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At least 379 records · Page 21

High-throughput calculations of charged point defect properties with semi-local density functional theory—performance benchmarks for materials screening applications

Abstract Calculations of point defect energetics with Density Functional Theory (DFT) can provide valuable insight into several optoelectronic, thermodynamic, and kinetic properties. These calculations commonly use methods ranging from semi-local functionals with a-posteriori corrections to more computationally intensive hybrid functional approaches. For applications of DFT-based high-throughput computation for data-driven materials discovery, point defect properties are of interest, yet are currently excluded from available materials databases. This work presents a benchmark analysis of automated, semi-local point defect calculations with a-posteriori corrections, compared to 245 “gold standard” hybrid calculations previously published. We consider three different a-posteriori correction sets implemented in an automated workflow, and evaluate the qualitative and quantitative differences among four different categories of defect information: thermodynamic transition levels, formation energies, Fermi levels, and dopability limits. We highlight qualitative information that can be extracted from high-throughput calculations based on semi-local DFT methods, while also demonstrating the limits of quantitative accuracy.

36 MATERIALS SCIENCE↗

Multi-approach assessment of the spatial distribution of the specific yield: application to the Crau plain aquifer, France

Spatially distributed values of the specific yield, a fundamental parameter for transient groundwater mass balance calculations, were obtained by means of three independent methods for the Crau plain, France. In contrast to its traditional use to assess recharge based on a given specific yield, the water-table fluctuation (WTF) method, applied using major recharging events, gave a first set of reference values. Then, large infiltration processes recorded by monitored boreholes and caused by major precipitation events were interpreted in terms of specific yield by means of a one-dimensional vertical numerical model solving Richards’ equations within the unsaturated zone. Finally, two gravity field campaigns, at low and high piezometric levels, were carried out to assess the groundwater mass variation and thus alternative specific yield values. The range obtained by the WTF method for this aquifer made of alluvial detrital material was 2.9– 26%, in line with the scarce data available so far. The average spatial value of specific yield by the WTF method (9.1%) is consistent with the aquifer scale value from the hydro-gravimetric approach. In this investigation, an estimate of the hitherto unknown spatial distribution of the specific yield over the Crau plain was obtained using the most reliable method (the WTF method). A groundwater mass balance calculation over the domain using this distribution yielded similar results to an independent quantification based on a stable isotope-mixing model. This agreement reinforces the relevance of such estimates, which can be used to build a more accurate transient hydrogeological model.

58 GEOSCIENCES↗

A new set of potential energy surfaces for HCO: Influence of Renner-Teller coupling on the bound and resonance vibrational states

It is commonly understood that the Renner-Teller effect can strongly influence the spectroscopy of molecules through coupling of electronic states. Here we investigate the vibrational bound states and low-lying resonances of the formyl radical treating the Renner-Teller coupled $ \tilde{X} $ 2 A' and à 2 A" states using the MultiConfiguration Time Dependent Hartree (MCTDH) method. The calculations were performed using the improved relaxation method for the bound states and a recently published extension to compute resonances. A new set of accurate global potential energy surfaces were computed at the explicitly correlated multireference configuration interaction (MRCI-F12) level and yielded remarkably close agreement with experiment in this application and thus enable future studies including photodissociation and collisional dynamics. Here, the results show the necessity of including the large contribution from a Davidson correction in the electronic structure calculations in order to appreciate the relatively small effect of the Renner-Teller coupling on the states considered here.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NEOS Data and the Origin of the 5 MeV Bump in the Reactor Antineutrino Spectrum

We perform a combined analysis of recent NEOS and Daya Bay data on the reactor antineutrino spectrum. This analysis includes approximately 1.5 million antineutrino events, which is the largest neutrino event sample analyzed to date. We use a double ratio which cancels flux model dependence and related uncertainties as well as the effects of the detector response model. We find at 3–4 standard deviation significance level, that plutonium-239 and plutonium-241 are disfavored as the single source for the so-called 5 MeV bump. This analysis method has general applicability and, in particular, with higher statistics data sets, will be able to shed significant light on the issue of the bump. With some caveats, this should also allow us to improve the sensitivity for sterile neutrino searches in NEOS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Asynchronous Truncated Multigrid-Reduction-in-Time

In this paper, we present the new “asynchronous truncated multigrid-reduction-in-time” (AT-MGRIT) algorithm for introducing time parallelism to the solution of discretized time-dependent problems. The new algorithm is based on the multigrid-reduction-in-time (MGRIT) approach, which, in certain settings, is equivalent to another common multilevel parallel-in-time method, Parareal. In contrast to Parareal and MGRIT that both consider a global temporal grid over the entire time interval on the coarsest level, the AT-MGRIT algorithm uses truncated local time grids on the coarsest level, each grid covering certain temporal subintervals. Further, these local grids can be solved completely in an independent way from each other, which reduces the sequential part of the algorithm and, thus, increases parallelism in the method. Here, we study the effect of using truncated local coarse grids on the convergence of the algorithm, both theoretically and numerically, and show, using challenging nonlinear problems, that the new algorithm consistently outperforms classical Parareal/MGRIT in terms of time to solution.

97 MATHEMATICS AND COMPUTING↗

Control optimization for parametric Hamiltonians by pulse reconstruction

Optimal control techniques provide a means to tailor the control pulses required to generate customized quantum gates, which helps to improve the resilience of quantum simulations to gate errors and device noise. However, the significant amount of (classical) computation required to generate customized gates can quickly undermine the effectiveness of this approach, especially when pulse optimization needs to be iterated. We propose a method to reduce the computational time required to generate the control pulse for a Hamiltonian that is parametrically dependent on a time-varying quantity. We use simple interpolation schemes to accurately reconstruct the control pulses from a set of pulses obtained in advance for a discrete set of predetermined parameter values. We obtain a reconstruction with very high fidelity and a significant reduction in computational effort. We report the results of the application of the proposed method to device-level quantum simulations of the unitary (real) time evolution of two interacting neutrons based on superconducting qubits.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

SIERRA Multimechanics Module: Aria User Manual - Version 4.56

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process ows via the incompressible Navier-Stokes equations specialized to a low Reynolds number (Re < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newtons method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic h-adaptivity and dynamic load balancing are some of Arias more advanced capabilities.

97 MATHEMATICS AND COMPUTING↗

SIERRA Multimechanics Module: Aria Thermal Theory Manual - Version 4.58

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number (R e < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newtons method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic-adaptivity and dynamic load balancing are some of Arias more advanced capabilities.

42 ENGINEERING↗

SIERRA Multimechanics Module: Aria User Manual - Version 4.58

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number ( %3C 1 ) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newtons method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic -adaptivity and dynamic load balancing are some of Arias more advanced capabilities.

97 MATHEMATICS AND COMPUTING↗

SIERRA Multimechanics Module: Aria User Manual (V.5.0)

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process %1Cows via the incompressible Navier-Stokes equations specialized to a low Reynolds number (Re < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newtons method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic h-adaptivity and dynamic load balancing are some of Arias more advanced capabilities.

97 MATHEMATICS AND COMPUTING↗

SIERRA Multimechanics Module: Aria Thermal Theory Manual (V.5.0)

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number ( Re < 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newtons method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic -adaptivity and dynamic load balancing are some of Arias more advanced capabilities.

97 MATHEMATICS AND COMPUTING↗

Digitalization, Management and Synthesis of Thermal Hydraulic Legacy Data Using Dynamical System Scaling

A unique attribute of the nuclear industry is the extent by which designers, developers, operators, and regulators pay attention to demonstrating the safety case. The safety case for nuclear systems is a written, traceable expression of safety, demonstrating the system’s protective measures against uncontrolled radiological releases. The nuclear installation resiliency or safety takes overriding priority over function and performance. The preparation of the safety case heavily relies on extensive experimental campaigns that challenge the target design under a spectrum of postulated accident scenarios. For safety reasons, these experiments are typically conducted in sub-scale test apparatuses intended to reproduce the postulated accident scenarios and event sequences realistically but subject to proven similarity criteria, often referred to as scaling analyses. Since the dawn of the nuclear industry, significant resources have been committed to the construction and operation of such test facilities and a massive amount of data has been generated. Such test data have been and are still used to validate the fundamental assumptions of nuclear power plant phenomena. As we move into the digital world, capturing this multi-decades worth of information in a transparent, easily accessible, and usable manner for the public and industry stakeholders is of paramount importance. Over the last few years FPoliSolutions has been actively developing an enterprise digital data ontology platform (FPoliDON) intended to do just that. The concept was introduced in a paper at the previous NURETH edition and has been significantly enhanced since. With the vision of helping designers use the data to assess their safety case evaluation models, the platform was designed not only to ontologically organize the experimental data, but also to guide the user in the complex analytics associated with the interpretation and use of such test results. A new feature which has been recently added is the ability for the user to access a library of sophisticated mathematical procedures for performing scaling analyses. For this purpose, the Dynamical System Scaling (DSS) procedure invented by Dr. Jose’ Reyes was formulated as one of the services in the digital platform. These methods have been demonstrated to provide an excelled mathematical apparatus to identify similarity criteria or quantify distortions between measured data and the target prototypical conditions. Moreover, DSS can provide a level of synthesis across SETs and IETs which has the promise to yield efficiency in the evaluation code assessment activities. This is often a daunting and expensive task to set up evaluation models that support the safety case of current and future nuclear power plants.

Reyes, Jose↗

Electronic Energies Are Not Enough: An Ion Mobility-Aided, Quantum Chemical Benchmark Analysis of H + GPGG Conformers

Peptides and proteins exist not as single, lowest energy structures but as ensembles of states separated by small barriers. In order to study these species we must be able to correctly identify their gas phase conformational distributions, and ion mobility spectrometry (IMS) has arisen as an experimental method for assessing the gas phase energetics of flexible peptides. Here, we present a thorough exploration and benchmarking of the low energy conformers of the small, hairpin peptide H+ GPGG with the aid of ion mobility spectrometry against a wide swath of density functionals (35 dispersion-corrected and uncorrected functionals represented by 21 unique exchange–correlation functionals) and wave function theory methods (15 total levels of theory). The three experimentally resolved IMS peaks were found to correspond to three distinct pairs of conformers, each pair composed of species differing only by the chair or boat configuration of the proline. Two of the H+ GPGG conformer pairs possess a cis configuration about the Pro–Gly1 peptide bond while the other adopts a trans configuration. While the experimental spectrum reports a higher intensity for the cis-1 conformer than the trans conformer, 13 WFT levels of theory, including a complete basis set CCSD(T) extrapolation, obtain trans to be favored in terms of the electronic energy. This same effect is seen in 14 of the 18 dispersion-corrected density functionals studied, whereas the remaining 17 functionals show more variety. Only when Gibbs free energies are considered do the WFT methods and dispersion-corrected functionals reflect the experimental distribution. CAM-B3LYP-D3BJ emerges as the best-performing density functional, matching the experimental distribution and the CCSD(T)/CBS relative energies within 6%. Further analysis reveals the trans conformer to be favored electronically, but entropically disfavored, leading to the experimental preference of the cis-1 conformer. Furthermore, these results highlight the danger in considering only the electronic energies, which is common practice in electronic structure theory predictions of conformational energy distributions. Additionally, the effects of temperature and scaling of the frequencies used in obtaining the Gibbs free energies are explored.

Energy↗

SU-F-R-36: Validating Quantitative Radiomic Texture Features for Oncologic PET: A Digital Phantom Study

Purpose: Radiomic texture features derived from the oncologic PET have recently been brought under intense investigation within the context of patient stratification and treatment outcome prediction in a variety of cancer types; however, their validity has not yet been examined. This work is aimed to validate radiomic PET texture metrics through the use of realistic simulations in the ground truth setting. Methods: Simulation of FDG-PET was conducted by applying the Zubal phantom as an attenuation map to the SimSET software package that employs Monte Carlo techniques to model the physical process of emission imaging. A total of 15 irregularly-shaped lesions featuring heterogeneous activity distribution were simulated. For each simulated lesion, 28 texture features in relation to the intensity histograms (GLIH), grey-level co-occurrence matrices (GLCOM), neighborhood difference matrices (GLNDM), and zone size matrices (GLZSM) were evaluated and compared with their respective values extracted from the ground truth activity map. Results: In reference to the values from the ground truth images, texture parameters appearing on the simulated data varied with a range of 0.73–3026.2% for GLIH-based, 0.02–100.1% for GLCOM-based, 1.11–173.8% for GLNDM-based, and 0.35–66.3% for GLZSM-based. For majority of the examined texture metrics (16/28), their values on the simulated data differed significantly from those from the ground truth images (P-value ranges from <0.0001 to 0.04). Features not exhibiting significant difference comprised of GLIH-based standard deviation, GLCO-based energy and entropy, GLND-based coarseness and contrast, and GLZS-based low gray-level zone emphasis, high gray-level zone emphasis, short zone low gray-level emphasis, long zone low gray-level emphasis, long zone high gray-level emphasis, and zone size nonuniformity. Conclusion: The extent to which PET imaging disturbs texture appearance is feature-dependent and could be substantial. It is thus advised that use of PET texture parameters for predictive and prognostic measurements in oncologic setting awaits further systematic and critical evaluation.

60 APPLIED LIFE SCIENCES↗

Push it to the limit: comparing periodic and local approaches to density functional theory for intermolecular interactions

With the aim of systematically comparing two popular approaches to density functional theory–all-electron calculations with local basis sets, and periodic calculations employing plane wave basis sets and norm-conserving pseudopotentials–we have computed complete-basis binding energies across the S22 set of intermolecular interactions, a dataset consisting of noncovalent interactions of small- and medium-sized molecules containing first- and second-row atoms, using the Troullier-Martins norm-conserving pseudopotentials with SPW92, a local spin-density approximation; and PBE, a generalised gradient approximation. Here, we have found that it is challenging to reach the basis set limit with these periodic calculations; for the methods and systems examined, a minimum vacuum distance of 30 Å between a system and its nearest images is necessary–unless some form of dipole correction is employed–as is a kinetic energy cutoff of at least 80 Ry. The trends in convergence with respect to vacuum size and kinetic energy cutoff are largely independent of the level of density functional approximation employed. A sense of the impact of each hyperparameter on basis set error provides a foundation for ensuring quality calculations in future studies and allows us to quantify the basis set errors incurred in existing studies on similar systems.

74 ATOMIC AND MOLECULAR PHYSICS↗

Green’s Function Coupled-Cluster Approach: Simulating Photoelectron Spectra for Realistic Molecular Systems

In this paper we present an efficient implementation for the analytical energy- dependent coupled cluster Green’s function with singles and doubles (GFCCSD) approach with our first practice being computing spectral functions of real molecular systems. Due to its algebraic structure, the presented method is highly scalable, and is capable of computing spectral function for a given molecular system in any energy region. Several typical examples have been given to demonstrate its capability of computing spectral functions not only in the valence band, but also in the core-level energy region. Satellite peaks have been observed in the inner valence band and core-level energy region where many-body effect becomes significant and single particle picture of ionization often breaks down. The accuracy test has been carried out by extensively comparing our GFCCSD results with experimental results as well as the theoretical results from other methods. It turns out GFCCSD method is able to provide qualitative or semi-quantitative level of description of ionization processes in both the core and valence regimes. To significantly improve the GFCCSD results for the main states, larger basis set can usually be employed, whereas the improvement of the GFCCSD results for the satellite states needs higher order many-body terms to be included in the GFCC implementation.

electronic structure theory↗

Guided ion beam and theoretical studies of the bond energy of SmS +

Previous work has shown that atomic samarium cations react with carbonyl sulfide to form SmS + + CO in an exothermic and barrierless process. To characterize this reaction further, the bond energy of SmS + is determined in the present study using guided ion beam tandem mass spectrometry. Reactions of SmS + with Xe, CO, and O 2 are examined. Results for collision-induced dissociation processes with all three molecules along with the endothermicity of the SmS + + CO → Sm + + COS exchange reaction are combined to yield D 0 (Sm + –S) = 3.37 ± 0.20 eV. The CO and O 2 reactions also yield a SmSO + product, with measured endothermicities that indicate D 0 (SSm + –O) = 3.73 ± 0.16 eV and D 0 (OSm + –S) = 1.38 ± 0.27 eV. The SmS + bond energy is compared with theoretical values characterized at several levels of theory, including CCSD(T) complete basis set extrapolations using all-electron basis sets. Multireference configuration interaction calculations with explicit spin-orbit calculations along with composite thermochemistry using the Feller-Peterson-Dixon method and all-electron basis sets were also explored for SmS+, and for comparison, SmO, SmO + , and EuO

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. Furthermore, a more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.

09 BIOMASS FUELS↗