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At least 19 records

Computational Spectroscopy of the Cr–Cr Bond in Coordination Complexes

In this work, we report the accurate computational vibrational analysis of the Cr–Cr bond in dichromium complexes using second-order multireference complete active space methods (CASPT2), allowing direct comparison with experimental spectroscopic data both to facilitate interpreting the low-energy region of the spectra and to provide insights into the nature of the bonds themselves. Recent technological development by the authors has realized such computation for the first time. Accurate simulation of the vibrational structure of these compounds has been hampered by their notorious multiconfigurational electronic structure that yields bond distances that do not correlate with bond order. Some measured Cr–Cr vibrational stretching modes, ν(Cr 2 ), have suggested weaker bonding, even for so-called ultrashort Cr–Cr bonds, while others are in line with the bond distance. Here, we optimize geometries and compute ν(Cr 2 ) with CASPT2 for three well-characterized complexes, Cr 2 (O 2 CCH 3 ) 4 (H 2 O) 2 , Cr 2 (mhp) 4 , and Cr 2 (dmp) 4 . We obtain CASPT2 harmonic ν(Cr 2 ) modes in good agreement with experiment at 282 cm –1 for Cr 2 (mhp) 4 and 353 cm –1 for Cr 2 (dmp) 4 , compute 50 Cr and 54 Cr isotope shifts, and demonstrate that the use of the so-called IPEA shift leads to improved Cr–Cr distances. Additionally, normal mode sampling was used to estimate anharmonicity along ν(Cr 2 ), leading to an anharmonic mode of 272 cm –1 for Cr 2 (mhp) 4 and 333 cm –1 for Cr 2 (dmp) 4 .

36 MATERIALS SCIENCE↗

Cis-Divacant Octahedral Fe(II) in a Dimensionally Reduced Family of 2-(Pyridin-2-yl)pyrrolide Complexes

Four-coordinate transition metal complexes can adopt a diverse array of coordination geometries, with square planar and tetrahedral coordination being the most prevalent. Previously, we reported the synthesis of a trinuclear Fe(II) complex, Fe 3 TPM 2 , supported by a three-fold symmetric 2-pyridylpyrrolide ligand (i.e., tris(5-(pyridin-2-yl)-1H-pyrrol-2-yl)methane), that featured a rare cis-divacant octahedral (CDO) geometry at each Fe(II) center. Here, a series of truncated 2-pyridylpyrrolide ligands is described that support mono- and binuclear Fe(II) complexes that also exhibit CDO geometries. Metallation of tetradentate ligand bis(5-(pyridin-2-yl)-1H-pyrrol-2-yl)methane (H 2 BPM) in THF results in a binuclear complex Fe 2 (BPM) 2 (THF) 2 in which both Fe(II) ions are octahedrally coordinated. The coordinated THF solvent ligands are labile: THF dissociation leads to Fe 2 (BPM) 2 , which features five-coordinate Fe(II) ions. The Fe–Fe distance in these binuclear complexes can be elongated by ligand methylation. Metalation of bis(5-(6-methylpyridin-2-yl)-1H-pyrrol-2-yl)methane (H 2 BPM Me ) in THF leads to the formation of four-coordinate, CDO Fe(II) centers in Fe(BPM Me ) 2 . Further ligand truncation affords bidentate ligands 2-(1H-pyrrol-2-yl)pyridine (PyrPyrrH) and 2-methyl-6-(1H-pyrrol-2-yl)pyridine (Pyr Me PyrrH). Metalation of these ligands in THF affords six-coordinate complexes Fe(PyrPyrr) 2 (THF) 2 and Fe(Pyr Me Pyrr) 2 (THF) 2 . Dissociation of labile solvent ligands provides access to fourcoordinate Fe(II) complexes. Ligand disproportionation at Fe(PyrPyrr) 2 results in the formation of Fe(PyrPyrr) 3 and Fe(0). Ligand methylation suppresses this disproportionation and enables isolation of Fe(Pyr Me Pyrr) 2 , which is rigorously CDO. Complete ligand truncation, by separating the 2-pyridylpyrrolide ligands into the constituent monodentate pyridyl and pyrrolide donors, affords Fe(Pyr) 2 (Pyrr) 2 in which the Fe(II) is tetrahedrally coordinated. Computational analysis indicates that the potential energy surface that dictates the coordination geometry in this family of four-coordinate complexes is fairly flat in the vicinity of CDO coordination. Furthermore, these synthetic studies provide the structural basis to explore the implications of CDO geometry on Fe-catalyzed reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Opportunities for enhancing MLCommons efforts while leveraging insights from educational MLCommons earthquake benchmarks efforts

MLCommons is an effort to develop and improve the artificial intelligence (AI) ecosystem through benchmarks, public data sets, and research. It consists of members from start-ups, leading companies, academics, and non-profits from around the world. The goal is to make machine learning better for everyone. In order to increase participation by others, educational institutions provide valuable opportunities for engagement. In this article, we identify numerous insights obtained from different viewpoints as part of efforts to utilize high-performance computing (HPC) big data systems in existing education while developing and conducting science benchmarks for earthquake prediction. As this activity was conducted across multiple educational efforts, we project if and how it is possible to make such efforts available on a wider scale. This includes the integration of sophisticated benchmarks into courses and research activities at universities, exposing the students and researchers to topics that are otherwise typically not sufficiently covered in current course curricula as we witnessed from our practical experience across multiple organizations. As such, we have outlined the many lessons we learned throughout these efforts, culminating in the need for benchmark carpentry for scientists using advanced computational resources. The article also presents the analysis of an earthquake prediction code benchmark while focusing on the accuracy of the results and not only on the runtime; notedly, this benchmark was created as a result of our lessons learned. Energy traces were produced throughout these benchmarks, which are vital to analyzing the power expenditure within HPC environments. Additionally, one of the insights is that in the short time of the project with limited student availability, the activity was only possible by utilizing a benchmark runtime pipeline while developing and using software to generate jobs from the permutation of hyperparameters automatically. It integrates a templated job management framework for executing tasks and experiments based on hyperparameters while leveraging hybrid compute resources available at different institutions. The software is part of a collection called cloudmesh with its newly developed components, cloudmesh-ee (experiment executor) and cloudmesh-cc (compute coordinator).

58 GEOSCIENCES↗

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures

Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures of multi-protein complexes and other macromolecular machines. A standalone prototype data resource for integrative structures called PDB-Dev was built, based on recommendations of the Integrative and Hybrid Methods (IHM) Task Force of the Worldwide Protein Data Bank (wwPDB). This effort included developing data standards and software tools for collecting, curating, validating, visualizing, archiving, and disseminating integrative structures that span diverse spatiotemporal scales and conformational states. Mechanisms have been created to validate integrative structures based on the experimental data underpinning them. Building upon this foundational framework, PDB-Dev has been further expanded to handle large dynamic macromolecular systems and integrative structures that combine, for example, experimental restraints with atomic coordinates computed by machine learning algorithms. Data standards and supporting tools have also been extended to capture information about biomolecular dynamics, such as conformational transitions and related kinetic data derived from biophysical methods. Recently, PDB-Dev was unified with the PDB archive and rebranded as PDB-IHM (pdb-ihm.org), further promoting FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data stewardship for integrative structural biology.

IHMCIF↗

Understanding the TiH (2-x) /TiO y System at Elevated Temperature: A Literature Review

Titanium hydride of varying TiH stoichiometry is used in pyrotechnic compositions. In order to yield consistent performance, manufacturing processes must be developed to ensure precise and reproducible material properties, including composition and morphology. Legacy synthesis protocols are not comprehensive nor are the required apparatuses still available. To guide the development of novel production procedures, this report reviews literature on relevant chemical reactions and diffusion events occurring at elevated temperature in the TiH (2-x) /TiO y system. Titanium hydride exposed to air spontaneously forms a passivating oxide layer. Upon heating, significant hydrogen release, which is accompanied by changes to the surface oxide layer, is noted by 375–400°C. At higher temperatures (above about 500°C) the oxide layer is reported to be essentially nonexistent as a result of oxide-layer dissolution processes and, potentially, oxide-layer reduction due to water formation. Based on the reviewed literature, we hypothesize that, by 500°C, the surface layer consists of an oxyhydride phase, which is a solid solution of oxygen in titanium hydride. We believe that hydrogen release from titanium hydride is controlled by the kinetics of molecular hydrogen desorption on the oxyhydride surface. No literature data is available for corresponding activation energies of the dynamic desorption process, and the equilibrium phase diagram of this three-component system remains largely unexplored as well. These gaps in knowledge might be addressed through coordinated computational modeling and experimental efforts.

36 MATERIALS SCIENCE↗

Connecting cation site location to alkane dehydrogenation activity in Ni/BEA catalysts

Ni-modified beta zeolite (Ni/BEA) catalysts activate carbon-hydrogen bonds in light alkanes, as demonstrated through isobutane reaction testing. Controlled synthesis of Ni/BEA allows for efficient introduction of ion-exchanged Ni sites at varying Ni loadings (0.43% - 1.8%). These catalysts exhibit site time yields (STY) for H2 production that increase with increasing Ni loading. A detailed analysis of secondary reactions and carbon deposition based on the relative molar flowrates of product C and H indicates that the observed increase in H2 STY with increasing Ni loading is likely attributed to both increasing alkane activation activity and increasing formation of hydrogen-deficient aromatic products retained within the catalyst pores. In situ diffuse-reflectance UV-visible-NIR absorbance and X-ray absorption spectroscopies indicate isolated, 4-coordinate Ni(2+) species for all loadings. Quantum mechanics/molecular mechanics modeling identifies two distinct Ni(2+) sites consistent with the structural characterization, but with differing relative stabilities due to their coordination environment. Computed reaction energetics for isobutane dehydrogenation demonstrate that the more stable Ni(2+) species at a six-membered 4Si-2Al ring, Ni-6MR, is less active for isobutane dehydrogenation than the less stable Ni(2+) at the five-membered 3Si-2Al ring, Ni-5MR. The differing local structure of the isolated cationic Ni sites in Ni/BEA offers a possible rationalization for the increased H2 STY observed at greater Ni loadings.

catalysts↗

Computation of generalised magnetic coordinates asymptotically close to the separatrix

Integrals to calculate generalised magnetic coordinates from an input magnetic flux function asymptotically close to the separatrix are presented, and implemented in the GPEC/DCON code suite. These integrals allow characterisation of the magnetic equilibrium of a diverted tokamak, in magnetic coordinates, arbitrarily close to the last closed flux surface, avoiding the numerical issues associated with calculating diverging field-line integrals near a magnetic x-point. Finally, these methods may assist ongoing efforts to develop robust asymptotic equilibrium behaviour for spectral 3D MHD codes at the separatrix.

equilibrium edge truncation↗

Reading Error Analysis (REA) Software Version 1

This is training presentation for REA (Reading Error Analysis) software. REA is designed for analyzing UGT scope reading errors and for developing reading points optimization algorithms.

97 MATHEMATICS AND COMPUTING↗

Direct computation of magnetic surfaces in Boozer coordinates and coil optimization for quasisymmetry

We propose a new method to compute magnetic surfaces that are parametrized in Boozer coordinates for vacuum magnetic fields. We also propose a measure for quasisymmetry on the computed surfaces and use it to design coils that generate a magnetic field that is quasisymmetric on those surfaces. The rotational transform of the field and complexity measures for the coils are also controlled in the design problem. Using an adjoint approach, we are able to obtain analytic derivatives for this optimization problem, yielding an efficient gradient-based algorithm. Starting from an initial coil set that presents nested magnetic surfaces for a large fraction of the volume, our method converges rapidly to coil systems generating fields with excellent quasisymmetry and low particle losses. In particular for low complexity coils, we are able to significantly improve the performance compared with coils obtained from the standard two-stage approach, e.g. reduce losses of fusion-produced alpha particles born at half-radius from $17.7\,\%$ to $6.6\,\%$ . We also demonstrate 16-coil configurations with alpha loss ${<}1\,\%$ and neoclassical transport magnitude $\epsilon _{\text {eff}}^{3/2}$ less than approximately $5\times 10^{-9}$ .

Physics↗

A Holistic Approach for Elucidating Local Structure, Dynamics, and Speciation in Molten Salts with High Structural Disorder

To examine ion solvation, exchange, and speciation for minority components in molten salts (MS) typically found as corrosion products, we propose a multimodal approach combining extended X-ray absorption fine structure (EXAFS) spectroscopy, optical spectroscopy, ab initio molecular dynamics (AIMD) simulations, and rate theory of ion exchange. Going beyond conventional EXAFS analysis, our method can accurately quantify populations of different coordination states of ions with highly disordered coordination environments via linear combination fitting of the EXAFS spectra of these coordination states computed from AIMD to the experimental EXAFS spectrum. In a case study of dilute Ni(II) dissolved in the ZnCl 2 +KCl melts, our method reveals heterogeneous distributions of coordination states of Ni(II) that are sensitive to variations in temperature and melt composition. These results are fully explained by the difference in the chloride exchange dynamics at varied temperatures and melt compositions. Finally, this insight will enable a better understanding and control of ion solubility and transport in MS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Author Correction: US oil and gas system emissions from nearly one million aerial site measurements

Correction to: Naturehttps://doi.org/10.1038/s41586-024-07117-5 Published online 13 March 2024 In the version of the article initially published, several errors were present and have been corrected in the HTML and PDF versions of the article and Supplementary Information. The main results, conclusions, and our interpretations of the data remain unchanged. See the new Supplementary Information Section S15 for a more detailed description of the errors corrected and the resulting effects on the analysis. Data processing and methods corrections Overflight count correction: We previously used pre-computed source coverage data for some Carbon Mapper campaigns that was computed differently than was required for our analysis. We have re-computed Carbon Mapper source coverage based on flightline polygons and source coordinates. Transition point computation, well sites: The updated version now correctly compares the cumulative emissions distribution of simulated well site emissions with that of aerially detected sources (rather than plumes) when computing the transition point. Transition point computation, midstream: Additionally, the transition point calculation has been corrected to exclude aerially detected midstream emissions below the transition point, which was previously leading to double counting of these emissions. This error was not present for upstream (well site) emissions. Calculation errors Unit error: We corrected a specific unit conversion error affecting well site emissions in the Kairos Fort Worth dataset. Across all datasets, we also correct the conversion factor for converting from standard volume to mass for midstream emissions. Sorting error: We correct code that was applying incorrect sorting when computing correction factors to account for partial detection at well sites. Small typographical corrections were made in Fig. 1b and SI Section S4.1. Data processing and methods corrections Overflight count correction: We previously used pre-computed source coverage data for some Carbon Mapper campaigns that was computed differently than was required for our analysis. We have re-computed Carbon Mapper source coverage based on flightline polygons and source coordinates. Transition point computation, well sites: The updated version now correctly compares the cumulative emissions distribution of simulated well site emissions with that of aerially detected sources (rather than plumes) when computing the transition point. Transition point computation, midstream: Additionally, the transition point calculation has been corrected to exclude aerially detected midstream emissions below the transition point, which was previously leading to double counting of these emissions. This error was not present for upstream (well site) emissions. Calculation errors Unit error: We corrected a specific unit conversion error affecting well site emissions in the Kairos Fort Worth dataset. Across all datasets, we also correct the conversion factor for converting from standard volume to mass for midstream emissions. Sorting error: We correct code that was applying incorrect sorting when computing correction factors to account for partial detection at well sites. Small typographical corrections were made in Fig. 1b and SI Section S4.1. The following practices may help researchers conducting similar analyses avoid making similar errors: 1, Clear, accessible documentation explaining the interpretation of all columns in data input tables and all internal variables within the model, 2, Simple cross-check calculations computed before and after unit conversions.

Sherwin, Evan D↗

Spherical fitting for oscilloscope film trace reading

This report describes a spherical fitting algorithm that can be used for estimating the oscilloscope film trace coordinates. This algorithm was adopted from a least square algebraic spherical fitting algorithm developed by the author earlier for photovoltaic velocimetry applications. Preliminary assessment suggests that the algorithm may be used for optimizing the coordinates manually digitized by the user, or may be used as an uncertainty estimator for the user’s film reading uncertainties.

97 MATHEMATICS AND COMPUTING↗

Coordinate Transformations

This whitepaper provides details for the background, conventions, definitions, transformation equations, examples, and implementation used in the Solid Body Geometry (SBG) transformations in Monte Carlo Application ToolKit (MCATK).

97 MATHEMATICS AND COMPUTING↗

Hydrated Metal and Metal-Nitrate Complexes in Water: Full Lanthanide(III) Series plus Miscellaneous Metal Ions

This is a dataset of hydrated metal complexes and metal–nitrate hydrated complexes intended for public use, reproducibility, and downstream structural analysis. A key feature is coverage across the full lanthanide(III) series (La–Lu), enabling systematic comparisons of coordination motifs and bonding trends across the entire lanthanide sequence. In addition to the lanthanides, the dataset also includes other metal ions such as UO2(VI), Fe(II), and Fe(III). The dataset provides optimized geometries for hydrated and nitrate-containing hydrated complexes, together with representative ab initio molecular dynamics (AIMD) trajectories saved in standard XYZ formats. The accompanying NWChem input decks enable reproduction of the reported calculations and provide a starting point for extending the simulations to related coordination environments. Computationally, DFT calculations employ the B3LYP functional with DFT-D3BJ dispersion corrections and a COSMO continuum solvent model (dielectric constant 78.4) to represent solvation beyond the explicitly treated first hydration shell. AIMD simulations are performed with the NWChem qmd module at 298 K, integrating nuclear motion with the velocity-Verlet algorithm and controlling temperature using a Nosé–Hoover thermostat. Trajectories are approximately 4.8 ps in length and are used primarily to assess short-time stability of candidate coordination motifs, including (for lanthanides) differences between 8- versus 9-water coordination and comparisons between nitrate-bound and nitrate-free hydrated complexes.

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗

Blueprint: Coordinated Vulnerability Disclosure (CVD) Adoption for Information Sharing and Analysis Center (ISAC)-Like Groups

The electric vehicle supply equipment (EVSE) industry is an incredibly diverse set of participants (EVSE manufacturers, charge network operators (CNOs), original equipment manufacturers (OEMs), etc.), and with the potential for an Information Sharing and Analysis Centers (ISAC) or ISAC-like group, it requires a series of guidance for doing a multiparty coordinated vulnerability disclosure (CVD) such that a group like this could be successful. This blueprint provides a template and guidance to stakeholders in the EVSE industry for conducting a multiparty CVD. It also formalizes what multiparty CVD could look like in an ISAC-like group with multiple entities as well as vulnerability coordinators by specifically calling out who in the ISAC-like group may be involved, and which industry members it may apply to. This blueprint leverages tools such as Vultron, VINCE, etc. along with open resources such as the Software Engineering Institutes guide for coordinated vulnerability disclosure, for the stakeholder in the EVSE industry to start up a CVD program of their own.

97 MATHEMATICS AND COMPUTING↗

Characterizing 4-string contact interaction using machine learning

Abstract The geometry of 4-string contact interaction of closed string field theory is characterized using machine learning. We obtain Strebel quadratic differentials on 4-punctured spheres as a neural network by performing unsupervised learning with a custom-built loss function. This allows us to solve for local coordinates and compute their associated mapping radii numerically. We also train a neural network distinguishing vertex from Feynman region. As a check, 4-tachyon contact term in the tachyon potential is computed and a good agreement with the results in the literature is observed. We argue that our algorithm is manifestly independent of number of punctures and scaling it to characterize the geometry ofn-string contact interaction is feasible.

Physics↗

An Eulerian Vlasov-Fokker–Planck algorithm for spherical implosion simulations of inertial confinement fusion capsules

Here, we present a numerical algorithm that enables a phase-space adaptive Eulerian Vlasov–Fokker–Planck (VFP) simulation of inertial confinement fusion (ICF) capsule implosions. The approach relies on extending a recent mass, momentum, and energy conserving phase-space moving-mesh adaptivity strategy to spherical geometry. In configuration space, we employ a mesh motion partial differential equation (MMPDE) strategy while, in velocity space, the mesh is expanded/contracted and shifted with the plasma’s evolving temperature and drift velocity. The mesh motion is dealt with by transforming the underlying VFP equations into a computational (logical) coordinate, with the resulting inertial terms carefully discretized to ensure conservation. To deal with the spatial and temporally varying dynamics in a spherically imploding system, we have developed a novel nonlinear stabilization strategy for MMPDE in the configuration space. The strategy relies on a nonlinear optimization procedure that optimizes between mesh quality and the volumetric rate change of the mesh to ensure both accuracy and stability of the solution. Implosions of ICF capsules are driven by several boundary conditions: (1) an elastic moving wall boundary; (2) a time-dependent Maxwellian Dirichlet boundary; and (3) a pressure-driven Lagrangian boundary. Of these, the pressure-driven Lagrangian boundary driver is new to our knowledge. The implementation of our strategy is verified through a set of test problems, including the Guderley and Van-Dyke implosion problems — the first-ever reported using a Vlasov–Fokker–Planck model.

1D2V↗

Solution Structures of Europium Terpyridyl Complexes with Nitrate and Triflate Counterions in Acetonitrile

Lanthanide–ligand complexes are key components of technological applications, and their properties depend on their structures in the solution phase, which are challenging to resolve experimentally or computationally. The coordination structure of the Eu 3+ ion in different coordination environments in acetonitrile is examined using ab initio molecular dynamics (AIMD) simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy. AIMD simulations are conducted for the solvated Eu 3+ ion in acetonitrile, both with or without a terpyridyl ligand, and in the presence of either triflate or nitrate counterions. EXAFS spectra are calculated directly from AIMD simulations and then compared to experimentally measured EXAFS spectra. In acetonitrile solution, both nitrate and triflate anions are shown to coordinate directly to the Eu 3+ ion forming either ten- or eight-coordinate solvent complexes where the counterions are binding as bidentate or monodentate structures, respectively. Coordination of a terpyridyl ligand to the Eu 3+ ion limits the available binding sites for the solvent and anions. In certain cases, the terpyridyl ligand excludes any solvent binding and limits the number of coordinated anions. The solution structure of the Eu-terpyridyl complex with nitrate counterions is shown to have a similar arrangement of Eu 3+ coordinating molecules as the crystal structure. Finally, this study illustrates how a combination of AIMD and EXAFS can be used to determine how ligands, solvent, and counterions coordinate with the lanthanide ions in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗