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At least 1,693 records · Page 94

Hydrated Anions: From Clusters to Bulk Solution with Quasi-Chemical Theory

The interactions of hydrated ions with molecular and macromolecular solution and interface partners are strong on a chemical energy scale. Here we recount the foremost ab initio theory for the evaluation of the hydration free energies of ions, namely, quasi-chemical theory (QCT). We focus on anions, particularly halides but also the hydroxide anion, because they have been outstanding challenges for all theories. For example, this work supports understanding the high selectivity for F – over Cl – in fluoride-selective ion channels despite the identical charge and the size similarity of these ions. QCT is built by the identification of inner-shell clusters, separate treatment of those clusters, and then the integration of those results into the broader-scale solution environment. Recent work has focused on a close comparison with mass-spectrometric measurements of ion-hydration equilibria. We delineate how ab initio molecular dynamics (AIMD) calculations on ion-hydration clusters, elementary statistical thermodynamics, and electronic structure calculations on cluster structures sampled from the AIMD calculations obtain just the free energies extracted from the cluster experiments. That theory–experiment comparison has not been attempted before the work discussed here, but the agreement is excellent with moderate computational effort. This agreement reinforces both theory and experiment and provides a numerically accurate inner-shell contribution to QCT. The inner-shell complexes involving heavier halides display strikingly asymmetric hydration clusters. Asymmetric hydration structures can be problematic for the evaluation of the QCT outer-shell contribution with the polarizable continuum model (PCM). Nevertheless, QCT provides a favorable setting for the exploitation of PCM when the inner-shell material shields the ion from the outer solution environment. For the more asymmetrically hydrated, and thus less effectively shielded, heavier halide ions clustered with waters, the PCM is less satisfactory. We therefore investigate an inverse procedure in which the inner-shell structures are sampled from readily available AIMD calculations on the bulk solutions. This inverse procedure is a remarkable improvement; our final results are in close agreement with a standard tabulation of hydration free energies, and the final composite results are independent of the coordination number on the chemical energy scale of relevance, as they should be. Finally, a comparison of anion hydration structure in clusters and bulk solutions from AIMD simulations emphasize some differences: the asymmetries of bulk solution inner-shell structures are moderated compared with clusters but are still present, and inner hydration shells fill to slightly higher average coordination numbers in bulk solution than in clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis of the Stereoisomeric Clusters 1,2-Os 3 (CO) 10 (trans-dpmn) and 1,2-Os 3 (CO) 10 (cis-dpmn) [where dpmn = 2,3-bis(diphenylphosphinomethyl)-5-norbornene]: DFT Evaluation of the Isomeric Clusters 1,2-Os 3 (CO) 10 (dpmn) and Isomer-Dependent Diphosphine Ligand Activation

The bicyclic diphosphines trans- and cis-2,3-bis(diphenylphosphinomethyl)-5-norbornene (dpmn) react with 1,2-Os 3 (CO) 10 (MeCN) 2 (1) to furnish the corresponding ligand-bridged clusters Os 3 (CO) 10 (trans-dpmn) (2) and Os 3 (CO) 10 (cis-dpmn) (3). Both new products have been isolated and the molecular structures established by X-ray diffraction analyses. The dihydroxyl-bridged cluster 1,2-Os 3 (CO) 8 (μ-OH) 2 (cis-dpmn) (4), which accompanied the formation of 3 in one reaction, has been isolated and characterized by mass spectrometry and X-ray crystallography. Whereas cluster 2 is stable in toluene at 373 K, 3 is thermally sensitive under identical conditions and undergoes loss of CO (2 equiv), coupled with the activation of three norbornene C-H bonds and one P-C(phenyl) bond, to furnish the dihydride cluster H 2 Os 3 (CO) 8 [μ 3 -2-PhPC -3 -endo-Ph 2 PCH 2 (C 7 H 7 )] (5). The solid-state structure of 5 confirms the multiple activation of the cis-dpmn ligand and accompanying formation of the face-capping 2-PhPC-3-endo-Ph 2 PCH 2 (C 7 H 7 ) moiety in the product. DFT calculations on 2 and 3 indicate that the former cluster is the thermodynamically more stable isomer, and the conversion of 3→ 5 + 2CO + benzene is computed to be exergonic by 12.7 kcal/mol and is entropically favored due to the release of the CO and benzene by-products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Planetary normal mode computation: Parallel algorithms, performance and reproducibility

This report is an extension of work entitled “Computing planetary interior normal modes with a highly parallel polynomial filtering eigensolver.” by Shi et al., [1] originally presented at the SC18 conference. A highly parallel polynomial filtered eigensolver was developed and exploited to calculate the planetary normal modes. The proposed method is ideally suited for computing interior eigenpairs for large-scale eigenvalue problems as it greatly enhances memory and computational efficiency. In this article, the second-order finite element method is used to further improve the accuracy as only the first-order finite element method was deployed in the previous work. The parallel algorithm, its parallel performance up to 20k processors, and the great computational accuracy are illustrated. The reproducibility of the previous work was successfully performed on the Student Cluster Competition at the SC19 conference by several participant teams using a completely different Mars-model dataset on different clusters. Both weak and strong scaling performances of the reproducibility by the participant teams were impressive and encouraging. The analysis and reflection of their results are demonstrated and future direction is discussed.

97 MATHEMATICS AND COMPUTING↗

New computing systems and their impact on structural analysis and design

A review is given of the recent advances in computer technology that are likely to impact structural analysis and design. The computational needs for future structures technology are described. The characteristics of new and projected computing systems are summarized. Advances in programming environments, numerical algorithms, and computational strategies for new computing systems are reviewed, and a novel partitioning strategy is outlined for maximizing the degree of parallelism. The strategy is designed for computers with a shared memory and a small number of powerful processors (or a small number of clusters of medium-range processors). It is based on approximating the response of the structure by a combination of symmetric and antisymmetric response vectors, each obtained using a fraction of the degrees of freedom of the original finite element model. The strategy was implemented on the CRAY X-MP/4 and the Alliant FX/8 computers. For nonlinear dynamic problems on the CRAY X-MP with four CPUs, it resulted in an order of magnitude reduction in total analysis time, compared with the direct analysis on a single-CPU CRAY X-MP machine.

Noor, Ahmed K.↗

Tycho: Realistically Simulating Exoplanets within Stellar Clusters. I. Improving the Monte Carlo Approach

To fully understand the diverse population of exoplanets, we must study their early lives within open clusters, the birthplace of most stars with masses >0.5M {sub ⊙} (including those currently in the field). Indeed, when we observe planets within clustered environments, we notice highly eccentric and odd systems that suggest the importance of dynamical pathways created by interactions with additional bodies (as in the case of HD 285507b). However, it has proven difficult to investigate these effects, as many current numerical solvers for the multi-scale N-body problem are simplified and limited in scope. To remedy this, we aim to create a physically complete computational solution to explore the role of stellar close encounters and interplanetary interactions in producing the observed exoplanet populations for both open cluster stars and field stars. We present a new code, Tycho, which employs a variety of different computational techniques, including multiple N-body integration methods, close encounter handling, modified Monte Carlo scattering experiments, and a variety of empirically informed initial conditions. We discuss the methodology in detail, and its implementation within the AMUSE software framework. Approximately 1% of our systems are promptly disrupted by star-star encounters contributing to the rogue planets occurrence rate. Additionally, we find that close encounters which that perturb long-period planets lead to 38.3% of solar-system-like planetary systems becoming long-term unstable.

79 ASTRONOMY AND ASTROPHYSICS↗

Constructing Water‐Stable Porous Organic Salts via Suppressed Proton Integration Using Fluorinated Tetrazole Tectons

Porous organic salts (POSs) are an emerging class of materials with ordered ionic architectures, offering excellent proton transfer and water uptake properties. However, conventional POS synthesis via strong acid–base neutralization (e.g., ─SO₃H and ─NH₂) leads to extensive hydrogen bonding with water, compromising stability in aqueous and water-lean environments. Here, we address this challenge by designing POSs with hydrophobic porous channels and minimal hydrogen bonding formation. Our key innovation is the use of fluorinated tetrazole as a weak acid tecton and a tetra-substituted imidazole precursor devoid of active protons as the base. Single-crystal analysis and computational modeling reveal that the structural integrity of the synthesized POSs arises primarily from cation–anion interactions, with water confined as clusters in the pores, independent of hydrogen bonding with the scaffold. Robustness of the POS structure under aqueous and water-lean conditions is confirmed by X-ray and neutron scattering, as well as computational modeling, confirming preserved packing and crystal structures. The stability of POS is further demonstrated in aqueous iodine capture, with imidazolium cations and C–F functionalizations serving as strong adsorption sites. As a result, the approach developed herein further pushes the boundary of POS materials to withstand both aqueous and water-lean conditions.

Fluorinated tecton↗

A Multi-Level Parallelization Concept for High-Fidelity Multi-Block Solvers

The integration of high-fidelity Computational Fluid Dynamics (CFD) analysis tools with the industrial design process benefits greatly from the robust implementations that are transportable across a wide range of computer architectures. In the present work, a hybrid domain-decomposition and parallelization concept was developed and implemented into the widely-used NASA multi-block Computational Fluid Dynamics (CFD) packages implemented in ENSAERO and OVERFLOW. The new parallel solver concept, PENS (Parallel Euler Navier-Stokes Solver), employs both fine and coarse granularity in data partitioning as well as data coalescing to obtain the desired load-balance characteristics on the available computer platforms. This multi-level parallelism implementation itself introduces no changes to the numerical results, hence the original fidelity of the packages are identically preserved. The present implementation uses the Message Passing Interface (MPI) library for interprocessor message passing and memory accessing. By choosing an appropriate combination of the available partitioning and coalescing capabilities only during the execution stage, the PENS solver becomes adaptable to different computer architectures from shared-memory to distributed-memory platforms with varying degrees of parallelism. The PENS implementation on the IBM SP2 distributed memory environment at the NASA Ames Research Center obtains 85 percent scalable parallel performance using fine-grain partitioning of single-block CFD domains using up to 128 wide computational nodes. Multi-block CFD simulations of complete aircraft simulations achieve 75 percent perfect load-balanced executions using data coalescing and the two levels of parallelism. SGI PowerChallenge, SGI Origin 2000, and a cluster of workstations are the other platforms where the robustness of the implementation is tested. The performance behavior on the other computer platforms with a variety of realistic problems will be included as this on-going study progresses.

Hatay, Ferhat F.↗

Scalable Out-of-Core Solvers on Xeon Phi Cluster

This paper documents the implementation of a distributive out-of-core (OOC) solver for performing LU and Cholesky factorizations of a large dense matrix on clusters of many-core programmable co-processors. The out-of- core algorithm combines both the left-looking and right-looking schemes aimed to minimize the movement of data between the CPU host and the co-processor, optimizing data locality as well as computing throughput. The OOC solver is built to align with the format of the ScaLAPACK software library, making it readily portable to any existing codes using ScaLAPACK. A runtime analysis conducted on Beacon (an Intel Xeon plus Intel Xeon Phi cluster which composed of 48 nodes of multi-core CPU and MIC) at the Na- tional Institute for Computational Sciences is presented. Comparison of the performance on the Intel Xeon Phi and GPU clusters are also provided.

D'Azevedo, Ed F↗

K-means-driven Gaussian Process data collection for angle-resolved photoemission spectroscopy

Abstract We propose the combination of k-means clustering with Gaussian Process (GP) regression in the analysis and exploration of 4D angle-resolved photoemission spectroscopy (ARPES) data. Using cluster labels as the driving metric on which the GP is trained, this method allows us to reconstruct the experimental phase diagram from as low as 12% of the original dataset size. In addition to the phase diagram, the GP is able to reconstruct spectra in energy-momentum space from this minimal set of data points. These findings suggest that this methodology can be used to improve the efficiency of ARPES data collection strategies for unknown samples. The practical feasibility of implementing this technology at a synchrotron beamline and the overall efficiency implications of this method are discussed with a view on enabling the collection of more samples or rapid identification of regions of interest.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Brief Summary of Research Results Supported by Institutional Computing under Project W11_MagUniv [Slides]

We continue to study the origin and dynamics of magnetic fields in galaxy clusters using a cosmological adaptive mesh refinement (AMR) Magneto-hydrodynamics (MHD) code called Enzo-MHD. We have performed large-scale simulations of formation of galaxy clusters, some of which are the largest ever performed in this kind of studies. We have collaborated with observers (Dr. F. Govoni and Dr. M. Murgia) to compare our simulations with observations, in terms of the Faraday rotation measurement, radio emissions in radio halo and relics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Mobility and clustering of barium ions and dications in high-pressure xenon gas

The clustering and drift properties of barium ions in xenon gas are explored theoretically, using density-functional theory and computational ion mobility theory, with the goal of better understanding barium ion transport for neutrinoless double beta decay. Here, we derive the equilibrium conformations, energies, and entropies of molecular ions in the Ba + -Xe and Ba 2 + -Xe systems, which yield a predictive model of cluster formation in high-pressure gas. In this work, we calculate ion-neutral interaction potential curves for these species and use them to predict effective molecular ion mobilities. Our calculation consistently reproduces experimental data on effective mobility and molecular ion formation for the Ba + system, and predicts strong cluster formation in the Ba 2 + system, dominated by stable [ BaXe 6 ] 2 + , [ BaXe 7 ] 2 + , [ BaXe 8 ] 2 + , and [ BaXe 9 ] 2 + complexes in the range of interest. Some implications for barium tagging in gas-phase neutrinoless double beta decay experiments are discussed, and the first predictions of pressure-dependent mobility of the doubly charged Ba 2 + species are presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Impact of amorphous pockets on displacement damage evolution in silicon

Silicon has long been known to exhibit amorphization in response to heavy particle bombardment. For doses below the total amorphization threshold, partial amorphization is observed in the form of scattered amorphous pockets. While extensive research has gone into modeling the formation and evolution of amorphous pockets in response to irradiation, no studies yet investigate their impact on the evolution of other damage such as interstitial supersaturation and clustering. In this study, we survey the impact of amorphous pockets on defect evolution in silicon when treated as static sinks. MD is first used to show that amorphous pockets provide energetically favorable sites for point defects relative to the crystalline bulk, supporting the hypothesis that they act as sinks. A 0-D cluster dynamics model is then constructed, taking an interstitial clustering model from the literature and including amorphous pockets as a sink species. We conduct our survey for temperatures between 30 and 400 °C and sink strengths between 1 to 6 x 10 10 cm −2 . Both implantation- and radiation-induced damage states are investigated using interstitial and vacancy concentrations as initial condition variables. We find that, due to the differing migration rates of the interstitial and the vacancy, amorphous pockets have a non-monotonic impact on the final damage state depending on the effective sink strength of the amorphous pockets, resulting in increased damage formation in regimes of intermediate amorphization. In conclusion, this result emphasizes the important role of amorphous pockets in governing the evolution of damage in partially amorphized crystalline materials.

36 MATERIALS SCIENCE↗

Charliecloud 101

This workshop will provide participants with background and hands-on experience to use basic containers for HPC applications. We will discuss what containers are, why they matter for HPC, and how they work. We’ll give an overview of Charliecloud, the unprivileged container solution from HPC Division, and walk participants through installing it on their own compute resource. Participants will build toy containers and a real HPC application, and then run them in parallel on an HPC Division cluster. This will be a highly interactive workshop with lots of Q&A.

97 MATHEMATICS AND COMPUTING↗

A static quantum embedding scheme based on coupled cluster theory

Here, we develop a static quantum embedding scheme that utilizes different levels of approximations to coupled cluster (CC) theory for an active fragment region and its environment. To reduce the computational cost, we solve the local fragment problem using a high-level CC method and address the environment problem with a lower-level Møller–Plesset (MP) perturbative method. This embedding approach inherits many conceptual developments from the hybrid second-order Møller–Plesset (MP2) and CC works by Nooijen [J. Chem. Phys. 111, 10815 (1999)] and Bochevarov and Sherrill [J. Chem. Phys. 122, 234110 (2005)]. We go beyond those works here by primarily targeting a specific localized fragment of a molecule and also introducing an alternative mechanism to relax the environment within this framework. We will call this approach MP-CC. We demonstrate the effectiveness of MP-CC on several potential energy curves and a set of thermochemical reaction energies, using CC with singles and doubles as the fragment solver, and MP2-like treatments of the environment. The results are substantially improved by the inclusion of orbital relaxation in the environment. Using localized bonds as the active fragment, we also report results for N=N bond breaking in azomethane and for the central C–C bond torsion in butadiene. We find that when the fragment Hilbert space size remains fixed (e.g., when determined by an intrinsic atomic orbital approach), the method achieves comparable accuracy with both a small and a large basis set. Additionally, our results indicate that increasing the fragment Hilbert space size systematically enhances the accuracy of observables, approaching the precision of the full CC solver.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SIAM Conference on Parallel Processing for Scientific Computing, 4th, Chicago, IL, Dec. 11-13, 1989, Proceedings

Attention is given to such topics as an evaluation of block algorithm variants in LAPACK and presents a large-grain parallel sparse system solver, a multiprocessor method for the solution of the generalized Eigenvalue problem on an interval, and a parallel QR algorithm for iterative subspace methods on the CM2. A discussion of numerical methods includes the topics of asynchronous numerical solutions of PDEs on parallel computers, parallel homotopy curve tracking on a hypercube, and solving Navier-Stokes equations on the Cedar Multi-Cluster system. A section on differential equations includes a discussion of a six-color procedure for the parallel solution of elliptic systems using the finite quadtree structure, data parallel algorithms for the finite element method, and domain decomposition methods in aerodynamics. Topics dealing with massively parallel computing include hypercube vs. 2-dimensional meshes and massively parallel computation of conservation laws. Performance and tools are also discussed.

Dongarra, Jack↗

Enabling Innovative Analysis on Heterogeneous Clusters through HTCdaskgateway

High energy particle (HEP) physics research is going through fundamental changes as we move to collect larger amounts of data from the Large Hadron Collider (LHC). Analysis facilities and distributed computing, through HTCs, have come together to create the next pythonic generation of analysis by utilizing HTCdaskgateway, a Dask gateway extension, allowing users to spawn workers compatible with both their analysis and heterogeneous clusters in line with authentication requirements. This is enabling physicists to engage with scientific python in ways they had not before because of domain specific C++ tools. An example of HTCdaskgateway’s use is Fermilab’s Elastic Analysis Facility.

Chavez, Elise [U. Wisconsin, Madison (main)]↗