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DOE OSTI2022

An immersed interface method for the 2D vorticity-velocity Navier-Stokes equations with multiple bodies

We present an immersed interface method for the vorticity-velocity form of the 2D Navier Stokes equations that directly addresses challenges posed by nonconvex immersed bodies, multiply connected domains, and the calculation of force distributions on immersed surfaces. The immersed interface method is re-interpreted as a polynomial extrapolation of flow quantities and boundary conditions into the immersed solid bodies, reducing computational cost and enabling simulations with nonconvex bodies that could not be discretized with previous immersed interface methods. In the flow, the vorticity transport equation is discretized using a conservative finite difference scheme and explicit Runge-Kutta time integration. The velocity reconstruction problem is transformed to a scalar Poisson equation that is discretized with conservative finite differences, and solved using an FFT-accelerated iterative algorithm. The use of conservative differencing throughout leads to exact enforcement of a discrete Kelvin's theorem, allowing for simulations with multiply connected domains and outflow boundaries that have challenged other immersed interface vortex methods. We also explore novel methods for recovering time-dependent pressure distributions on immersed bodies within a vorticity-based method and present a novel control volume formulation for recovering aerodynamic moments from only the vorticity and velocity fields. The method achieves second order spatial accuracy and third order temporal accuracy, and is validated on a variety of 2D flows in internal and free-space domains.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Multi-element flow-driven spectral chaos (ME-FSC) method for uncertainty quantification of dynamical systems

The flow-driven spectral chaos (FSC) is a recently developed method for tracking and quantifying uncertainties in the long-time response of stochastic dynamical systems using the spectral approach. The method uses a novel concept called enriched stochastic flow maps as a means to construct an evolving finite-dimensional random function space that is both accurate and computationally efficient in time. In this paper, we present a multi-element version of the FSC method (the ME-FSC method for short) to tackle (mainly) those dynamical systems that are inherently discontinuous over the probability space. In ME-FSC, the random domain is partitioned into several elements, and then the problem is solved separately on each random element using the FSC method. Subsequently, results are aggregated to compute the probability moments of interest using the law of total probability. To demonstrate the effectiveness of the ME-FSC method in dealing with discontinuities and long-time integration of stochastic dynamical systems, four representative numerical examples are presented in this paper, including the Van-der-Pol oscillator problem and the Kraichnan-Orszag three-mode problem. Results show that the ME-FSC method is capable of solving problems that have strong nonlinear dependencies over the probability space, both reliably and at low computational cost.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Effects of surface runoff and infiltration partition methods on hydrological modeling: A comparison of four schemes in two watersheds in the Northeastern US

The ratio according to which the precipitation/snowmelt is divided into surface and subsurface water is of primary importance to watershed scale hydrological modeling. The present study compared four different surface runoff and infiltration partition methods in the Richards-equation-based SWAT model (RSWAT), i.e., daily curve number method (DC-RSWAT), hourly curve number method (HC-RSWAT), Green-Ampt method (GA-RSWAT), and effective infiltration capacity method (EIC-RSWAT). These four versions of RSWAT and a daily-curve-number-based SWAT (DC-SWAT) were used to simulate daily flow rate (from 2001 to 2015) at the outlets of the Tuckahoe Creek Watershed (TCW) and Greensboro Watershed (GW) of the Chesapeake Bay in Maryland. Parameter sensitivity analysis, calibration, and prediction uncertainty analysis were conducted. The results indicate that surface runoff and infiltration partition methods have pronounced impacts on model performance. Comparative analysis showed that DC-RSWAT outperformed other versions of RSWAT for both calibration (from 2001 to2007) and validation (from 2008 to 2015) periods in the two test watersheds. In general, DC-RSWAT achieved more accurate deterministic flow simulation and reliable uncertainty estimation than other versions. As such, daily-curve-number method is recommended for surface runoff and infiltration partition in RSWAT for simulating stream flow.

hydrology, modeling, streamflow↗

DOE OSTI2021

Development of a rapid viability RT-PCR (RV-RT-PCR) method to detect infectious SARS-CoV-2 from swabs

Since the rapid onset of the COVID-19 pandemic, its causative virus, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), continues to spread and increase the number of fatalities. To expedite studies on understanding potential surface transmission of the virus and to aid environmental epidemiological investigations, here we developed a rapid viability reverse transcriptase PCR (RV-RT-PCR) method that detects viable (infectious) SARS-CoV-2 from swab samples in <1 day compared to several days required by current gold-standard cell-culture-based methods. The method integrates cell-culture-based viral enrichment in a 96-well plate format with gene-specific RT-PCR-based analysis before and after sample incubation to determine the cycle threshold (C T ) difference (ΔC T ). An algorithm based on ΔC T ≥ 6 representing ~ 2-log or more increase in SARS-CoV-2 RNA following enrichment determines the presence of infectious virus. The RV-RT-PCR method with 2-hr viral infection and 9-hr post-infection incubation periods includes ultrafiltration to concentrate virions, resulting in detection of <50 SARS-CoV-2 virions in swab samples in 17 h (for a batch of 12 swabs), compared to days typically required by the cell-culture-based method. The SARS-CoV-2 RV-RT-PCR method may also be useful in clinical sample analysis and antiviral drug testing, and could serve as a model for developing rapid methods for other viruses of concern.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

A phase quantification method based on EBSD data for a continuously cooled microalloyed steel

Mechanical properties of steels depend on the phase constitutions of the final microstructures which can be related to the processing parameters. Therefore, accurate quantification of different phases is necessary to investigate the relationships between processing parameters, final microstructures and mechanical properties. Point counting on micrographs observed by optical or scanning electron microscopy is widely used as a phase quantification method, and different phases are discriminated according to their morphological characteristics. However, it is difficult to differentiate some of the phase constituents with similar morphology. Differently, for EBSD based phase quantification methods, besides morphological characteristics, other parameters derived from the orientation information can also be used for discrimination. In this research, a phase quantification method based on EBSD data in the unit of grains was proposed to identify and quantify the complex phase constitutions of a microalloyed steel subjected to accelerated coolings. Characteristics of polygonal ferrite/quasi-polygonal ferrite, acicular ferrite and bainitic ferrite on grain averaged misorientation angles, aspect ratios, high angle grain boundary fractions and grain sizes were analysed and used to develop the identification criteria for each phase. Comparing the results obtained by this EBSD based method and point counting, it was found that this EBSD based method can provide accurate and reliable phase quantification results for microstructures with relatively slow cooling rates. - Highlights: •A phase quantification method based on EBSD data in the unit of grains was proposed. •The critical grain area above which GAM angles are valid parameters was obtained. •Grain size and grain boundary misorientation were used to identify acicular ferrite. •High cooling rates deteriorate the accuracy of this EBSD based method.

36 MATERIALS SCIENCE↗

DOE OSTI2021

A Poisson equation method for prescribing fully developed non-Newtonian inlet conditions for computational fluid dynamics simulations in models of arbitrary cross-section

Prescribing inlet boundary conditions for computational fluid dynamics (CFD) simulations of internal flow in complex geometries such as anatomical vascular models is challenging. In the absence of patient-specific inlet velocity data, a common approach for long blood vessels is to assume that the inlet flow is fully developed. In vessels of irregular cross section, however, prescribing fully developed conditions is complicated due to the lack of a general closed-form analytical solution. In this study, we develop a simple Poisson equation method for prescribing fully developed inlet conditions for the flow of either Newtonian or non-Newtonian fluids in CFD models of arbitrary cross-section. We first derive the generalized Poisson equation for fully developed flow of a non-Newtonian fluid and we then develop and verify a methodology for numerically computing the solution on any planar boundary domain. In addition, we develop a simple extension of the method for prescribing a non-orthogonal inlet velocity that represents fully developed flow from an upstream tube that is connected to the CFD inlet at a non-orthogonal angle. This may be used to investigate a common source of uncertainty in CFD simulations of internal flow that is due to a lack of information concerning the exact streamwise flow direction at the inlets. Comparison to several Newtonian and non-Newtonian benchmark verification solutions shows the method to be extremely accurate. As a practical demonstration case, we use the method to prescribe fully developed conditions on multiple non-circular inlets for the non-Newtonian flow of blood in a patient-specific model of the inferior vena cava (IVC). Finally, we further demonstrate the utility of the method by performing a sensitivity study using the patient-specific IVC model, wherein we investigate the influence of inlet velocity flow direction on the non-Newtonian IVC hemodynamics. Given its simplicity and computational efficiency, the method is shown to be far superior to alternative approaches for prescribing fully developed inlet conditions in such complicated geometries. In conclusion, to facilitate the adoption of our Poisson equation method, we have distributed our OpenFOAM source code and the associated test cases from this study as open-source software.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Enhanced photocatalytic degradation of methylene blue: Preparation of TiO{sub 2}/reduced graphene oxide nanocomposites by direct sol-gel and hydrothermal methods

Highlights: • TiO{sub 2}-RGO nanocomposites presented, in all the cases studied, improved photocatalytic properties compared to bare TiO{sub 2}. • An optimal composition, in terms of TiO{sub 2}/RGO ratio was found in both series nanocomposites. • Nanocomposites of sol-gel method presented improved textural properties than those of hydrothermal method. • Optimization in the preparation, needed to obtain materials with finer properties for effective application in environmental. - Abstract: In this study, two different preparation methods of titanium dioxide nanoparticles/reduced graphene oxide nanocomposites were investigated using direct sol-gel method followed by hydrothermal treatment or simple hydrothermal route. A different amount of graphene (1- 20%) was mixed with TiO{sub 2} for both series of samples in order to improve the photocatalytic activity. The influence of the preparation method on the physico-chemical properties was established by different characterization methods and the photocatalytic degradation of methylene blue (MB) under UV light irradiation was used as test reaction. The highest photocatalytic activity was observed for the nanocomposites containing 10 wt% of graphene. The elimination of MB can reach 93% and 82% for the nanocomposites with 10 wt% graphene prepared by the sol-gel and hydrothermal methods, respectively. These photocatalysts are promising for practical application in nanotechnology.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Development of a high-throughput method for processing sponge-stick samples to detect viable Bacillus anthracis spores

Since the national validation of the sponge-stick based method for detection of Bacillus anthracis spores in environmental samples, there have not been focused efforts to address the low throughput nature of the method, which processes only one sample at one time. Sample processing remains a serious bottleneck for rapidly analyzing large numbers of samples expected from a biological warfare attack. Therefore, we developed a high-throughput method to simultaneously process multiple sponge-stick samples to be better prepared for rapid response and recovery after wide area anthrax incidents. In this method, sponges are placed in 50 mL tubes containing 25 mL extraction buffer and shaken to release spores, after which the suspension is recovered for analysis. Here, we determined that an additional extraction step, conducted in the same tubes with 10 mL buffer, further increased spore recovery from sponge-stick by approximately 10 %. We determined that orbital shaking and multi-tube vortexing were both more effective than reciprocating shaking for recovering spores. We conducted simultaneous processing of up to 12 sponge-stick samples and demonstrated comparable spore recovery efficiencies to the traditional low-throughput stomacher-based method (approximately 60 % recovery at 10 2 -spore level and 75 % recovery at 10 4 -spore level for both methods in three replicate experiments, P > 0.05 for two-tailed t-tests for each experiment and spore level). We also demonstrated that our high-throughput method could be integrated with Rapid Viability-Polymerase Chain Reaction (RV-PCR) analysis and could detect levels as low as 40 spores per sponge even when challenged by a PCR particulate contaminant.

Anthrax↗

DOE OSTI2020

Comparison of gamma-ray spectral analysis methods for thick-walled UF 6 cylinders

Three data analysis methods were compared for gamma ray spectra collected by planar and coaxial high-purity germanium detectors (HPGe) on thick-walled uranium hexafluoride cylinders. The cylinder contents range from natural to low-enriched uranium (4.95% 235 U). Each spectrum was analyzed with the traditional 185.7 keV enrichment meter method, a 185.7/1001 keV ratio method, and the Fixed Energy Response Function Analysis with Multiple Efficiency (FRAM) software that utilizes low- and high-energy gamma rays and X-rays. When results for all cylinders were compared, the enrichment meter method and the 185.7/1001 keV peak ratio method consistently provided the most accurate data for all detector types. The error on the enrichment calculations analyzed with FRAM did not meet the international target value whereas those calculated with the enrichment meter and ratio method did. Enrichments calculated by FRAM were found to skew to higher values on natural uranium and to lower values on low-enriched uranium. FRAM calculated the least-precise enrichments; replicate analyses of single cylinders resulted in 235 U values that varied by as much as 19%. FRAM does have the significant advantages in that it does not require the use of calibration cylinders, infinite thickness criteria are not necessary, and it can be applied to any HPGe detector. Finally, if calibration cylinders are available, the enrichment meter and 185.7/1001 peak ratio are the recommended methods as they are the most accurate and precise.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

252 Cf yield calibration method for nuclear material accountancy and safeguards practitioners

Californium-252 is an isotope commonly encapsulated as a physically small but strong spontaneous fission neutron source for applications in industry, academia, and research. Within the nuclear safeguards community, a well-characterized 252 Cf source is often used as an accessible alternative for plutonium in calibrations measurements, which require the absolute source strength. Current methods of source strength quantification can provide an accurate estimate, approximately 1% uncertainty under optimal conditions, but are typically costly and time consuming. An alternative method was developed to determine 252 Cf source strength using passive neutron correlation counting (PNCC). The PNCC method enables institutions and facilities to perform 252 Cf source calibration measurements in-house using detection systems that are common within the nuclear safeguards community. This novel method was previously successfully demonstrated using neutron multiplicity well counters. However, the previous evaluation utilized detection systems with high neutron detection efficiencies, greater than 60%. The purpose of the current study is to extend the previous evaluation and demonstrate the feasibility of the PNCC 252 Cf calibration method for suite of coincidence counters with lower neutron detection efficiencies, between 15% and 35%, which are more commonly encountered in the field, as well as to provide a step-by-step guide to using the method. The neutron source used in this evaluation was previously certified by the National Institutes of Science and Technology (NIST), which provides a reference for the accuracy of the PNCC method. In conclusion, the present source yield calculations demonstrate excellent agreement with a NIST calibration technique and achieve a standard uncertainty below the target 1%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2019

Evaluation of the continuous dilatometer method of silicon carbide thermometry for passive irradiation temperature determination

Silicon carbide (SiC) is a primary candidate for passive irradiation temperature monitoring, and continuous dilatometry (CD) has been proposed as the key method for extracting irradiation temperatures from SiC thermometry samples. The CD method was evaluated to determine the sensitivity of the technique to the analysis procedure, as well as its accuracy and precision. Analysis found that the CD method had a ±20 °C sensitivity to the algorithm used to determine the irradiation temperatures. Comparison of the CD method with the continuous length change method for SiC thermometry showed CD is a more viable method of extracting irradiation temperatures. In conclusion, a comparison of irradiation temperatures determined by CD with those from active thermocouple measurements further validated the CD method for accurately and precisely determining irradiation temperatures in materials test reactor irradiations.

36 MATERIALS SCIENCE↗

DOE OSTI2023

High precision tests of QCD without scale or scheme ambiguities: The 40th anniversary of the Brodsky–Lepage–Mackenzie method

A key issue in making precise predictions in QCD is the uncertainty in setting the renormalization scale μ r and thus determining the correct values of the QCD running coupling α s (μ r ) at each order in the perturbative expansion of a QCD observable. It has often been conventional to simply set the renormalization scale to the typical scale of the process Q and vary it in the range μ r $\in$ [Q/2, 2Q] in order to estimate the theoretical error. This is the practice of Conventional Scale Setting (CSS). The resulting CSS prediction will however depend on the theorist’s choice of renormalization scheme and the resulting pQCD series will diverge factorially. It will also disagree with renormalization scale setting used in QED and electroweak theory thus precluding grand unification. A solution to the renormalization scale-setting problem is offered by the Principle of Maximum Conformality (PMC), which provides a systematic way to eliminate the renormalization scale-and-scheme dependence in perturbative calculations. The PMC method has rigorous theoretical foundations, it satisfies Renormalization Group Invariance (RGI) and preserves all self-consistency conditions derived from the renormalization group. The PMC cancels the renormalon growth, reduces to the Gell-Mann–Low scheme in the N c → 0 Abelian limit and leads to scale- and scheme-invariant results. The PMC has now been successfully applied to many high-energy processes. In this article we summarize recent developments and results in solving the renormalization scale and scheme ambiguities in perturbative QCD. In particular, we present a recently developed method the PMC ∞ and its applications, comparing the results with CSS. The method preserves the property of renormalizable SU(N)/U(1) gauge theories defined as Intrinsic Conformality (iCF). This property underlies the scale invariance of physical observables and leads to a remarkably efficient method to solve the conventional renormalization scale ambiguity at every order in pQCD. This new method reflects the underlying conformal properties displayed by pQCD at NNLO, eliminates the scheme dependence of pQCD predictions and is consistent with the general properties of the PMC. A new method to identify conformal and β-terms, which can be applied either to numerical or to theoretical calculations is also shown. We present results for the thrust and C-parameter distributions in e + e - annihilation showing errors and comparison with the CSS. We also show results for a recent innovative comparison between the CSS and the PMC ∞ applied to the thrust distribution investigating both the QCD conformal window and the QED N c → 0 limit. In order to determine the thrust distribution along the entire renormalization group flow from the highest energies to zero energy, we consider the number of flavors near the upper boundary of the conformal window. In this flavor-number regime the theory develops a perturbative infrared interacting fixed point. These results show that PMC ∞ leads to higher precision and introduces new interesting features in the PMC. In fact, this method preserves with continuity the position of the peak, showing perfect agreement with the experimental data already at NNLO. We also show a detailed comparison of the PMC ∞ with the other PMC approaches: the multi-scale-setting approach (PMCm) and the single-scale-setting approach (PMCs) by comparing their predictions for three important fully integrated quantities R e+e- , R$_Τ$ and Γ (H→$b\bar{b}$) up to the four-loop accuracy.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Harmonizing solar induced fluorescence across spatial scales, instruments, and extraction methods using proximal and airborne remote sensing: A multi-scale study in a soybean field

Solar-induced chlorophyll fluorescence (SIF) has been widely used to track vegetation photosynthesis at different scales ranging from in-situ measurements to satellite products. Airborne platforms sample SIF data at a spatial scale intermediate between in-situ and satellite, matching that of ground measurement (e.g. flux tower footprints and other field sampling), enabling us to explore causes of SIF variation and validate satellite-based SIF products. However, harmonizing SIF across sensors and platforms (correcting for systematic errors to yield a consistent, comparable SIF product) is challenging because SIF can be retrieved in different absorption windows, with different instruments and methods complicating the comparison between different observational levels (i.e., ground, airborne, satellites) and between sites equipped with different instruments with varying optical properties (spectral resolution and sampling intervals, spatial resolution). Additionally, the spatial and temporal variability of atmospheric properties can influence the retrieval of the weak SIF signal. Because of these complications, direct comparisons of airborne and ground SIF across scales are rarely attempted. Here, in this study, we combined airborne SIF data with simultaneous ‘ground truth’ data collected by stationary and mobile platforms in a soybean field in Nebraska, USA. In this effort, we tested several SIF extraction methods, including Fraunhofer Line Discrimination (FLD), improved Fraunhofer Line Discrimination (iFLD), Spectral Fitting Method (SFM), SpecFit, and a Singular Vector Decomposition (SVD) method. The SpecFit method was sensitive to the 715–740 nm water bands and removing the water bands in the fitting process yielded better agreement between the airborne and ground SIF spectra. Accurate estimation of the ground level downwelling irradiance obtained by ground measurements over a calibration target improved agreement between airborne and ground SIF retrievals at the O 2 A band, and allowed us to derive a SIF dataset with improved agreement across platforms and sampling scales. This experimental approach provided a method for generating comparable SIF signals across instruments, methods and platforms, which is critical to understanding the SIF-GPP relationship at different scales and to cross-validate the diversity of platforms used for satellite products calibration and validation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Benchmarking Concentration and Extraction Methods for Wastewater-Based Surveillance of Eight Human Respiratory Viruses: Implications for Rapid Application to Novel Pathogens

To provide early warning and support a rapid response to a novel virus through wastewater surveillance, it would be ideal to understand in advance which concentration and extraction methods are likely to be effective for dPCR-based methods, depending on virus characteristics. In this study, we spiked raw wastewater samples with eight human respiratory viruses and processed them with four methods that concentrate and/or extract nucleic acids from both liquid and solid fractions (Promega, Nanotrap, and InnovaPrep) or only the solid fraction of wastewater (Solids). Our findings provide encouraging evidence that all four methods combined with dPCR could detect an emerging virus in wastewater, although they differed in sensitivity. The pattern of recovery efficiency for adenoviruses, coronaviruses, and influenza A viruses was consistent across methods, with Promega producing higher median recovery efficiencies, while distinct patterns were observed for coxsackieviruses. We also normalized the concentration data with two endogenous fecal indicators, PMMoV and Carjivirus (formerly crAssphage). We found that normalization could reduce method-associated differences if the indicator exhibited a recovery pattern similar to that of the target virus. These findings can guide the selection of concentration and extraction methods for wastewater monitoring based on the properties of target viruses, thus enhancing pandemic preparedness.

Biological and medical sciences↗

DOE OSTI2017

Assessment of Different Discrete Particle Methods Ability To Predict Gas-Particle Flow in a Small-Scale Fluidized Bed

Several discrete particle methods exist in the open literature to simulate fluidized bed systems, such as discrete element method (DEM), time driven hard sphere (TDHS), coarse-grained particle method (CGPM), coarse grained hard sphere (CGHS), and multi-phase particle-in-cell (MP-PIC). These different approaches usually solve the fluid phase in a Eulerian fixed frame of reference and the particle phase using the Lagrangian method. The first difference between these models lies in tracking either real particles or lumped parcels. The second difference is in the treatment of particle-particle interactions: by calculating collision forces (DEM and CGPM), using momentum conservation laws (TDHS and CGHS), or based on particle stress model (MP-PIC). These major model differences lead to a wide range of results accuracy and computation speed. However, these models have never been compared directly using the same experimental dataset. In this research, a small-scale fluidized bed is simulated with these methods using the same open-source code MFIX. The results indicate that modeling the particle-particle collision by TDHS increases the computation speed while maintaining good accuracy. Also, lumping few particles in a parcel increases the computation speed with little loss in accuracy. However, modeling particle-particle interactions with solids stress leads to a big loss in accuracy with a little increase in computation speed. The MP-PIC method predicts an unphysical particle-particle overlap, which results in incorrect voidage distribution and incorrect overall bed hydrodynamics. Based on this study, we recommend using the CGHS method for fluidized bed simulations due to its computational speed that rivals that of MPPIC while maintaining a much better accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Toward a QUBO-Based Density Matrix Electronic Structure Method

Density matrix electronic structure theory is used in many quantum chemistry methods to “alleviate” the computational cost that arises from directly using wave functions. Although density matrix based methods are computationally more efficient than wave function based methods, significant computational effort is involved. Because the Schrödinger equation needs to be solved as an eigenvalue problem, the time-to-solution scales cubically with the system size in mean-field type approaches such as Hartree–Fock and density functional theory and is solved as many times in order to reach charge or field self-consistency. We hereby propose and study a method to compute the density matrix by using a quadratic unconstrained binary optimization (QUBO) solver. This method could be useful to solve the problem with quantum computers and, more specifically, quantum annealers. Our proposed approach is based on a direct construction of the density matrix using a QUBO eigensolver. We explore the main parameters of the algorithm focusing on precision and efficiency. We show that, while direct construction of the density matrix using a QUBO formulation is possible, the efficiency and precision have room for improvement. Moreover, calculations performed with quantum annealing on D-Wave’s new Advantage quantum computer are compared with results obtained with classical simulated annealing, further highlighting some problems of the proposed method. Finally, we also suggest alternative methods that could lead to a more efficient QUBO-based density matrix construction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree–Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. Here, the accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, R cut . R cut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small R cut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Physics-Informed Neural Network Method for Forward and Backward Advection-Dispersion Equations

Advection-dispersion equations (ADEs) are commonly used to describe transport phenomena in porous media. Even though mature discretization-based numerical methods for ADEs exist, some challenges still remain, especially when it comes to solving advection-dominated forward ADEs and diffusion-dominated backward ADEs. The latter problem usually arises in the source identification context and leads to numerically unstable grid-based solutions that require a form of regularization or should be treated as an inverse problem that is computationally more expensive because it requires solving the forward problem multiple times. In this study, we propose a discretization-free approach based on the physics-informed neural network (PINN) method for solving coupled ADE and Darcy flow equations with space-dependent hydraulic conductivity. In this approach, the hydraulic conductivity, hydraulic head, and concentration fields are approximated with deep neural networks (DNNs). We assume that the conductivity field is given by its values on a grid, and we use these values to train the conductivity DNN. The head and concentration DNNs are trained by minimizing the residuals of the flow equation and ADE and using the initial and boundary conditions as additional constraints. The PINN method is applied to one- and two-dimensional forward ADE problems, where its performance for various P\'{e}clet numbers ($Pe$) is compared with the analytical and numerical solutions. We find that the PINN method is accurate with errors of less than 1\% and outperforms some conventional discretization-based methods for $Pe$ larger that 100. Next, we demonstrate that the PINN method remains accurate for the backward ADEs, with the relative errors in most cases staying under 5\% compared to the reference concentration field. Finally, we show that when available, the concentration measurements can be easily incorporated in the PINN method and significantly improve (by more than 50\% in the considered cases) the accuracy of the PINN solution of the backward ADE.

He, Qizhi↗