for ultimate focusing. We show that the curved geometries satisfy the Bragg condition everywhere and phase requirement for point focusing, and effectively focus hard x-rays to a scale close to the wavelength.Comment: 18 pages, 12 figure

Ion beam lithography for Fresnel zone plates in X-ray microscopy

Fresnel Zone Plates (FZP) are to date very successful focusing optics for X-rays. Established methods of fabrication are rather complex and based on electron beam lithography (EBL). Here, we show that ion beam lithography (IBL) may advantageously simplify their preparation. A FZP operable from the extreme UV to the limit of the hard X-ray was prepared and tested from 450 eV to 1500 eV. The trapezoidal profile of the FZP favorably activates its 2nd order focus. The FZP with an outermost zone width of 100 nm allows the visualization of features down to 61, 31 and 21 nm in the 1st, 2nd and 3rd order focus respectively. Measured efficiencies in the 1st and 2nd order of diffraction reach the theoretical predictions

Complete Strain Mapping of Nanosheets of Tantalum Disulfide

Quasi-two-dimensional (quasi-2D) materials hold promise for future electronics because of their unique band structures that result in electronic and mechanical properties sensitive to crystal strains in all three dimensions. Quantifying crystal strain is a prerequisite to correlating it with the performance of the device, and calls for high resolution but spatially resolved rapid characterization methods. Here we show that using fly-scan nano X-ray diffraction we can accomplish a tensile strain sensitivity below 0.001% with a spatial resolution of better than 80 nm over a spatial extent of 100 $\mu$m on quasi 2D flakes of 1T-TaS2. Coherent diffraction patterns were collected from a $\sim$ 100 nm thick sheet of 1T-TaS2 by scanning 12keV focused X-ray beam across and rotating the sample. We demonstrate that the strain distribution around micron and sub-micron sized 'bubbles' that are present in the sample may be reconstructed from these images. The experiments use state of the art synchrotron instrumentation, and will allow rapid and non-intrusive strain mapping of thin film samples and electronic devices based on quasi 2D materials

Evolution of vegetation and climate variability on the Tibetan Plateau over the past 1.74 million years

The Tibetan Plateau exerts a major influence on Asian climate, but its long-term environmental history remains largely unknown. We present a detailed record of vegetation and climate changes over the past 1.74 million years in a lake sediment core from the Zoige Basin, eastern Tibetan Plateau. Results show three intervals with different orbital- and millennial-scale features superimposed on a stepwise long-term cooling trend. The interval of 1.74–1.54 million years ago is characterized by an insolation-dominated mode with strong ~20,000-year cyclicity and quasi-absent millennial-scale signal. The interval of 1.54–0.62 million years ago represents a transitional insolation-ice mode marked by ~20,000- and ~40,000-year cycles, with superimposed millennial-scale oscillations. The past 620,000 years are characterized by an ice-driven mode with 100,000-year cyclicity and less frequent millennial-scale variability. A pronounced transition occurred 620,000 years ago, as glacial cycles intensified. These new findings reveal how the interaction of low-latitude insolation and high-latitude ice-volume forcing shaped the evolution of the Tibetan Plateau climate.publishedVersio

Self-absorption correction on 2D X-ray fluorescence maps

Abstract X-ray fluorescence mapping (XRF) is a highly efficient and non-invasive technique for quantifying material composition with micro and nanoscale spatial resolutions. Quantitative XRF analysis, however, confronts challenges from the long-lasting problem called self-absorption. Moreover, correcting two-dimensional XRF mapping datasets is particularly difficult because it is an ill-posed inverse problem. Here we report a semi-empirical method that can effectively correct 2D XRF mapping data. The correction error is generally less than 10% from a comprehensive evaluation of the accuracy in various configurations. The proposed method was applied to quantify the composition distribution around the grain boundaries in an electrochemically corroded stainless steel sample. Highly localized Cr enrichment was found around the crack sites, which was invisible before the absorption correction