An Efficient and Accurate Car-Parrinello-like Approach to Born-Oppenheimer Molecular Dynamics

We present a new method which combines Car-Parrinello and Born-Oppenheimer molecular dynamics in order to accelerate density functional theory based ab-initio simulations. Depending on the system a gain in efficiency of one to two orders of magnitude has been observed, which allows ab-initio molecular dynamics of much larger time and length scales than previously thought feasible. It will be demonstrated that the dynamics is correctly reproduced and that high accuracy can be maintained throughout for systems ranging from insulators to semiconductors and even to metals in condensed phases. This development considerably extends the scope of ab-initio simulations.Comment: 4 pages, 3 figures; Accepted by Phys. Rev. Lett. for publicatio

Pyrite in contact with supercritical water: the desolation of steam

The supercritical water and pyrite interface has been studied by DFT calculations. A surprisingly dry surface has been found which points to a new reactivity under extreme conditions which has relevance in the iron–sulfur world prebiotic chemistry of the early Earth.</p

Negative thermal expansion of ScF3: First principles vs empirical molecular dynamics

The calculations were performed on the Paul Scherrer Institute cluster Merlin4, HPC resources of the Swiss National Supercomputing Centre in Lugano (project ID s626) as well as at the Latvian SuperCluster (LASC). Authors are greatly indebted to S. Ali, D. Gryaznov, R.A. Evarestov, M. Isupova, A. Kalinko, V. Kashcheyevs, V. Pankratov, S. Piskunov, A. I. Popov, J. Purans, F. Rocca, L. Shirmane, P. Zˇguns, and Yu. F. Zhukovskii for many stimulating discussions. Financial support provided by project No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001) under the activity “Post-doctoral research aid” realized at the Institute of Solid State Physics, University of Latvia is greatly acknowledged.The crystal lattice of cubic scandium fluorine (ScF3) exhibits negative thermal expansion (NTE) over a wide range of temperatures from 10 K to 1100 K. Here the NTE effect in ScF3 is studied using atomistic simulations based on empirical and ab initio molecular dynamics (AIMD) in the isobaric-isothermal (NpT) ensemble. The temperature dependence of the average lattice constant, the Sc-F-Sc bond angle distribution and the radial distribution functions were obtained. Crossover from the NTE to positive thermal expansion occurring at about 1100 K is reproduced by AIMD simulations in agreement with the known experiment data. At the same time, empirical MD model fails to reproduce the NTE behaviour and suggests an expansion of the ScF3 lattice with increasing temperature. However, both MD models predict strong anisotropy of fluorine atom thermal vibration amplitude, being larger in the direction orthogonal to the Sc-F-Sc atom chain.ISSP UL project No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001); Institute of Solid State Physics, University of Latvia as the Center of Excellence has received funding from the European Union’s Horizon 2020 Framework Programme H2020-WIDESPREAD-01-2016-2017-TeamingPhase2 under grant agreement No. 739508, project CAMART

Interpretation of the Cu K-edge EXAFS spectra of Cu3N using ab initio molecular dynamics

Financial support provided by ERDF project No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001) under the activity “Post-doctoral research aid” realized at the Institute of Solid State Physics, University of Latvia is greatly acknowledged. This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under the project ID s681 .Cubic copper nitride (Cu3N) has anti-perovskite structure, and its properties are strongly affected by anisotropic thermal vibrations of copper atoms. Ab initio molecular dynamics (AIMD) simulations were performed in the temperature range from 300 K to 700 K in order to probe the details of Cu3N lattice dynamics. The Cu K-edge extended X-ray absorption fine structure (EXAFS) spectrum of bulk Cu3N was used to validate AIMD simulations at 300 K. The AIMD results suggest strong anharmonicity of the Cu–N and Cu–Cu bonds, the rigidity of NCu6 octahedra and strong correlation in atomic motion within –N–Cu–N– atom chains as well as support anisotropy of copper thermal vibrations.National Centre for Supercomputing Applications; Institute of Solid State Physics, Chinese Academy of Sciences; European Regional Development Fund 1.1.1.2/16/I/001,1.1.1.2/VIAA/l/16/147; Swiss National Supercomputing Centre grant under the project ID s681; Institute of Solid State Physics, University of Latvia as the Center of Excellence has received funding from the European Union’s Horizon 2020 Framework Programme H2020-WIDESPREAD-01-2016-2017-TeamingPhase2 under grant agreement No. 739508, project CAMART

Unraveling the interlayer and intralayer coupling in two-dimensional layered MoS2_2 by X-ray absorption spectroscopy and ab initio molecular dynamics simulations

Understanding interlayer and intralayer coupling in two-dimensional layered materials (2DLMs) has fundamental and technological importance for their large-scale production, engineering heterostructures, and development of flexible and transparent electronics. At the same time, the quantification of weak interlayer interactions in 2DMLs is a challenging task, especially, from the experimental point of view. Herein, we demonstrate that the use of X-ray absorption spectroscopy in combination with reverse Monte Carlo (RMC) and ab initio molecular dynamics (AIMD) simulations can provide useful information on both interlayer and intralayer coupling in 2DLM 2H$_c$-MoS$_2$. The analysis of the low-temperature (10-300 K) Mo K-edge extended X-ray absorption fine structure (EXAFS) using RMC simulations allows for obtaining information on the means-squared relative displacements $\sigma^2$ for nearest and distant Mo-S and Mo-Mo atom pairs. This information allowed us further to determine the strength of the interlayer and intralayer interactions in terms of the characteristic Einstein frequencies $\omega_E$ and the effective force constants $\kappa$ for the nearest ten coordination shells around molybdenum. The studied temperature range was extended up to 1200 K employing AIMD simulations which were validated at 300 K using the EXAFS data. Both RMC and AIMD results provide evidence of the reduction of correlation in thermal motion between distant atoms and suggest strong anisotropy of atom thermal vibrations within the plane of the layers and in the orthogonal direction

Analysis of the U L3-edge X-ray absorption spectra in UO2 using molecular dynamics simulations

This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under the project ID s444. The resource allocation within the PSI share at CSCS and on the PSI compute cluster Merlin4 is also acknowledged. D. B. is grateful for a fellowship within the Sciex-NMS programme. A. K. was supported by Latvian Science Council Grant no. 187/2012.Uranium L3-edge X-ray absorption spectroscopy was used to study the atomic structure of uranium dioxide (UO2). The extended X-ray absorption fine structure (EXAFS) was interpreted within the ab initio multiple-scattering approach combined with classical molecular dynamics to account for thermal disorder effects. Nine force-field models were validated, and the role of multiple-scattering contributions was evaluated.Swiss National Supercomputing Centre project ID s444; Latvian Science Council grant no. 187/2012; Institute of Solid State Physics, University of Latvia as the Center of Excellence has received funding from the European Union’s Horizon 2020 Framework Programme H2020-WIDESPREAD-01-2016-2017-TeamingPhase2 under grant agreement No. 739508, project CAMART

Analysis of the U L3-edge X-ray absorption spectra in UO2 using molecular dynamics simulations

This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under the project ID s444. The resource allocation within the PSI share at CSCS and on the PSI compute cluster Merlin4 is also acknowledged. D. B. is grateful for a fellowship within the Sciex-NMS programme. A. K. was supported by Latvian Science Council Grant no. 187/2012.Uranium L3-edge X-ray absorption spectroscopy was used to study the atomic structure of uranium dioxide (UO2). The extended X-ray absorption fine structure (EXAFS) was interpreted within the ab initio multiple-scattering approach combined with classical molecular dynamics to account for thermal disorder effects. Nine force-field models were validated, and the role of multiple-scattering contributions was evaluated.Swiss National Supercomputing Centre project ID s444; Latvian Science Council grant no. 187/2012; Institute of Solid State Physics, University of Latvia as the Center of Excellence has received funding from the European Union’s Horizon 2020 Framework Programme H2020-WIDESPREAD-01-2016-2017-TeamingPhase2 under grant agreement No. 739508, project CAMART

Title: Water Structure as a Function of Temperature from X-ray Scattering Experiments and Ab Initio Molecular Dynamics

We present high-quality x-ray scattering experiments on pure water taken over a temperature range of 2°C to 77°C using a synchrotron beam line at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory. The ALS x-ray scattering intensities are qualitatively different in trend of maximum intensity over this temperature range compared to older x-ray experiments. While the common procedure is to report both the intensity curve and radial distribution function(s), the proper extraction of the real-space pair correlation functions from the experimental scattering is very difficult due to uncertainty introduced in the experimental corrections, the proper weighting of OO, OH, and HH contributions, and numerical problems of Fourier transforming truncated data in Q-space. Instead we consider the direct calculation of xray scattering spectra using electron densities derived from density functional theory based on real-space configurations generated with classical water models. The simulation of the experimental intensity is therefore definitive for determining radial distribution functions over a smaller Q-range. We find that the TIP4P, TIP5P and polarizable TIP4P-Pol2 water models, with DFT-LDA densities, show very good agreement with the experimental intensities, and TIP4P-Pol2 in particular shows quantitative agreement over the full temperature range. The resulting radial distribution functions from TIP4P-Pol2 provide the current best benchmarks for real-space water structure over the biologically relevant temperature range studied here. 1 Introduction Liquid water structure is characterized by x-ray (or neutron) diffraction that measures experimental intensities as a function of momentum transfer, Q=4πsin(θ/2)/λ, where λ is the wavelength and θ is the scattering angle with respect to the incident beam. The most recent x-ray data taken at ambient conditions at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory exhibited significant differences when compared to the scattering curves of past x-ray experiments The intensity is the true experimental observable in which error-bars are well-defined. However, it is typical practice for water scattering experiments to also report radial distributions in addition to the intensity profile, primarily because it is more convenient and practical to consider water structure in terms of real-space distribution functions (1) ( In this study we consider the direct calculation of x-ray scattering spectra using ab-initio density functional theory with the LDA functional over the temperature range studied by experiment. The generation of the real-space &quot;snapshots&quot; could come from either a first 3 principles molecular dynamics calculation Experimental Methods Experimental setup. The data collection was performed at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory on beam line 7.3.3. Doubly distilled and degassed water was used in each experiment, and several data sets with independent fillings of the sample holder were collected at each temperature (2°C, 11°C, 22°C, 33°C, 44°C, 55°C, 66°C, and 77°C). A silicon monochrometer was used to produce an x-ray beam with spot size on the order of 100µm, with 99% of the energy at 12.800 ± 0.001 keV or a wavelength of 0.9686Å. This wavelength provided the best compromise between sufficient flux and maximizing our 4 accessible Q-range. Data sets were collected with a flat slab water sample using a transmisson geometry, with the sample tilted with respect to the incoming x-ray beam by an angle of 30 o . A Bruker Charge Coupled Device (CCD) area detector, mounted on a Huber diffractometer and with dimensions of 9.6cm x 9.6cm collected the diffracted x-rays. In order to realize the full range of 0.1Å -1 &lt; Q &lt;11.1Å -1 provided in this study, the data were collected with the detector in three different positions which were pieced together for the final result. The sample to detector positions were determined to 100µm precision while the angle between the xray beam and the normal to detector face were characterized on the order of mrads. The geometries at each detector position were determined by collecting PbS powder patterns with the powder placed within the sample holder and fitting the resulting sharp Bragg rings to determine all the geometric parameters. A more detailed description of this procedure can be found in previous work Experimental corrections. The collected raw intensity data was transformed to a circularly integrated scattering cross-section on a per electron scale versus Q. The following divides the corrections into two parts. The first deals with corrections that must be applied generally to all detector positions such as absorption, geometric corrections, and polarization of the radiation. The second set of corrections deals with overlapping data from different panels and thus the contribution of background and sample holder scattering. Corrections to the intensities due to absorption by air, water, and window material are given by the form where I o is the intensity if there were no absorption in the sample, I is the measured intensity, t is the thickness, τ is the angle between the plane of the sample and the incident x-ray beam, and ν has the form ν=cosθsinτ+sinθcosφcosτ. The absorption coefficients, µ ρ , can be obtained from http://www-cxro.lbl.gov/optical_constants using a tabulated format based on 6 When the incident radiation is plane-polarized as in our experiment, the in-plane and outof-plane polarization is treated separately, and the measured intensities must be rescaled by the factor ( The data were also corrected for the 1/r 2 fall off of intensity, and correction for pixel orientation with respect to the incident radiation. We discovered that detector manufacturers attempt to provide a correction of this sort in their bundled software for data read-out. Corrections to the image collected by the CCD includes distortions introduced by the fiber optic tapers connecting the plate to the chip, a dark current correction that takes into account photoelectrons ejected by thermal motions in the CCDs and any low-level background radiation in the experimental hutch, and finally a flat field correction that provides a correction for variations in pixel sensitivity. This correction involves a calibration measurement that collects a reference image intensity using either a radioactive source or scattering from a fluorescent material at a set distance from the detector. The image is used to generate a scale factor for each pixel such that, when applied to the flat field image, each pixel measures the same intensity. The set distance with which this correction is calibrated varies among manufacturers. If the calibration experiment involves a relatively small source to detector distance, then the geometric corrections (1/r 2 fall off, pixel orientation) are implicitly taken into account by the manufacturer in the flat field correction. This is the case for the Bruker detector, so we need to &quot;uncorrect&quot; the collected image for the manufacturers geometry, and reapply the correct geometric corrections for our experiment. This is an insidious problem since these detector corrections are applied 7 before the &quot;raw image&quot; is available to the experimentalist, and the correction is not documented in the manufacturer literature. We next turn to the procedure for the subtraction of background that is required in order to match segments of the intensity over the full range of Q in this experiment