Journal of Applied Crystallography
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Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.enCopyright (c) 2017 International Union of Crystallography2017-11-21International Union of CrystallographyInternational Union of Crystallographyhttp://journals.iucr.orgurn:issn:1600-5767Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.text/htmlJournal of Applied Crystallography, Volume 50, Part 6, 2017textweekly62002-02-01T00:00+00:006502017-11-21Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallography1561urn:issn:1600-5767med@iucr.orgNovember 20172017-11-21Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
//journals.iucr.org/j/issues/2017/06/00/isscontsbdy.html
Still imageAdvancing reverse Monte Carlo structure refinements to the nanoscale
http://scripts.iucr.org/cgi-bin/paper?kc5063
Over the past decade, the RMCProfile software package has evolved into a powerful computational framework for atomistic structural refinements using a reverse Monte Carlo (RMC) algorithm and multiple types of experimental data. However, realizing the full potential of this method, which can provide a consistent description of atomic arrangements over several length scales, requires a computational speed much higher than that permitted by the current software. This problem has been addressed via substantial optimization and development of RMCProfile, including the introduction of the new parallel-chains RMC algorithm. The computing speed of this software has been increased by nearly two orders of magnitude, as demonstrated using the refinements of a simulated structure with two distinct correlation lengths for the atomic displacements. The new developments provide a path for achieving even faster performance as more advanced computing hardware becomes available. This version of RMCProfile permits refinements of atomic configurations of the order of 500 000 atoms (compared to the current limit of 20 000), which sample interatomic distances up to 10 nm (versus 3 nm currently). Accurate, computationally efficient corrections of the calculated X-ray and neutron total scattering data have been developed to account for the effects of instrumental resolution. These corrections are applied in both reciprocal and real spaces, thereby enabling RMC fitting of an atomic pair distribution function, which is obtained as the Fourier transform of the total-scattering intensity, over the entire nanoscale distance range accessible experimentally.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Eremenko, M.Krayzman, V.Gagin, A.Levin, I.2017-10-11doi:10.1107/S1600576717013140International Union of CrystallographyThe computing speed of reverse Monte Carlo structure refinements has been improved by up to two orders of magnitude, which significantly expands the capabilities of this method.ENlocal structurereverse Monte CarloscatteringOver the past decade, the RMCProfile software package has evolved into a powerful computational framework for atomistic structural refinements using a reverse Monte Carlo (RMC) algorithm and multiple types of experimental data. However, realizing the full potential of this method, which can provide a consistent description of atomic arrangements over several length scales, requires a computational speed much higher than that permitted by the current software. This problem has been addressed via substantial optimization and development of RMCProfile, including the introduction of the new parallel-chains RMC algorithm. The computing speed of this software has been increased by nearly two orders of magnitude, as demonstrated using the refinements of a simulated structure with two distinct correlation lengths for the atomic displacements. The new developments provide a path for achieving even faster performance as more advanced computing hardware becomes available. This version of RMCProfile permits refinements of atomic configurations of the order of 500 000 atoms (compared to the current limit of 20 000), which sample interatomic distances up to 10 nm (versus 3 nm currently). Accurate, computationally efficient corrections of the calculated X-ray and neutron total scattering data have been developed to account for the effects of instrumental resolution. These corrections are applied in both reciprocal and real spaces, thereby enabling RMC fitting of an atomic pair distribution function, which is obtained as the Fourier transform of the total-scattering intensity, over the entire nanoscale distance range accessible experimentally.text/htmlAdvancing reverse Monte Carlo structure refinements to the nanoscaletext6502017-10-11Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Improved orientation sampling for indexing diffraction patterns of polycrystalline materials
http://scripts.iucr.org/cgi-bin/paper?po5106
Orientation mapping is a widely used technique for revealing the microstructure of a polycrystalline sample. The crystalline orientation at each point in the sample is determined by analysis of the diffraction pattern, a process known as pattern indexing. A recent development in pattern indexing is the use of a brute-force approach, whereby diffraction patterns are simulated for a large number of crystalline orientations and compared against the experimentally observed diffraction pattern in order to determine the most likely orientation. Whilst this method can robustly identify orientations in the presence of noise, it has very high computational requirements. In this article, the computational burden is reduced by developing a method for nearly optimal sampling of orientations. By using the quaternion representation of orientations, it is shown that the optimal sampling problem is equivalent to that of optimally distributing points on a four-dimensional sphere. In doing so, the number of orientation samples needed to achieve a desired indexing accuracy is significantly reduced. Orientation sets at a range of sizes are generated in this way for all Laue groups and are made available online for easy use.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Larsen, P.M.Schmidt, S.2017-10-11doi:10.1107/S1600576717012882International Union of CrystallographyA method for generating high-quality discretizations of SO(3) is described and compared with existing methods.ENorientation samplingpattern indexingforward modellingquaternionsspherical coveringsOrientation mapping is a widely used technique for revealing the microstructure of a polycrystalline sample. The crystalline orientation at each point in the sample is determined by analysis of the diffraction pattern, a process known as pattern indexing. A recent development in pattern indexing is the use of a brute-force approach, whereby diffraction patterns are simulated for a large number of crystalline orientations and compared against the experimentally observed diffraction pattern in order to determine the most likely orientation. Whilst this method can robustly identify orientations in the presence of noise, it has very high computational requirements. In this article, the computational burden is reduced by developing a method for nearly optimal sampling of orientations. By using the quaternion representation of orientations, it is shown that the optimal sampling problem is equivalent to that of optimally distributing points on a four-dimensional sphere. In doing so, the number of orientation samples needed to achieve a desired indexing accuracy is significantly reduced. Orientation sets at a range of sizes are generated in this way for all Laue groups and are made available online for easy use.text/htmlImproved orientation sampling for indexing diffraction patterns of polycrystalline materialstext6502017-10-11Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00A valence-selective X-ray fluorescence holography study of an yttrium oxide thin film
http://scripts.iucr.org/cgi-bin/paper?to5163
The first direct valence-selective structure determination by X-ray fluorescence holography is reported. The method is applied to investigate an epitaxial thin film of the rare earth monoxide YO, which has recently been synthesized by pulsed laser deposition. The surface of the sample is easily oxidized to Y2O3. In order to separate the structural information connected with the two different valence states of Y, the X-ray fluorescence holography measurements were performed close to the Y K absorption edge. Using the shift of the absorption edge for the different valence states, very different relative contributions of YO and Y2O3 are obtained. Thus, it is possible to distinguish the crystal structures of YO and Y2O3 in the thin-film sample.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Stellhorn, J.R.Hosokawa, S.Happo, N.Tajiri, H.Matsushita, T.Kaminaga, K.Fukumura, T.Hasegawa, T.Hayashi, K.2017-10-11doi:10.1107/S1600576717012821International Union of CrystallographyThe first direct valence-selective structure determination by X-ray fluorescence holography is presented. This method uses the fluorescence intensity variation of specific elements close to the K absorption edge. Thereby, the different crystal structures in a mixed Y2+/Y3+ thin film of yttrium oxide are distinguished.ENX-ray fluorescence holographyvalence selectivityyttrium oxidethin-film analysisThe first direct valence-selective structure determination by X-ray fluorescence holography is reported. The method is applied to investigate an epitaxial thin film of the rare earth monoxide YO, which has recently been synthesized by pulsed laser deposition. The surface of the sample is easily oxidized to Y2O3. In order to separate the structural information connected with the two different valence states of Y, the X-ray fluorescence holography measurements were performed close to the Y K absorption edge. Using the shift of the absorption edge for the different valence states, very different relative contributions of YO and Y2O3 are obtained. Thus, it is possible to distinguish the crystal structures of YO and Y2O3 in the thin-film sample.text/htmlA valence-selective X-ray fluorescence holography study of an yttrium oxide thin filmtext6502017-10-11Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Melting and freezing temperatures of confined Bi nanoparticles over a wide size range
http://scripts.iucr.org/cgi-bin/paper?rg5131
The size dependences of the melting and freezing temperatures, Tm and Tf, respectively, of spherical Bi nanoparticles embedded in a sodium borate glass were determined by applying a new experimental procedure based on the combined and simultaneous use of small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS). This experimental procedure is particularly useful for materials in which a widely polydisperse set of nanoparticles are embedded. The results provide additional and stronger evidence supporting the main previous conclusions: (i) the melting and freezing temperatures both decrease linearly for increasing reciprocal radius (1/R); and (ii) the effect of undercooling is suppressed for Bi nanoparticles with radii smaller than a critical value equal to 1.8 nm. These results confirm a previously proposed low-resolution structural model for Bi nanocrystals below their melting temperature and with radius R > 1.8 nm, which consists of a crystalline core surrounded by a disordered shell. In the present work, a number of samples with different and partially overlapping radius distributions were studied, allowing the determination of Tm(R) and Tf(R) functions over a wide range of radii (1 < R < 11 nm). Comparison of the experimentally determined Tm(R) and Tf(R) functions corresponding to different samples indicates good reproducibility of the experimental results. This allowed the verification of the robustness of the experimental procedure based on in situ combined use of SAXS and WAXS for determination of the radius dependence of the melting and freezing temperatures of spherical nanoparticles in dilute solution.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Degenhardt, H.F.Kellermann, G.Craievich, A.F.2017-10-11doi:10.1107/S1600576717012997International Union of CrystallographyThe size dependences of the melting and crystallization temperatures of spherical Bi nanoparticles embedded in glass were determined using combined small- and wide-angle X-ray scattering measurements for nanoparticle radii ranging from 1 to 11 nm. The results provide additional and stronger evidence supporting previous conclusions showing that, below the melting temperature, Bi nanocrystals with radii larger than 1.8 nm consist of a crystalline core surrounded by a disordered shell.ENsmall-angle X-ray scatteringnanocrystalswide-angle X-ray scatteringmeltingcrystallizationnanoparticlesThe size dependences of the melting and freezing temperatures, Tm and Tf, respectively, of spherical Bi nanoparticles embedded in a sodium borate glass were determined by applying a new experimental procedure based on the combined and simultaneous use of small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS). This experimental procedure is particularly useful for materials in which a widely polydisperse set of nanoparticles are embedded. The results provide additional and stronger evidence supporting the main previous conclusions: (i) the melting and freezing temperatures both decrease linearly for increasing reciprocal radius (1/R); and (ii) the effect of undercooling is suppressed for Bi nanoparticles with radii smaller than a critical value equal to 1.8 nm. These results confirm a previously proposed low-resolution structural model for Bi nanocrystals below their melting temperature and with radius R > 1.8 nm, which consists of a crystalline core surrounded by a disordered shell. In the present work, a number of samples with different and partially overlapping radius distributions were studied, allowing the determination of Tm(R) and Tf(R) functions over a wide range of radii (1 < R < 11 nm). Comparison of the experimentally determined Tm(R) and Tf(R) functions corresponding to different samples indicates good reproducibility of the experimental results. This allowed the verification of the robustness of the experimental procedure based on in situ combined use of SAXS and WAXS for determination of the radius dependence of the melting and freezing temperatures of spherical nanoparticles in dilute solution.text/htmlMelting and freezing temperatures of confined Bi nanoparticles over a wide size rangetext6502017-10-11Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Inverse pole figure mapping of bulk crystalline grains in a polycrystalline steel plate by pulsed neutron Bragg-dip transmission imaging
http://scripts.iucr.org/cgi-bin/paper?nb5198
A new mapping procedure for polycrystals using neutron Bragg-dip transmission is presented. This is expected to be useful as a new materials characterization tool which can simultaneously map the crystallographic direction of grains parallel to the incident beam. The method potentially has a higher spatial resolution than neutron diffraction imaging. As a demonstration, a Bragg-dip neutron transmission experiment was conducted at J-PARC on beamline MLF BL10 NOBORU. A large-grained Si–steel plate was used. Since this specimen included multiple grains along the neutron beam transmission path, it was a challenging task for existing methods to analyse the direction of the crystal lattice of each grain. A new data-analysis method for Bragg-dip transmission measurements was developed based on database matching. As a result, the number of grains and their crystallographic direction along the neutron transmission path have been determined.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Sato, H.Shiota, Y.Morooka, S.Todaka, Y.Adachi, N.Sadamatsu, S.Oikawa, K.Harada, M.Zhang, S.Su, Y.Kamiyama, T.Ohnuma, M.Furusaka, M.Shinohara, T.Kiyanagi, Y.2017-10-11doi:10.1107/S1600576717012900International Union of CrystallographyPulsed neutron Bragg-dip transmission is an efficient method for determining the crystallographic direction of crystals lying parallel to the incident beam. The method can be used for crystalline grain identification with a spatial resolution higher than that achievable by neutron diffraction imaging.ENpulsed neutron Bragg-dip transmission imaginggrain orientation mappinginverse pole figureslarge-area bulk analysisA new mapping procedure for polycrystals using neutron Bragg-dip transmission is presented. This is expected to be useful as a new materials characterization tool which can simultaneously map the crystallographic direction of grains parallel to the incident beam. The method potentially has a higher spatial resolution than neutron diffraction imaging. As a demonstration, a Bragg-dip neutron transmission experiment was conducted at J-PARC on beamline MLF BL10 NOBORU. A large-grained Si–steel plate was used. Since this specimen included multiple grains along the neutron beam transmission path, it was a challenging task for existing methods to analyse the direction of the crystal lattice of each grain. A new data-analysis method for Bragg-dip transmission measurements was developed based on database matching. As a result, the number of grains and their crystallographic direction along the neutron transmission path have been determined.text/htmlInverse pole figure mapping of bulk crystalline grains in a polycrystalline steel plate by pulsed neutron Bragg-dip transmission imagingtext6502017-10-11Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements
http://scripts.iucr.org/cgi-bin/paper?rg5136
Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes' theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO3 film fabricated on top of SrTiO3. The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites.Copyright (c) 2017 Masato Anada et al.urn:issn:1600-5767Anada, M.Nakanishi-Ohno, Y.Okada, M.Kimura, T.Wakabayashi, Y.2017-10-20doi:10.1107/S1600576717013292International Union of CrystallographyReverse Monte Carlo software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference.ENBayesian inferencecrystal truncation rodsperovskite filmsMonte CarloMonte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes' theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO3 film fabricated on top of SrTiO3. The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites.text/htmlBayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurementstext6502017-10-20Copyright (c) 2017 Masato Anada et al.Journal of Applied Crystallographyresearch papers00Whole-nanoparticle atomistic modeling of the schwertmannite structure from total scattering data
http://scripts.iucr.org/cgi-bin/paper?po5094
Schwertmannite is a poorly crystalline nanometric iron sulfate oxyhydroxide. This mineral shows a structural variability under different environments. Because of that, the determination of its structure and, consequently, of its physical–chemical properties is quite challenging. This article presents a detailed structural investigation of the structure of schwertmannite conducted under different approaches: X-ray absorption spectroscopy, Rietveld refinement, and a combined reverse Monte Carlo and Debye function analysis of the whole nanoparticle structure. The schwertmannite model presented here is, to the auhors' knowledge, the most complete model so far reported.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Sestu, M.Navarra, G.Carrero, S.Valvidares, S.M.Aquilanti, G.Pérez-Lopez, R.Fernandez-Martinez, A.2017-10-20doi:10.1107/S160057671701336XInternational Union of CrystallographyA single-particle structural model of schwertmannite is proposed from a combined multi-technique approach, using a novel reverse Monte Carlo/Debye scattering equation parallel code.ENschwertmanniteiron oxidesstructural modelingsulfatesreverse Monte CarloDebye scattering equationpair distribution function analysesSchwertmannite is a poorly crystalline nanometric iron sulfate oxyhydroxide. This mineral shows a structural variability under different environments. Because of that, the determination of its structure and, consequently, of its physical–chemical properties is quite challenging. This article presents a detailed structural investigation of the structure of schwertmannite conducted under different approaches: X-ray absorption spectroscopy, Rietveld refinement, and a combined reverse Monte Carlo and Debye function analysis of the whole nanoparticle structure. The schwertmannite model presented here is, to the auhors' knowledge, the most complete model so far reported.text/htmlWhole-nanoparticle atomistic modeling of the schwertmannite structure from total scattering datatext6502017-10-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00The electrostatic potential of dynamic charge densities
http://scripts.iucr.org/cgi-bin/paper?ks5578
A procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the BayMEM software package. Our approach is also discussed with respect to the Ewald summation method. It is argued that a meaningful ESP can only be obtained if identical thermal smearing is applied to the nuclear (positive) and electronic (negative) parts of the dynamic charge densities. The method is applied to structure models of dl-serine at three different temperatures of 20, 100 and 298 K. The ESP at locations near the atomic nuclei exhibits a drastic reduction with increasing temperature, the largest difference between the ESP from the static charge density and the ESP of the dynamic charge density being at T = 20 K. These features demonstrate that zero-point vibrations are sufficient for changing the spiky nature of the ESP at the nuclei into finite values. On 0.5 e Å−3 isosurfaces of the electron densities (taken as the molecular surface relevant to intermolecular interactions), the dynamic ESP is surprisingly similar at all temperatures, while the static ESP of a single molecule has a slightly larger range and is shifted towards positive potential values.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Hübschle, C.B.van Smaalen, S.2017-10-20doi:10.1107/S1600576717013802International Union of CrystallographyThe electrostatic potential (ESP) is computed for dynamic charge densities corresponding to multipole models and maximum-entropy densities. Convergence of the reciprocal-space summation is guaranteed by the Gaussian form of the Debye–Waller factor. Applications to serine demonstrate only a weak temperature dependence of the ESP on molecular surfaces relevant to intermolecular interactions.ENelectrostatic potentialcharge densityelectron densityX-ray diffractionmultipole modelA procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the BayMEM software package. Our approach is also discussed with respect to the Ewald summation method. It is argued that a meaningful ESP can only be obtained if identical thermal smearing is applied to the nuclear (positive) and electronic (negative) parts of the dynamic charge densities. The method is applied to structure models of dl-serine at three different temperatures of 20, 100 and 298 K. The ESP at locations near the atomic nuclei exhibits a drastic reduction with increasing temperature, the largest difference between the ESP from the static charge density and the ESP of the dynamic charge density being at T = 20 K. These features demonstrate that zero-point vibrations are sufficient for changing the spiky nature of the ESP at the nuclei into finite values. On 0.5 e Å−3 isosurfaces of the electron densities (taken as the molecular surface relevant to intermolecular interactions), the dynamic ESP is surprisingly similar at all temperatures, while the static ESP of a single molecule has a slightly larger range and is shifted towards positive potential values.text/htmlThe electrostatic potential of dynamic charge densitiestext6502017-10-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Phase retrieval of coherent diffractive images with global optimization algorithms
http://scripts.iucr.org/cgi-bin/paper?jo5035
Coherent diffractive imaging (CDI) or lensless microscopy has recently been of great interest as a promising alternative to electron microscopy in achieving atomic spatial resolution. Reconstruction of images in real space from a single experimental diffraction pattern in CDI is based on applying iterative phase-retrieval (IPR) algorithms, such as the hybrid input–output and the error reduction algorithms. For noisy data, these algorithms might suffer from stagnation or trapping in local minima. Generally, the different local minima have many common as well as complementary features and might provide useful information for an improved estimate of the object. Therefore, a linear combination of a number of chosen minima, termed a basis set, gives an educated initial estimate, which might accelerate the search for the global solution. In this study, a genetic algorithm (GA) is combined with an IPR algorithm to tackle the stagnation and trapping in phase-retrieval problems. The combined GA–IPR has been employed to reconstruct an irregularly shaped hole and has proven to be reliable and robust. With the concept of basis set, it is strongly believed that many effective local and global optimization frameworks can be combined in a similar manner to solve the phase problem.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Truong, N.X.Whittaker, E.Denecke, M.A.2017-10-20doi:10.1107/S1600576717013012International Union of CrystallographyPhase-retrieval algorithms combined with global optimization techniques have been shown to be robust and reliable, and to outperform phase-retrieval algorithms used in coherent diffractive imaging.ENcoherent diffractive imagingphase-retrieval methodshigh-order harmonic generationEUV imagingCoherent diffractive imaging (CDI) or lensless microscopy has recently been of great interest as a promising alternative to electron microscopy in achieving atomic spatial resolution. Reconstruction of images in real space from a single experimental diffraction pattern in CDI is based on applying iterative phase-retrieval (IPR) algorithms, such as the hybrid input–output and the error reduction algorithms. For noisy data, these algorithms might suffer from stagnation or trapping in local minima. Generally, the different local minima have many common as well as complementary features and might provide useful information for an improved estimate of the object. Therefore, a linear combination of a number of chosen minima, termed a basis set, gives an educated initial estimate, which might accelerate the search for the global solution. In this study, a genetic algorithm (GA) is combined with an IPR algorithm to tackle the stagnation and trapping in phase-retrieval problems. The combined GA–IPR has been employed to reconstruct an irregularly shaped hole and has proven to be reliable and robust. With the concept of basis set, it is strongly believed that many effective local and global optimization frameworks can be combined in a similar manner to solve the phase problem.text/htmlPhase retrieval of coherent diffractive images with global optimization algorithmstext6502017-10-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Variant selection in surface martensite
http://scripts.iucr.org/cgi-bin/paper?nb5203
A significant variant selection is reported in isothermal martensite formed on the surface of an Fe–30% Ni sample. The selection phenomenon is modelled using different descriptions of the martensitic phase transformation. In particular, matrices based on the phenomenological theory of martensite crystallography, the Jaswon and Wheeler distortion, and the continuous face centred cubic–body centred cubic distortion are compared. All descriptions allow good predictions of the variant selection. However, the Jaswon and Wheeler distortion and the continuous distortion better account for other features of the surface martensite, such as the {225}γ habit plane and the accommodation mechanism by twin-related variant pairing.Copyright (c) 2017 Annick P. Baur et al.urn:issn:1600-5767Baur, A.P.Cayron, C.Logé, R.E.2017-10-20doi:10.1107/S160057671701398XInternational Union of CrystallographyVariant selection is reported in martensite formed on the surface of an Fe–30% Ni sample. Predictive models of the phenomenon based on different crystallographic descriptions of the transformation are proposed and compared.ENsurface martensitevariant selectionphenomenological theory of martensite crystallography (PTMC)continuous f.c.c.–b.c.c. distortionA significant variant selection is reported in isothermal martensite formed on the surface of an Fe–30% Ni sample. The selection phenomenon is modelled using different descriptions of the martensitic phase transformation. In particular, matrices based on the phenomenological theory of martensite crystallography, the Jaswon and Wheeler distortion, and the continuous face centred cubic–body centred cubic distortion are compared. All descriptions allow good predictions of the variant selection. However, the Jaswon and Wheeler distortion and the continuous distortion better account for other features of the surface martensite, such as the {225}γ habit plane and the accommodation mechanism by twin-related variant pairing.text/htmlVariant selection in surface martensitetext6502017-10-20Copyright (c) 2017 Annick P. Baur et al.Journal of Applied Crystallographyresearch papers00Generalized skew-symmetric interfacial probability distribution in reflectivity and small-angle scattering analysis
http://scripts.iucr.org/cgi-bin/paper?vg5072
Generalized skew-symmetric probability density functions are proposed to model asymmetric interfacial density distributions for the parameterization of any arbitrary density profiles in the `effective-density model'. The penetration of the densities into adjacent layers can be selectively controlled and parameterized. A continuous density profile is generated and discretized into many independent slices of very thin thickness with constant density values and sharp interfaces. The discretized profile can be used to calculate reflectivities via Parratt's recursive formula, or small-angle scattering via the concentric onion model that is also developed in this work.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Jiang, Z.Chen, W.2017-11-03doi:10.1107/S1600576717013632International Union of CrystallographyGeneralized skew-symmetric interfacial probability density functions are used to model arbitrary interfacial density profiles for the analysis of reflectivity and small-angle scattering.ENinterface density profileroughnessreflectivitysmall-angle scatteringform factorsGeneralized skew-symmetric probability density functions are proposed to model asymmetric interfacial density distributions for the parameterization of any arbitrary density profiles in the `effective-density model'. The penetration of the densities into adjacent layers can be selectively controlled and parameterized. A continuous density profile is generated and discretized into many independent slices of very thin thickness with constant density values and sharp interfaces. The discretized profile can be used to calculate reflectivities via Parratt's recursive formula, or small-angle scattering via the concentric onion model that is also developed in this work.text/htmlGeneralized skew-symmetric interfacial probability distribution in reflectivity and small-angle scattering analysistext6502017-11-03Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Application of forward models to crystal orientation refinement
http://scripts.iucr.org/cgi-bin/paper?po5102
Two approaches are proposed for the refinement of electron diffraction pattern indexing. The approaches require two basic ingredients: an accurate physics-based forward model and an algorithm to search the local orientation neighborhood. Forward models for electron backscatter diffraction (EBSD) and electron channeling pattern (ECP) modalities are coupled with either a multi-resolution brute-force search algorithm or a bound optimization by quadratic approximation algorithm. The efficacy of the methods is evaluated for varying levels of error in the pattern projection center. The EBSD modality shows an orientation improvement when the projection center error is within ±1% of the full detector width, whereas the ECP modality shows improvement up to a ±5% error. The algorithms are applied to an experimental EBSD scan for partially recrystallized 90/10 brass; the results show that the refinement is necessary to remove the artifacts introduced by the discrete sampling nature of the dictionary indexing method. Finally, a pattern center correction factor is derived for orientations obtained from dictionary indexing for large-area EBSD scans.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Singh, S.Ram, F.De Graef, M.2017-11-03doi:10.1107/S1600576717014200International Union of CrystallographyTwo algorithms reliant on physics-based forward models are proposed to refine crystal orientations: a multi-resolution brute-force local search and a derivative-free optimization. The efficacy of these methods is evaluated for the electron backscatter diffraction and electron channeling pattern modalities using simulated patterns with known orientations.ENelectron backscatter diffractionEBSDmodelinglarge-area scansTwo approaches are proposed for the refinement of electron diffraction pattern indexing. The approaches require two basic ingredients: an accurate physics-based forward model and an algorithm to search the local orientation neighborhood. Forward models for electron backscatter diffraction (EBSD) and electron channeling pattern (ECP) modalities are coupled with either a multi-resolution brute-force search algorithm or a bound optimization by quadratic approximation algorithm. The efficacy of the methods is evaluated for varying levels of error in the pattern projection center. The EBSD modality shows an orientation improvement when the projection center error is within ±1% of the full detector width, whereas the ECP modality shows improvement up to a ±5% error. The algorithms are applied to an experimental EBSD scan for partially recrystallized 90/10 brass; the results show that the refinement is necessary to remove the artifacts introduced by the discrete sampling nature of the dictionary indexing method. Finally, a pattern center correction factor is derived for orientations obtained from dictionary indexing for large-area EBSD scans.text/htmlApplication of forward models to crystal orientation refinementtext6502017-11-03Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Modeling the polarized X-ray scattering from periodic nanostructures with molecular anisotropy
http://scripts.iucr.org/cgi-bin/paper?ge5043
There is a need to characterize nanoscale molecular orientation in soft materials, and polarized scattering is a powerful means to measure this property. However, few approaches have been demonstrated that quantitatively relate orientation to scattering. Here, a modeling framework to relate the molecular orientation of nanostructures to polarized resonant soft X-ray scattering measurements is developed. A variable-angle transmission measurement called critical-dimension X-ray scattering enables the characterization of the three-dimensional shape of periodic nanostructures. When this measurement is conducted at resonant soft X-ray energies with different polarizations to measure soft material nanostructures, the scattering contains convolved information about the nanostructure shape and the preferred molecular orientation as a function of position, which is extracted by fitting using inverse iterative algorithms. A computationally efficient Born approximation simulation of the scattering has been developed, with a full tensor treatment of the electric field that takes into account biaxial molecular orientation, and this approach is validated by comparing it with a rigorous coupled wave simulation. The ability of various sample models to generate unique best fit solutions is then analyzed by generating simulated scattering pattern sets and fitting them with an inverse iterative algorithm. The interaction of the measurement geometry and the change in orientation across a periodic repeat unit leads to distinct asymmetry in the scattering pattern which must be considered for an accurate fit of the scattering.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Liman, C.D.Germer, T.A.Sunday, D.F.DeLongchamp, D.M.Kline, R.J.2017-11-03doi:10.1107/S160057671701408XInternational Union of CrystallographyA modeling framework to relate the molecular orientation of nanostructures to polarized resonant soft X-ray scattering measurements using the Born approximation and a full tensor treatment is described.ENpolarized resonant soft X-ray scatteringanisotropic nanostructureselectromagnetic modelingcritical-dimension small-angle X-ray scatteringCDSAXSThere is a need to characterize nanoscale molecular orientation in soft materials, and polarized scattering is a powerful means to measure this property. However, few approaches have been demonstrated that quantitatively relate orientation to scattering. Here, a modeling framework to relate the molecular orientation of nanostructures to polarized resonant soft X-ray scattering measurements is developed. A variable-angle transmission measurement called critical-dimension X-ray scattering enables the characterization of the three-dimensional shape of periodic nanostructures. When this measurement is conducted at resonant soft X-ray energies with different polarizations to measure soft material nanostructures, the scattering contains convolved information about the nanostructure shape and the preferred molecular orientation as a function of position, which is extracted by fitting using inverse iterative algorithms. A computationally efficient Born approximation simulation of the scattering has been developed, with a full tensor treatment of the electric field that takes into account biaxial molecular orientation, and this approach is validated by comparing it with a rigorous coupled wave simulation. The ability of various sample models to generate unique best fit solutions is then analyzed by generating simulated scattering pattern sets and fitting them with an inverse iterative algorithm. The interaction of the measurement geometry and the change in orientation across a periodic repeat unit leads to distinct asymmetry in the scattering pattern which must be considered for an accurate fit of the scattering.text/htmlModeling the polarized X-ray scattering from periodic nanostructures with molecular anisotropytext6502017-11-03Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00ECCI, EBSD and EPSC characterization of rhombohedral twinning in polycrystalline α-alumina deformed in a D-DIA apparatus
http://scripts.iucr.org/cgi-bin/paper?nb5201
Rhombohedral twinning in alumina (aluminium oxide, α-Al2O3) is an important mechanism for plastic deformation under high-temperature–pressure conditions. Rhombohedral twins in a polycrystalline alumina sample deformed in a D-DIA apparatus at 965 K and 4.48 GPa have been characterized. Three classes of grains were imaged, containing single, double and mosaic twins, using electron channeling contrast imaging (ECCI) in a field emission scanning electron microscope. These twinned grains were analyzed using electron backscatter diffraction (EBSD). The methodology for twin identification presented here is based on comparison of theoretical pole figures for a rhombohedral twin with experimental pole figures obtained with EBSD crystal orientation mapping. An 85°〈02{\overline 2}1〉 angle–axis pair of misorientation was identified for rhombohedral twin boundaries in alumina, which can be readily used in EBSD post-processing software to identify the twin boundaries in EBSD maps and distinguish the rhombohedral twins from basal twins. Elastic plastic self-consistent (EPSC) modeling was then used to model the synchrotron X-ray diffraction data from the D-DIA experiments utilizing the rhombohedral twinning law. From these EPSC models, a critical resolved shear stress of 0.25 GPa was obtained for rhombohedral twinning under the above experimental conditions, which is internally consistent with the value estimated from the applied load and Schmid factors determined by EBSD analysis.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Kaboli, S.Burnley, P.C.2017-11-03doi:10.1107/S1600576717013991International Union of CrystallographyThis study presents rhombohedral twin characterization in plastically deformed alumina at high-pressure and -temperature conditions using electron channeling contrast imaging (ECCI) in a field emission scanning electron microscope, electron backscatter diffraction (EBSD) and elastic plastic self-consistent (EPSC) numerical modeling on synchrotron X-ray diffraction data.ENrhombohedral twinselectron channeling contrast imagingECCIelectron backscatter diffractionEBSDelastic plastic self-consistent modelingEPSCRhombohedral twinning in alumina (aluminium oxide, α-Al2O3) is an important mechanism for plastic deformation under high-temperature–pressure conditions. Rhombohedral twins in a polycrystalline alumina sample deformed in a D-DIA apparatus at 965 K and 4.48 GPa have been characterized. Three classes of grains were imaged, containing single, double and mosaic twins, using electron channeling contrast imaging (ECCI) in a field emission scanning electron microscope. These twinned grains were analyzed using electron backscatter diffraction (EBSD). The methodology for twin identification presented here is based on comparison of theoretical pole figures for a rhombohedral twin with experimental pole figures obtained with EBSD crystal orientation mapping. An 85°〈02{\overline 2}1〉 angle–axis pair of misorientation was identified for rhombohedral twin boundaries in alumina, which can be readily used in EBSD post-processing software to identify the twin boundaries in EBSD maps and distinguish the rhombohedral twins from basal twins. Elastic plastic self-consistent (EPSC) modeling was then used to model the synchrotron X-ray diffraction data from the D-DIA experiments utilizing the rhombohedral twinning law. From these EPSC models, a critical resolved shear stress of 0.25 GPa was obtained for rhombohedral twinning under the above experimental conditions, which is internally consistent with the value estimated from the applied load and Schmid factors determined by EBSD analysis.text/htmlECCI, EBSD and EPSC characterization of rhombohedral twinning in polycrystalline α-alumina deformed in a D-DIA apparatustext6502017-11-03Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00A peak-finding algorithm based on robust statistical analysis in serial crystallography
http://scripts.iucr.org/cgi-bin/paper?yr5023
The recent development of serial crystallography at synchrotron and X-ray free-electron laser (XFEL) sources is producing crystallographic datasets of ever increasing volume. The size of these datasets is such that fast and efficient analysis presents a range of challenges that have to be overcome to enable real-time data analysis, which is essential for the effective management of XFEL experiments. Among the blocks which constitute the analysis pipeline, one major bottleneck is `peak finding', whose goal is to identify the Bragg peaks within (often) noisy diffraction patterns. Development of faster and more reliable peak-finding algorithms will allow for efficient processing and storage of the incoming data, as well as the optimal use of diffraction data for structure determination. This paper addresses the problem of peak finding and, by extension, `hit finding' in crystallographic XFEL datasets, by exploiting recent developments in robust statistical analysis. The approach described here involves two basic steps: (1) the identification of pixels which contain potential peaks and (2) modeling of the local background in the vicinity of these potential peaks. The presented framework can be generalized to include both complex background models and alternative models for the Bragg peaks.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Hadian-Jazi, M.Messerschmidt, M.Darmanin, C.Giewekemeyer, K.Mancuso, A.P.Abbey, B.2017-11-03doi:10.1107/S1600576717014340International Union of CrystallographyThis manuscript addresses the problem of peak finding and, by extension, `hit finding' in crystallographic X-ray free-electron laser datasets, by exploiting recent developments in robust statistical analysis.ENX-ray free-electron lasers (XFELs)serial crystallographypeak findingrobust statisticsThe recent development of serial crystallography at synchrotron and X-ray free-electron laser (XFEL) sources is producing crystallographic datasets of ever increasing volume. The size of these datasets is such that fast and efficient analysis presents a range of challenges that have to be overcome to enable real-time data analysis, which is essential for the effective management of XFEL experiments. Among the blocks which constitute the analysis pipeline, one major bottleneck is `peak finding', whose goal is to identify the Bragg peaks within (often) noisy diffraction patterns. Development of faster and more reliable peak-finding algorithms will allow for efficient processing and storage of the incoming data, as well as the optimal use of diffraction data for structure determination. This paper addresses the problem of peak finding and, by extension, `hit finding' in crystallographic XFEL datasets, by exploiting recent developments in robust statistical analysis. The approach described here involves two basic steps: (1) the identification of pixels which contain potential peaks and (2) modeling of the local background in the vicinity of these potential peaks. The presented framework can be generalized to include both complex background models and alternative models for the Bragg peaks.text/htmlA peak-finding algorithm based on robust statistical analysis in serial crystallographytext6502017-11-03Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Effect of phenol red dye on monocrystal growth, crystalline perfection, and optical and dielectric properties of zinc (tris) thiourea sulfate
http://scripts.iucr.org/cgi-bin/paper?ks5572
In this work, the growth of large size (∼25 × 29 × 5 mm and ∼25 × 24 × 6 mm) colorful single crystals of zinc (tris) thiourea sulfate (ZTS) in the presence of 0.05–2 wt% phenol red (PR) dye was achieved using a simple and low-cost technique. Powder X-ray diffraction patterns confirm the presence of PR dye, which is indicated by an enhancement of the Raman peak intensities, a shift in their position and the appearance of a few extra peaks. The quality of the grown crystals was assessed by high-resolution X-ray diffraction, which shows that the crystalline perfection of 1 wt% PR-dyed ZTS crystals is better than that of 2 wt% PR-dyed crystals. The measured UV–vis absorbance spectra show two additional, strong absorption bands at ∼430 and 558 nm in the dyed crystals, due to the presence of PR dye, along with a band at ∼276 nm which is present for all crystals but is slightly shifted for the dyed crystals. Photoluminescence spectra were recorded at two excitation wavelengths (λexc = 310 and 385 nm). The luminescence intensity is found to be enriched in dyed crystals, with some extra emission bands. An enhancement in the value of the dielectric constant and a.c. electrical conductivity was also observed in the dyed ZTS crystals.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Shkir, M.Ganesh, V.AlFaify, S.Maurya, K.K.Vijayan, N.2017-11-14doi:10.1107/S1600576717014339International Union of CrystallographyIn this article, the effect of phenol red dye on key structural, crystalline perfection, optical, photoluminescence and dielectric properties of zinc (tris) thiourea sulfate single crystals is reported.ENphenol red dyecrystal growthFT-Raman spectroscopyscanning electron microscopySEMoptical propertiesdielectric responsephotoluminescenceIn this work, the growth of large size (∼25 × 29 × 5 mm and ∼25 × 24 × 6 mm) colorful single crystals of zinc (tris) thiourea sulfate (ZTS) in the presence of 0.05–2 wt% phenol red (PR) dye was achieved using a simple and low-cost technique. Powder X-ray diffraction patterns confirm the presence of PR dye, which is indicated by an enhancement of the Raman peak intensities, a shift in their position and the appearance of a few extra peaks. The quality of the grown crystals was assessed by high-resolution X-ray diffraction, which shows that the crystalline perfection of 1 wt% PR-dyed ZTS crystals is better than that of 2 wt% PR-dyed crystals. The measured UV–vis absorbance spectra show two additional, strong absorption bands at ∼430 and 558 nm in the dyed crystals, due to the presence of PR dye, along with a band at ∼276 nm which is present for all crystals but is slightly shifted for the dyed crystals. Photoluminescence spectra were recorded at two excitation wavelengths (λexc = 310 and 385 nm). The luminescence intensity is found to be enriched in dyed crystals, with some extra emission bands. An enhancement in the value of the dielectric constant and a.c. electrical conductivity was also observed in the dyed ZTS crystals.text/htmlEffect of phenol red dye on monocrystal growth, crystalline perfection, and optical and dielectric properties of zinc (tris) thiourea sulfatetext6502017-11-14Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00A combined characterization of clusters in naturally aged Al–Cu–(Li, Mg) alloys using small-angle neutron and X-ray scattering and atom probe tomography
http://scripts.iucr.org/cgi-bin/paper?ks5575
A new methodology for the characterization of solute clusters leading to compositional fluctuations is presented and discussed. The methodology makes use of contrast variation arising from a combination of small-angle scattering using neutrons and X-rays, and adapts a model for solute correlation to extract the chemistry and length scale of clustered states after quench and after natural ageing. In three subsets of the Al–Cu system, Cu-rich clusters are reported for all cases. The presence of Mg strongly enhances Cu clustering in the naturally aged state and results in more than double the number of clusters in the complex Al–Cu–Li–Mg system. The results are compared with those obtained using atom probe tomography.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Ivanov, R.Deschamps, A.De Geuser, F.2017-11-14doi:10.1107/S1600576717014443International Union of CrystallographyCompositional fluctuations arising from Cu-rich solute clusters in Al–Cu alloys with additions of Li and Mg are characterized by combined small-angle neutron and X-ray scattering.ENsmall-angle scatteringsolute clusterscompositional fluctuationsAl–Cu alloysA new methodology for the characterization of solute clusters leading to compositional fluctuations is presented and discussed. The methodology makes use of contrast variation arising from a combination of small-angle scattering using neutrons and X-rays, and adapts a model for solute correlation to extract the chemistry and length scale of clustered states after quench and after natural ageing. In three subsets of the Al–Cu system, Cu-rich clusters are reported for all cases. The presence of Mg strongly enhances Cu clustering in the naturally aged state and results in more than double the number of clusters in the complex Al–Cu–Li–Mg system. The results are compared with those obtained using atom probe tomography.text/htmlA combined characterization of clusters in naturally aged Al–Cu–(Li, Mg) alloys using small-angle neutron and X-ray scattering and atom probe tomographytext6502017-11-14Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Spherical harmonics analysis based on the Reuss model in elastic macro strain and stress determination by powder diffraction
http://scripts.iucr.org/cgi-bin/paper?ks5550
In this paper a new approach to macro strain/stress analysis by generalized spherical harmonics is presented. It consists of expanding the stress tensor weighted by texture in a series of generalized spherical harmonics with the ground state of expansion specific to the classical Reuss model of an isotropic polycrystal. Like previously reported models having a ground state of hydrostatic type [Popa & Balzar (2001). J Appl Cryst. 34, 187–195] and of Voigt type [Popa et al. (2014). J Appl Cryst. 34, 154–159], the actual model is appropriate for use with Rietveld refinement.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Popa, N.C.2017-11-14doi:10.1107/S1600576717014431International Union of CrystallographyThis article presents a stress tensor spherical harmonics expansion with the Reuss ground state, which is used for macro strain/stress investigation by powder diffraction.ENmacro strain/stressspherical harmonicsReuss modelpowder diffractionselection rulesIn this paper a new approach to macro strain/stress analysis by generalized spherical harmonics is presented. It consists of expanding the stress tensor weighted by texture in a series of generalized spherical harmonics with the ground state of expansion specific to the classical Reuss model of an isotropic polycrystal. Like previously reported models having a ground state of hydrostatic type [Popa & Balzar (2001). J Appl Cryst. 34, 187–195] and of Voigt type [Popa et al. (2014). J Appl Cryst. 34, 154–159], the actual model is appropriate for use with Rietveld refinement.text/htmlSpherical harmonics analysis based on the Reuss model in elastic macro strain and stress determination by powder diffractiontext6502017-11-14Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Combinatorial appraisal of transition states for in situ pair distribution function analysis
http://scripts.iucr.org/cgi-bin/paper?kc5062
In situ total scattering measurements are increasingly utilized to follow atomic and nanoscale structural details of phase transitions and other transient processes in materials. This contribution presents an automated method and associated tool set to analyze series of diffraction and pair distribution function data with a linear combination of end-member states. It is demonstrated that the combinatorial appraisal of transition states (CATS) software tracks phase changes, relative phase fractions and length scales of interest in experimental data series. It is further demonstrated, using a series of local structure data simulations, that the misfit of such a model can reveal details of phase aggregation and growth related to the pair distribution function's sensitivity to interphase correlations. CATS may be applied to quantitative evaluation of many transient processes, including amorphous-to-crystalline phase transitions, the evolution of solid-solution behaviors, the precipitation and growth of aggregates, and other atomic to nanoscale details of crystallization and phase transformation phenomena.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Olds, D.Peterson, P.F.Crawford, M.K.Neilson, J.R.Wang, H.-W.Whitfield, P.S.Page, K.2017-11-20doi:10.1107/S1600576717015163International Union of CrystallographyA method and software tool are introduced to fit a series of pair distribution function data through a phase transition or to detect and track a specific structural feature of interest using a linear combination of two end-member states. The misfit between the model combination and the data can reveal underlying details regarding the nature and length scale of intermediate structures.ENtotal scatteringpair distribution function (PDF)interfacesphase transitionsgrowthhierarchical structuresIn situ total scattering measurements are increasingly utilized to follow atomic and nanoscale structural details of phase transitions and other transient processes in materials. This contribution presents an automated method and associated tool set to analyze series of diffraction and pair distribution function data with a linear combination of end-member states. It is demonstrated that the combinatorial appraisal of transition states (CATS) software tracks phase changes, relative phase fractions and length scales of interest in experimental data series. It is further demonstrated, using a series of local structure data simulations, that the misfit of such a model can reveal details of phase aggregation and growth related to the pair distribution function's sensitivity to interphase correlations. CATS may be applied to quantitative evaluation of many transient processes, including amorphous-to-crystalline phase transitions, the evolution of solid-solution behaviors, the precipitation and growth of aggregates, and other atomic to nanoscale details of crystallization and phase transformation phenomena.text/htmlCombinatorial appraisal of transition states for in situ pair distribution function analysistext6502017-11-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Full elastic strain tensor determination at the phase scale in a powder metallurgy nickel-based superalloy using X-ray Laue microdiffraction
http://scripts.iucr.org/cgi-bin/paper?nb5207
Laue microdiffraction is used to determine the full elastic strain tensor of the γ and γ′ phases in grains of a nickel-based superalloy with a coarse-grained microstructure. A `rainbow' filter and an energy dispersive point detector are employed to measure the energy of Bragg reflections. For the two techniques, an uncertainty of ±2.5 × 10−3 Å is obtained for the undetermined crystal lattice parameter. Our measurements show that the filter method provides better confidence, energy resolution, accuracy and acquisition time. The sensitivity of each method with respect to the γ–γ′ lattice mismatch is demonstrated with measurements in samples with average precipitate sizes of 200 and 2000 nm. For the 200 nm precipitate size, the lattice mismatch is less than 2 × 10−3 Å and the dilatational strains are close to ±1.5 × 10−3 depending on the considered phase. For the 2000 nm precipitate size, the lattice mismatch is close to 8 × 10−3 Å and almost no elastic strain occurs in the microstructure.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Altinkurt, G.Fèvre, M.Robach, O.Micha, J.-S.Geandier, G.Dehmas, M.2017-11-20doi:10.1107/S1600576717014558International Union of CrystallographyLaue microdiffraction coupled with energy measurements is used to determine the full elastic strain tensor related to the γ and γ′ phases in a coarse-grained nickel-based superalloy. Model microstructures with a 200 or 2000 nm average precipitate size are investigated.ENLaue microdiffractionfull strain tensornickel-based superalloysphase sensitivityLaue microdiffraction is used to determine the full elastic strain tensor of the γ and γ′ phases in grains of a nickel-based superalloy with a coarse-grained microstructure. A `rainbow' filter and an energy dispersive point detector are employed to measure the energy of Bragg reflections. For the two techniques, an uncertainty of ±2.5 × 10−3 Å is obtained for the undetermined crystal lattice parameter. Our measurements show that the filter method provides better confidence, energy resolution, accuracy and acquisition time. The sensitivity of each method with respect to the γ–γ′ lattice mismatch is demonstrated with measurements in samples with average precipitate sizes of 200 and 2000 nm. For the 200 nm precipitate size, the lattice mismatch is less than 2 × 10−3 Å and the dilatational strains are close to ±1.5 × 10−3 depending on the considered phase. For the 2000 nm precipitate size, the lattice mismatch is close to 8 × 10−3 Å and almost no elastic strain occurs in the microstructure.text/htmlFull elastic strain tensor determination at the phase scale in a powder metallurgy nickel-based superalloy using X-ray Laue microdiffractiontext6502017-11-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Characteristic diffuse scattering from distinct line roughnesses
http://scripts.iucr.org/cgi-bin/paper?rg5132
Lamellar gratings are widely used diffractive optical elements; gratings etched into Si can be used as structural elements or prototypes of structural elements in integrated electronic circuits. For the control of the lithographic manufacturing process, a rapid in-line characterization of nanostructures is indispensable. Numerous studies on the determination of regular geometry parameters of lamellar gratings from optical and extreme ultraviolet (EUV) scattering highlight the impact of roughness on the optical performance as well as on the reconstruction of these structures. Thus, a set of nine lamellar Si gratings with a well defined line edge roughness or line width roughness were designed. The investigation of these structures using EUV small-angle scattering reveals a strong correlation between the type of line roughness and the angular scattering distribution. These distinct scattering patterns open new paths for the unequivocal characterization of such structures by EUV scatterometry.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Fernández Herrero, A.Pflüger, M.Probst, J.Scholze, F.Soltwisch, V.2017-11-20doi:10.1107/S1600576717014455International Union of CrystallographyThe impact of the edge roughness of laterally periodic nanostructures on the scattering pattern is investigated. The applicability of existing analytical approaches for the description of real samples is discussed.ENEUV scatterometryline edge roughnessline width roughnessresonance diffuse scatteringLamellar gratings are widely used diffractive optical elements; gratings etched into Si can be used as structural elements or prototypes of structural elements in integrated electronic circuits. For the control of the lithographic manufacturing process, a rapid in-line characterization of nanostructures is indispensable. Numerous studies on the determination of regular geometry parameters of lamellar gratings from optical and extreme ultraviolet (EUV) scattering highlight the impact of roughness on the optical performance as well as on the reconstruction of these structures. Thus, a set of nine lamellar Si gratings with a well defined line edge roughness or line width roughness were designed. The investigation of these structures using EUV small-angle scattering reveals a strong correlation between the type of line roughness and the angular scattering distribution. These distinct scattering patterns open new paths for the unequivocal characterization of such structures by EUV scatterometry.text/htmlCharacteristic diffuse scattering from distinct line roughnessestext6502017-11-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Protein crystals IR laser ablated from aqueous solution at high speed retain their diffractive properties: applications in high-speed serial crystallography
http://scripts.iucr.org/cgi-bin/paper?te5026
In order to utilize the high repetition rates now available at X-ray free-electron laser sources for serial crystallography, methods must be developed to softly deliver large numbers of individual microcrystals at high repetition rates and high speeds. Picosecond infrared laser (PIRL) pulses, operating under desorption by impulsive vibrational excitation (DIVE) conditions, selectively excite the OH vibrational stretch of water to directly propel the excited volume at high speed with minimized heating effects, nucleation formation or cavitation-induced shock waves, leaving the analytes intact and undamaged. The soft nature and laser-based sampling flexibility provided by the technique make the PIRL system an interesting crystal delivery approach for serial crystallography. This paper demonstrates that protein crystals extracted directly from aqueous buffer solution via PIRL-DIVE ablation retain their diffractive properties and can be usefully exploited for structure determination at synchrotron sources. The remaining steps to implement the technology for high-speed serial femtosecond crystallography, such as single-crystal localization, high-speed sampling and synchronization, are described. This proof-of-principle experiment demonstrates the viability of a new laser-based high-speed crystal delivery system without the need for liquid-jet injectors or fixed-target mounting solutions.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Schulz, E.C.Kaub, J.Busse, F.Mehrabi, P.Müller-Werkmeister, H.M.Pai, E.F.Robertson, W.D.Miller, R.J.D.2017-11-20doi:10.1107/S1600576717014479International Union of CrystallographyThis paper describes a proof-of-principle study demonstrating that protein crystals ablated by a picosecond infrared laser retain their diffractive properties. The crystals were ejected at high speed from an aqueous solution, collected and then used for structure determination by serial synchrotron crystallography.ENserial synchrotron crystallographySSXpicosecond infrared lasersPIRLfixed targetssample deliveryIn order to utilize the high repetition rates now available at X-ray free-electron laser sources for serial crystallography, methods must be developed to softly deliver large numbers of individual microcrystals at high repetition rates and high speeds. Picosecond infrared laser (PIRL) pulses, operating under desorption by impulsive vibrational excitation (DIVE) conditions, selectively excite the OH vibrational stretch of water to directly propel the excited volume at high speed with minimized heating effects, nucleation formation or cavitation-induced shock waves, leaving the analytes intact and undamaged. The soft nature and laser-based sampling flexibility provided by the technique make the PIRL system an interesting crystal delivery approach for serial crystallography. This paper demonstrates that protein crystals extracted directly from aqueous buffer solution via PIRL-DIVE ablation retain their diffractive properties and can be usefully exploited for structure determination at synchrotron sources. The remaining steps to implement the technology for high-speed serial femtosecond crystallography, such as single-crystal localization, high-speed sampling and synchronization, are described. This proof-of-principle experiment demonstrates the viability of a new laser-based high-speed crystal delivery system without the need for liquid-jet injectors or fixed-target mounting solutions.text/htmlProtein crystals IR laser ablated from aqueous solution at high speed retain their diffractive properties: applications in high-speed serial crystallographytext6502017-11-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00Lattice thermal expansion of Pu1−yAmyO2−x plutonium–americium mixed oxides
http://scripts.iucr.org/cgi-bin/paper?kc5064
Plutonium–americium mixed oxides, Pu1−yAmyO2−x, with various Am contents (y = 0.018, 0.077, 0.21, 0.49, 0.80 and 1.00) were studied in situ by high-temperature X-ray diffraction. In this study, the lattice thermal expansion of the six compounds subjected to heat treatments up to 1773 K under reconstituted air (N2 + 21% O2 + ∼5 vpm H2O) was investigated. The materials remained monophasic throughout the experiments and, depending upon the americium content, the lattice parameter of the face-centred cubic phase deviated from linear lattice expansion at elevated temperatures as a result of the progressive reduction of Am4+ to Am3+.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Vauchy, R.Joly, A.Valot, C.2017-11-20doi:10.1107/S1600576717014832International Union of CrystallographyThe lattice thermal expansion of Pu1−yAmyO2−x mixed oxides was studied in situ in reconstituted air by high-temperature X-ray diffraction. The lattice parameter of the face-centred cubic phase constituting the materials studied exhibited a more pronounced deviation from linearity as a function of both temperature and americium content in the mixed oxides.ENhigh-temperature X-ray diffractionlattice thermal expansionactinidesplutoniumamericiumtransplutonium elementsmixed oxidesnuclear fuelMOXradiotoxicitytransmutationPlutonium–americium mixed oxides, Pu1−yAmyO2−x, with various Am contents (y = 0.018, 0.077, 0.21, 0.49, 0.80 and 1.00) were studied in situ by high-temperature X-ray diffraction. In this study, the lattice thermal expansion of the six compounds subjected to heat treatments up to 1773 K under reconstituted air (N2 + 21% O2 + ∼5 vpm H2O) was investigated. The materials remained monophasic throughout the experiments and, depending upon the americium content, the lattice parameter of the face-centred cubic phase deviated from linear lattice expansion at elevated temperatures as a result of the progressive reduction of Am4+ to Am3+.text/htmlLattice thermal expansion of Pu1−yAmyO2−x plutonium–americium mixed oxidestext6502017-11-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyresearch papers00NanoPDF64: software package for theoretical calculation and quantitative real-space analysis of powder diffraction data of nanocrystals
http://scripts.iucr.org/cgi-bin/paper?po5098
NanoPDF64 is a tool designed for structural analysis of nanocrystals based on examination of powder diffraction data with application of real-space analysis. The program allows for fast building of models of nanocrystals consisting of up to several hundred thousand atoms with either cubic or hexagonal close packed structure. The nanocrystal structure may be modified by introducing stacking faults, density modulation waves (i.e. the core–shell model) and thermal atomic vibrations. The program calculates diffraction patterns and, by Fourier transform, the reduced pair distribution functions G(r) for the models. Experimental G(r)s may be quantitatively analyzed by least-squares fitting with an analytical formula.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Skrobas, K.Stelmakh, S.Gierlotka, S.Palosz, B.F.2017-10-20doi:10.1107/S1600576717013152International Union of CrystallographyNanoPDF64 is a software package for analysis of pair distribution functions of nanocrystals. It is also capable of calculating theoretical powder diffraction patterns and pair distribution functions for atomistic models of nanocrystals.ENnanocrystalspair distribution functionspowder diffractionNanoPDF64 is a tool designed for structural analysis of nanocrystals based on examination of powder diffraction data with application of real-space analysis. The program allows for fast building of models of nanocrystals consisting of up to several hundred thousand atoms with either cubic or hexagonal close packed structure. The nanocrystal structure may be modified by introducing stacking faults, density modulation waves (i.e. the core–shell model) and thermal atomic vibrations. The program calculates diffraction patterns and, by Fourier transform, the reduced pair distribution functions G(r) for the models. Experimental G(r)s may be quantitatively analyzed by least-squares fitting with an analytical formula.text/htmlNanoPDF64: software package for theoretical calculation and quantitative real-space analysis of powder diffraction data of nanocrystalstext6502017-10-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00CarbonXS GUI: a graphical front-end for CarbonXS
http://scripts.iucr.org/cgi-bin/paper?po5093
The crystallographic structure of disordered carbons impacts their performance in components for fuel cells, batteries and catalyst supports. Obtaining parameters such as lattice constants and crystal domain size requires an appropriate model for these carbons, a task accomplished with the Fortran program CarbonXS published in 1993. CarbonXS GUI contains an updated version of CarbonXS and a graphical user interface wrapper. This new version provides a graphical method of configuring and operating CarbonXS, a calculation mode to simulate diffraction patterns, and immediate feedback in the form of fit–source and difference plots. CarbonXS GUI is available for free on Windows, Linux and Mac OSX at http://github.com/lktsui/carbon_xs_gui.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Tsui, L.Garzon, F.2017-11-14doi:10.1107/S1600576717015035International Union of CrystallographyCarbonXS GUI is a graphical user interface to CarbonXS. It is used to fit the X-ray diffraction patterns of disordered and graphitized carbon materials to extract structural parameters such as coherence size and strain.ENcarbonX-ray diffractioncomputer programsThe crystallographic structure of disordered carbons impacts their performance in components for fuel cells, batteries and catalyst supports. Obtaining parameters such as lattice constants and crystal domain size requires an appropriate model for these carbons, a task accomplished with the Fortran program CarbonXS published in 1993. CarbonXS GUI contains an updated version of CarbonXS and a graphical user interface wrapper. This new version provides a graphical method of configuring and operating CarbonXS, a calculation mode to simulate diffraction patterns, and immediate feedback in the form of fit–source and difference plots. CarbonXS GUI is available for free on Windows, Linux and Mac OSX at http://github.com/lktsui/carbon_xs_gui.text/htmlCarbonXS GUI: a graphical front-end for CarbonXStext6502017-11-14Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographycomputer programs00A method to perform modulated structure studies using the program ZMC
http://scripts.iucr.org/cgi-bin/paper?po5110
The Monte Carlo simulation toolkit ZMC provides a general method for Monte Carlo simulation of disordered molecular displacements, orientations and site occupations. It is part of a suite of programs that allows convenient calculation of three-dimensional reciprocal space diffraction intensities. Such intensities are useful for extensive structure interpretations from diffraction experiments. Some physical properties can also be calculated from the simulation. This article reports the implementation of an integrated ZMC module that facilitates the construction of modulated molecular crystals and allows the corresponding calculation of modulation satellites. Use of the module is explained and examples illustrated. The method is ideally suited for novice treatment of modulated structure features and also as a basic platform to explore complex structure/properties relationships using atomistic simulation techniques.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Chan, E.J.Goossens, D.J.2017-11-20doi:10.1107/S1600576717015023International Union of CrystallographyA relatively simple method for users new to modulated structures to implement such structural features in an atomistic Monte Carlo modelling program (ZMC) is described. The relevance and usefulness of such a method are outlined.ENmodulated structurediffuse scatteringmolecular simulationsoftware toolsphase transitionsThe Monte Carlo simulation toolkit ZMC provides a general method for Monte Carlo simulation of disordered molecular displacements, orientations and site occupations. It is part of a suite of programs that allows convenient calculation of three-dimensional reciprocal space diffraction intensities. Such intensities are useful for extensive structure interpretations from diffraction experiments. Some physical properties can also be calculated from the simulation. This article reports the implementation of an integrated ZMC module that facilitates the construction of modulated molecular crystals and allows the corresponding calculation of modulation satellites. Use of the module is explained and examples illustrated. The method is ideally suited for novice treatment of modulated structure features and also as a basic platform to explore complex structure/properties relationships using atomistic simulation techniques.text/htmlA method to perform modulated structure studies using the program ZMCtext6502017-11-20Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographycomputer programs003DBVSMAPPER: a program for automatically generating bond-valence sum landscapes. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?to9016
An equation in the article by Sale & Avdeev [J. Appl. Cryst. (2012), 45, 1054–1056] is corrected.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Sale, M.Avdeev, M.2017-11-14doi:10.1107/S1600576717016119International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2012), 45, 1054–1056.ENbond-valence sumsbond-valence sum mappingbond-valence energy landscapeisosurfacesautomationion-conduction pathwaystopologyCIFPerlMaterials StudioAn equation in the article by Sale & Avdeev [J. Appl. Cryst. (2012), 45, 1054–1056] is corrected.text/html3DBVSMAPPER: a program for automatically generating bond-valence sum landscapes. Corrigendumtext6502017-11-14Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallographyaddenda and errata00