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We present a method based on second linear response time-dependent density func- tional theory (TDDFT) to calculate permanent and transition multipoles of excited states, which are required to compute excited-state absorption/emission spectra, multi- photon optical processes, among others. In previous work, we examined computations based on second linear response theory in which linear response TDDFT was employed twice. In contrast, the present methodology only requires information from a single linear response calculation to compute the excited-state properties. These are eval- uated analytically through various algebraic operations involving electron repulsion integrals and excitation vectors. The present derivation focuses on full many-body wave functions instead of single orbitals, as in our previous approach. Here, we test the proposed method by applying it to several diatomic and triatomic molecules. This shows that the computed excited-state dipoles are consistent with respect to reference equation-of-motion coupled cluster calculations.
Pulsed laser photolysis experiments with laser-induced fluorescence detection of NH 2 set an upper limit to the rate constant for reaction with N 2 O of k < 1 × 10 −15 cm 3 molecule −1 s −1 at 513 K. Computations were based on geometries and anharmonic frequency analysis (B2PLYP-D3/cc-pVTZ) followed by coupled cluster calculations extrapolated to the infinite basis set limit, with corrections for core−valence electron correlation, scalar relativistic effects, and correlation up to CCSDT(Q). Species that showed multireference character were quantified with MRCI(7,7)+Q/cc-pVTZ theory. Rate constants were obtained for the dominant product channel H 2 NN + NO, along with HN 3 + OH, H 2 NO + N 2 , NNH + HNO, ON(NH) 2 and HNNH + NO. The last channel is slow even at 2500 K, contrary to an early empirical estimate and confirming recent suggestions. Modeling of literature experiments on oxidation of NH 3 by N 2 O shows that all channels are too slow to make a significant impact on the loss of N 2 O in ammonia flames. Similarly, the direct NH 3 + N 2 O reaction is found to be negligibly slow.
One of the main unsolved problems of cosmology is how to maximize the extraction of information from nonlinear data. If the data are nonlinear the usual approach is to employ a sequence of statistics (N-point statistics, counting statistics of clusters, density peaks or voids etc.), along with the corresponding covariance matrices. However, this approach is computationally prohibitive and has not been shown to be exhaustive in terms of information content. Here we instead develop a hierarchical Bayesian approach, expanding the likelihood around the maximum posterior of linear modes, which we solve for using optimization methods. By integrating out the modes using perturbative expansion of the likelihood we construct an initial power spectrum estimator, which for a fixed forward model contains all the cosmological information if the initial modes are gaussian distributed. We develop a method to construct the window and covariance matrix such that the estimator is explicitly unbiased and nearly optimal. We then generalize the method to include the forward model parameters, including cosmological and nuisance parameters, and primordial non-gaussianity. We apply the method in the simplified context of nonlinear structure formation, using either simplified 2-LPT dynamics or N-body simulations as the nonlinear mapping between linear and nonlinear density, and 2-LPT dynamics in the optimization steps used to reconstruct the initial density modes. We demonstrate that the method gives an unbiased estimator of the initial power spectrum, providing among other a near optimal reconstruction of linear baryonic acoustic oscillations.
Numerical simulations in cosmology require trade-offs between volume, resolution and run-time that limit the volume of the Universe that can be simulated, leading to sample variance in predictions of ensemble-average quantities such as the power spectrum or correlation function(s). Sample variance is particularly acute at large scales, which is also where analytic techniques can be highly reliable. This provides an opportunity to combine analytic and numerical techniques in a principled way to improve the dynamic range and reliability of predictions for clustering statistics. In this paper we extend the technique of Zel'dovich control variates, previously demonstrated for 2-point functions in real space, to reduce the sample variance in measurements of 2-point statistics of biased tracers in redshift space. We demonstrate that with this technique, we can reduce the sample variance of these statistics down to their shot-noise limit out to k ~ 0.2 h Mpc -1 . This allows a better matching with perturbative models and improved predictions for the clustering of e.g. quasars, galaxies and neutral Hydrogen measured in spectroscopic redshift surveys at very modest computational expense. We discuss the implementation of ZCV, give some examples and provide forecasts for the efficacy of the method under various conditions.
The advent of high-throughput DNA sequencing techniques has permitted very high quality de novo assemblies of genomes, but raise an issue of requiring large amounts of computer memory to resolve the large genome graphs generated by most overlap graph de novo assemblers. To address these limitations, we present a novel algorithmic approach; Scalable Overlap-graph Reduction Algorithms (SORA). SORA adapts string graph reduction algorithms for the genome assembly using a distributed computing platform. To efficiently compute coverage for enormous paths in the graphs, SORA uses Apache Spark which is a cluster-based engine designed on top of Hadoop to handle very large datasets in the cloud. The experimental results show that SORA can process a nearly one billion edge graph in a distributed cloud cluster as well as smaller graphs on a local cluster with a short turnaround time. Moreover, our algorithms scale almost linearly with increasing numbers of virtual instances in the cloud. SORA is freely available for download at https://github.com/BioHPC/SORA/.
The Berkeley eXtensible Environment (BXE) provides a cloud environment for hardware designers and computer architects to design, build, and simulate their custom architectures on an on-premises FPGA cluster. Utilizing the Chipyard, MoSAIC, and FireSim frameworks, users are provided an environment where they can assemble SoC designs from an existing library of components or import their own source code. Once their designs are ready, they can utilize the FireSim framework provided by BXE to deploy and simulate their designs on the FPGA. Users aren't limited to a single FPGA; they can deploy multiple instances across multiple FPGAs, acting like a rack of servers, or partition their large design across multiple FPGAs, ganging multiple FPGAs into a single simulated system.
Texas A and M University is conducting isothermal flow tests in a wire-wrapped, 61-pin hexagonal fuel bundle to support the research on advanced nuclear fuel development sponsored by the Department of Energy (DOE). The purpose of these tests is to produce high spatial- and temporal-resolution measurements of the flow and pressure measurements at different locations of the test bundle. The data resulting from these tests will be used to benchmark numerical simulations of the experiments using both industry-standard Reynolds-averaged Navier-Stokes (RANS) based Computation Fluid Dynamics (CFD) methods and a highly resolved Large Eddy Simulation (LES) computer code. This article described the main features of the experimental facility, its capabilities in producing experimental data of pressure drop and velocity fields at different axial locations and within different exterior and interior sub-channels, using advanced flow visualization techniques. Examples of experimental data outputs and typical locations of the measurements that will included in the research scope are also shown in this article. (authors)
In Light Water Reactor (LWR) cores, the nuclear fuel rods are arranged together as rod bundles in a triangular or square pattern. The fuel rod bundles are supported by the spacer grids with mixing vanes. An understanding of spacer grid and mixing vanes effect is important since it has a direct impact on the turbulence structure in the flow and the heat removal efficiency from the fuel rod surface. Although a considerable amount of literature has been published on the experimental investigation of spacer grid and mixing vanes effect, the measurements were mainly focused on single-phase flow. The influence of spacer grid and mixing vanes on two-phase flow is yet to be fully understood. Some preliminary research efforts have been invested in nuclear community. For example, Wheeler et al. experimentally studied the effects of spacer grid in air-water two-phase flow. Although mixing vanes are not considered, they presented interesting results of time-averaged two-phase flow quantities at upstream and downstream locations of the spacer grid. Over the past decades, the rapid development of High-Performance Computing (HPC) is allowing for the increasingly larger-scale high-fidelity simulations. Thanks to this favorable historical trend, Direct Numerical Simulation (DNS), integrated with Interface Tracking Methods (ITM), has been emerging as a valuable tool to complement and expand our ability to understand the two-phase flow phenomenon. Meanwhile, in order to make best use of the large-scale two-phase flow simulations, advanced data analysis techniques are being developed, as they enable the extraction of detailed parameters about individual bubble behavior. The level set ITM is utilized in our DNS flow solver, which makes use of a signed distance field. The gas-liquid interface is modeled by the zero level set. The level set method can be readily used to distinguish different phases based on the sign of corresponding level set value (e.g. the sign is positive in the liquid phase while negative in the gas phase.). However, the traditional level set approach is not able to collect calculated values and associate with specific bubbles when multiple (even thousands of) bubbles present in the simulations of two-phase flow. This drawback hinders the collection of useful bubble information, which can give us valuable insights about bubbly flows. For example, how the different local fluid conditions could affect bubble interfacial forces, bubble deformation level, and eventually the bubble distribution throughout the whole domain. A bubble tracking methodology has been developed to address the drawbacks and improve the data collection efficiency of level set based two-phase flow simulations. In the present work, a single Pressurized Water Reactor (PWR) subchannel with reduced size spacer grid and mixing vanes is chosen as the computational domain. The springs and dimples of the spacer grid are not represented for simplicity in the present investigation. The bubble tracking methodology is applied to the simulations of two-phase bubbly flow through spacer grid and mixing vanes region. In the intended simulation, the liquid turbulence will be fully resolved by DNS while the two-phase behaviors are captured by level set ITM. Bubble tracking data are to be processed to investigate the spacer grid and mixing vanes effect on two-phase bubbly flow. (authors)
Approximate solutions to the ab initio electronic structure problem have been a focus of theoretical and computational chemistry research for much of the past century, with the goal of predicting relevant energy differences to within “chemical accuracy” (1 kcal/mol). For small organic molecules, or in general, for weakly correlated main group chemistry, a hierarchy of single-reference wave function methods has been rigorously established, spanning perturbation theory and the coupled cluster (CC) formalism. For these systems, CC with singles, doubles, and perturbative triples is known to achieve chemical accuracy, albeit at O(N7) computational cost. In addition, a hierarchy of density functional approximations of increasing formal sophistication, known as Jacob’s ladder, has been shown to systematically reduce average errors over large datasets representing weakly correlated chemistry. However, the accuracy of such computational models is less clear in the increasingly important frontiers of chemical space including transition metals and f-block compounds, in which strong correlation can play an important role in reactivity. A stochastic method, phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC), has been shown to be capable of producing chemically accurate predictions even for challenging molecular systems beyond the main group, with relatively low O(N3 − N4) cost and near-perfect parallel efficiency. Herein, we present our perspectives on the past, present, and future of the ph-AFQMC method. We focus on its potential in transition metal quantum chemistry to be a highly accurate, systematically improvable method that can reliably probe strongly correlated systems in biology and chemical catalysis and provide reference thermochemical values (for future development of density functionals or interatomic potentials) when experiments are either noisy or absent. Finally, we discuss the present limitations of the method and where we expect near-term development to be most fruitful.
Over a three year period, from 2016-2019, this project demonstrated the scientific benefits of integrating the Titan supercomputer at Oak Ridge Leadership Computing Facility into traditional high throughput grid based distributed computing systems managed by PanDA, the workflow management system used for the execution of all distributed computing applications by the ATLAS experiment at the Large Hadron Collider. PanDA manages millions of batch jobs daily at hundreds of clusters worldwide on request by thousands of physicist users, and processes more than an exabyte of data annually using grid middleware. High levels of operational use of Titan was sustained by PanDA in order to meet the physics goals of ATLAS. The success of this project led to the use of other supercomputers worldwide by ATLAS, and to the adoption of PanDA by other experiments and other scientists. Multiple innovative operational and computer science research goals were achieved supporting the use of supercomputers for scientific domains with large scale distributed data and distributed processing needs.
Physical networks formed by ionizable polymers with ionic clusters as crosslinks are controlled by coupled dynamics that transcend from ionic clusters through chain motion to macroscopic response. Here, the coupled dynamics, across length scales, from the ionic clusters to the networks in toluene swollen polystyrene sulfonate networks, were directly correlated, as the electrostatic environment of the physical crosslinks was altered. The multiscale insight is attained by coupling neutron spin echo measurements with molecular dynamics simulations, carried out to times typical of relaxation of polymers in solutions. The experimental dynamic structure factor is in outstanding agreement with the one calculated from computer simulations, as the networks are perturbed by elevating the temperature and changing the electrostatic environment. In toluene, the long-lived clusters remain stable over hundreds of ns across a broad temperature range, while the polymer network remains dynamic. In conclusion, though the size of the clusters changes as the dielectric constant of the solvent is modified through the addition of ethanol, they remain stable but morph, enhancing the polymer chain dynamics.
The U.S. Department of Energy is conducting a program focused on developing a process for the conversion of biomass to bio-based fuels and co-products. Biomass-derived syngas is converted thermochemically within a temperature range of 240 to 330°C and at elevated pressure (e.g., 1200 psig) over a catalyst. Ethanol is the desired reaction product, although other side compounds are produced, including C 3 to C 5 alcohols; higher (i.e., greater than C 1 ) oxygenates such as methyl acetate, ethyl acetate, acetic acid and acetaldehyde; and higher hydrocarbon gases such as methane, ethane/ethene, propane/propene, etc. Saturated hydrocarbon gases (especially methane) are undesirable because they represent a diminished yield of carbon to the desired ethanol product and represent compounds that must be steam reformed at high energy cost to reproduce CO and H 2 . Ethanol produced by the thermochemical reaction of syngas could be separated and blended directly with gasoline to produce a liquid transportation fuel. Additionally, higher oxygenates and unsaturated hydrocarbon side products such as olefins also could be further processed to liquid fuels. The goal of the current project is the development of a Rh-based catalyst with high activity and selectivity to C 2 + oxygenates. This report chronicles an effort to characterize numerous supports and catalysts to identify particular traits that could be correlated with the most active and/or selective catalysts. Carbon and silica supports and catalysts were analyzed. Generally, analyses provided guidance in the selection of acceptable catalyst supports. For example, supports with high surface areas due to a high number of micropores were generally found to be poor at producing oxygenates, possibly because of mass transfer limitations of the products formed out of the micropores. To probe fundamental aspects of the complicated reaction network of CO with H 2 , a computational/ theoretical investigation using quantum mechanical and ab initio molecular dynamics calculations was initiated in 2009. Computational investigations were performed first to elucidate understanding of the nature of the catalytically active site. Thermodynamic calculations revealed that Mn likely exists as a metallic alloy with Rh in Rh-rich environments under reducing conditions at the temperatures of interest. After determining that reduced Rh-Mn alloy metal clusters were in a reduced state, the activation energy barriers of numerous transition state species on the catalytically active metal particles were calculated to compute the activation barriers of several reaction pathways that are possible on the catalyst surface. Comparison of calculations with a Rh nanoparticle versus a Rh-Mn nanoparticle revealed that the presence of Mn enabled the reaction pathway of CH with CO to form an adsorbed CHCO species, which was a precursor to C 2 + oxygenates. The presence of Mn did not have a significant effect on the rate of CH 4 production. Ir was observed during empirical catalyst screening experiments to improve the activity and selectivity of Rh-Mn catalysts. Thus, the addition of Ir to the Rh-Mn nanoparticles also was probed computationally. Simulations of Rh-Mn-Ir nanoparticles revealed that, with sufficient Ir concentrations, the Rh, Mn and Ir presumably would be well mixed within a nanoparticle. Activation barriers were calculated for Rh-Mn-Ir nanoparticles for several C-, H-, and O-containing transitional species on the nanoparticle surface. It was found that the presence of Ir opened yet another reactive pathway whereby HCO is formed and may undergo insertion with CHx surface moieties. The reaction pathway opened by the presence of Ir is in addition to the CO + CH pathway opened by the presence of Mn. Similar to Mn, the presence of Ir was not found to not affect the rate of CH 4 production.
The Project 8 collaboration aims to measure the absolute neutrino mass or improve on the current limit by measuring the tritium beta decay electron spectrum. We present the current distributed computing model for the Project 8 experiment. Project 8 is in its second phase of data taking with a near continuous data rate of 1Gbps. The current computing model uses DIRAC (Distributed Infrastructure with Remote Agent Control) for its workflow and data management. A detailed meta-data assignment using the DIRAC File Catalog is used to automate raw data transfers and subsequent stages of data processing. The DIRAC system is deployed on containers managed using a Kubernetes cluster to provide a scalable infrastructure. A modified DIRAC Site Director provides the ability to submit jobs using Singularity on opportunistic High-Performance Computing (HPC) sites.
Iron–sulfur (Fe–S) clusters are common biological cofactors that facilitate vital redox reactions. Despite extensive research, the molecular basis of redox potential tuning in ferredoxin-like proteins remains an active area of debate. In this study, we combine statistical analysis of over one thousand [4Fe–4S]-containing protein structures from the Protein Data Bank (PDB) with broken-symmetry and extended broken-symmetry density functional theory to examine how cysteine ligand orientations and environmental screening affect redox properties of the clusters. We identified five main ligand configurations, three of which are predominant in natural structures. Among these, the adiabatic electron affinity differs by less than 0.1 V, indicating that, while geometry plays a secondary role, it allows localized fine-tuning of redox properties. In contrast, electrostatic and solvation effects primarily determine the overall potential range.
Exploiting the machinery of Constrained Density Functional Theory (CDFT), we propose a variational method for calculating low-lying excited states of molecular systems. We dub this method eXcited CDFT (XCDFT). Excited states are obtained by self-consistently constraining a user-defined population of electrons, N c , in the virtual space of a reference set of occupied orbitals. By imposing this population to be N c = 1.0, we computed the first excited state of 15 molecules from a test set. Our results show that XCDFT achieves an accuracy in the predicted excitation energy only slightly worse than linear-response time-dependent DFT (TDDFT), but without incurring into problems of variational collapse typical of the more commonly adopted ΔSCF method. In addition, we selected a few challenging processes to test the limits of applicability of XCDFT. We find that in contrast to TDDFT, XCDFT is capable of reproducing energy surfaces featuring conical intersections (azobenzene and H3) with correct topology and correct overall energetics also away from the intersection. Venturing to condensed-phase systems, XCDFT reproduces the TDDFT solvatochromic shift of benzaldehyde when it is embedded by a cluster of water molecules. Finally, we find XCDFT to be a competitive method among single-reference methods for computations of excited states in terms of time to solution, rate of convergence, and accuracy of the result.
Missing data are prevalent issue in analyses involving data collection. The problem of missing data is exacerbated for multisource analysis, where data from multiple sensors are combined to arrive at a single conclusion. In this scenario, it is more likely to occur and can lead to discarding a large amount of data collected; however, the information from observed sensors can be leveraged to estimate those values not observed. We propose two methods for imputation of multisource data, both of which take advantage of potential correlation between data from different sensors, through ridge regression and a state-space model. These methods, as well as the common median imputation, are applied to data collected from a variety of sensors monitoring an experimental facility. Performance of imputation methods is compared with the mean absolute deviation; however, rather than using this metric to solely rank themethods,we also propose an approach to identify significant differences. Imputation techniqueswill also be assessed by their ability to produce appropriate confidence intervals, through coverage and length, around the imputed values. Finally, performance of imputed datasets is compared with a marginalized dataset through a weighted k-means clustering. In general, we found that imputation through a dynamic linearmodel tended to be the most accurate and to produce the most precise confidence intervals, and that imputing the missing values and down weighting them with respect to observed values in the analysis led to the most accurate performance.
Large scale graph processing is a major research area for Big Data exploration. Vertex centric programming models like Pregel are gaining traction due to their simple abstraction that allows for scalable execution on distributed systems naturally. However, there are limitations to this approach which cause vertex centric algorithms to under-perform due to poor compute to communication overhead ratio and slow convergence of iterative superstep. In this paper we introduce GoFFish a scalable sub-graph centric framework co-designed with a distributed persistent graph storage for large scale graph analytics on commodity clusters. We introduce a sub-graph centric programming abstraction that combines the scalability of a vertex centric approach with the flexibility of shared memory sub-graph computation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation.