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DOE OSTI2022

Latent Space Dynamics Identification

LaSDI is a data-driven physical simulation software that forms a latent space for a given high-fidelity model and discovers a set of ordinary differential equations for the latent space dynamics. It allows a fast and accurate solution process, which is useful for multi-query decision making applications, such as design optimization and uncertainty quantification. The performance of the LaSDI framework is demonstrated on four different problems, i.e., 1D and 2D Burgers equations, nonlinear heat conduction, and radial advection problems. Both linear and nonlinear compression techniques, such as neural network and proper orthogonal decomposition, are used to form a latent space. A concept of local dynamics identification procedure is introduced to enable a parametric model, which enhances the accuracy level over a given parameter space.

Fries, William↗

DOE OSTI2024

CMLM (Co-Optimized Machine-Learned Manifolds) [SWR-23-41]

Co-optimized Machine-Learned Manifolds (CMLM) is a data-driven approach for developing reduced-order manifold models for high-dimensional chemically reacting systems. It involves a specially designed neural network, the training of which simultaneously optimizes linear combinations of species that define the manifold, nonlinear mapping to outputs of interest such as reaction rates, and (optionally) subfilter closure for large eddy simulation. This software package provides an implementation of the CMLM approach in Python using the PyTorch machine learning library. A few example cases are included, showing how the tool can be applied to different types of data from 0D and 1D reacting simulations performed using Cantera. The neural networks can be saved in a format that is readable by the Pele suite of combustion solvers for use in reacting computational fluid dynamics simulations. This software repository contains several python scripts to perform various tasks associated with the Co-optimized Machine Learned Manifolds (CMLM) model, which is described in Perry, Henry de Frahan, and Yellapantula, CNF, 2022 (https://doi.org/10.1016/j.combustflame.2022.112286). This includes not only the code that defines the CMLM model, but also scripts to generate suitable training data, scripts to pre-process the data, scripts to train the CMLM model, and scripts to plot the output, as well as various other helper files. The scripts depend on several commonly used python libraries for data analysis and chemical reaction computations. The trained models that result from this tool are designed to work with the an interface being implemented in the Pele suite of reacting flow solvers (https://github.com/AMReX-Combustion).

Perry, Bruce↗

DOE OSTI2025

BHResist [SWR-25-57]

BHResist is a pure python library for computing thermal resistance within single-u, double-u, and coaxial grouted borehole heat exchangers. For single and double u-tube configurations, the methods use the 1st-order closed-form multipole approximations, which typically produces results with less than 1% error when compared to the 10th-order multipole method. Coaxial borehole methods apply a simple 1D resistance network method. This is intended to be a lightweight library that can be easily imported into any other Python tool, with no bulky dependencies.

Mitchell, Matt [National Renewable Energy Laborato↗

DOE OSTI2025

Atmospheric Profile Builder

APBuilder is a software tool designed to generate atmospheric profiles for use with AC2Dr by downloading weather model data and transforming it into 1D or 2D binary profiles. These binary profiles serve as required inputs for AC2Dr, an LLNL-developed, open source, two-dimensional numerical solver for the acoustic wave equation based on the finite difference method.

Kim, Keehoon [Lawrence Livermore National Laborato↗

DOE OSTI2025

pyAXEAP1-GUI package

SF-25-076 pyAXEAP1-GUI package is an X-ray emission spectroscopy (XES) data analysis package in the Python language. It can transfer the collected images from a 2D detector into spectra and display XES and RXES data as 3Dimages, 2D images and 1D profiles.

Berno, Alexander↗

DOE OSTI2026

OPEN ALPHADIFFRACT

Open-source release of the AlphaDiffract data generation and training system. Includes only the public Materials Project dataset retrievers.AlphaDiffract is a deep learning framework that achieves state-of-the-art performance in predicting the crystal system, space group, and lattice parameters directly from PXRD patterns. AlphaDiffract utilizes a 1D adaptation of the ConvNeXt architecture, a modern convolutional neural network that integrates key design principles from transformers, coupledwith dedicated prediction heads for each crystallographic property.

Prince, Michael [Argonne National Laboratory (ANL)↗

DOE OSTI2025

Equivariant Graph Attention Network - 3D Conformers & Feature Fusion

EGAN-3F (Equivariant Graph Attention Network - 3D Conformers & Feature Fusion) presents an innovative approach for predicting binding affinity between small molecules and protein targets, a fundamental task in drug discovery. Traditional structure-based methods often depend on protein-ligand complex structures obtained from crystallography or molecular docking. In contrast, ligand-only machine learning models using 1D or 2D representations such as SMILES have been developed to predict binding affinity without structural information about the target; however, their accuracy is often limited due to the lack of 3D ligand information. EGAN-3F addresses this limitation by integrating spatially aware graph learning with traditional descriptor-based features. We systematically investigate how combining 2D and 3D molecular representations enhances binding affinity prediction from SMILES strings. This approach underscores the importance of modeling conformational diversity and incorporating chemically meaningful descriptors to improve predictive accuracy. The key innovation of EGAN-3F lies in its ability to achieve robust ligand-based binding affinity predictions without requiring protein-ligand complex structures, effectively bridging the gap between purely structural and ligand-only modeling paradigms.

Shim, Heesung [Lawrence Livermore National Laborat↗

DOE OSTI2026

torch-einshard v1.0

torch-einshard is a Python library for describing local and distributed PyTorch tensor computations with compact, einsum-like notation. Its expressions name logical axes, specify how they are sharded across a PyTorch DeviceMesh, and represent partial reductions. The library automatically performs contractions, permutations, reshaping, splitting, gathering, reduction, reduce-scatter, and repartitioning while preserving autograd. Additional features include sharding-aware FFTs, tensor rolls, halo exchange, sliding windows, 1D–3D convolutions, uneven-shard handling, parameter initialization and gradient management, and cost-based execution planning. It is designed for scientific machine learning and large-model workloads, including tensor-, sequence-, and spatial-parallel MLPs, attention, convolutions, and spectral operations. Compared with manually combining torch.einsum and distributed collectives, torch-einshard expresses both the mathematical operation and data placement in one readable formula. This reduces boilerplate and synchronization errors, keeps forward and backward communication consistent, and allows the library to select optimized collective strategies without changing model code.

Morozov, Dmitriy [Lawrence Berkeley National Labor↗

DOE OSTI2021

A Shallow-Water Model for Convective Self-Aggregation

Randomly distributed convective storms can self-aggregate in the absence of large-scale forcings. Here we present a 1D shallow-water model to study the convective self-aggregation. This model simulates the dynamics of the planetary boundary layer and represents convection as a triggered process. Once triggered, convection lasts for finite time and occupies finite length. Here we show that the model can successfully simulate self-aggregation, and that the results are robust to a wide range of parameter values. In the simulations, convection excites gravity waves. The gravity waves then form a standing wave pattern, separating the domain into convectively active and inactive regions. We analyze the available potential energy (APE) budget and show that convection generates APE, providing energy for self-aggregation. By performing dimensional analysis, we develop a scaling theory for the size of convective aggregation, which is set by the gravity wave speed, damping time scale, and number density of convective storms. This paper provides a simple modeling framework to further study convective self-aggregation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

A Triple-Moment Representation of Ice in the Predicted Particle Properties (P3) Microphysics Scheme

In the original Predicted Particle Properties (P3) bulk microphysics scheme, all ice-phase hydrometeors are represented by one or more “free” ice categories, where the physical properties evolve smoothly through changes to the four prognostic variables (per category), and with a two-moment representation of the particle size distribution. As such, the spectral dispersion cannot evolve independently, which thus results in limitations in representation of ice—in particular, hail—due to necessary constraints in the scheme to prevent excessive gravitational size sorting. To overcome this, P3 has been modified to include a three-moment representation of the size distribution of each ice category through the addition of a fifth prognostic variable, the sixth moment of the size distribution. The details of the three-moment ice parameterization in P3 are provided. The behavior of the modified scheme, with the single-ice-category configuration, is illustrated through simulations in a simple 1D kinematic model framework as well as with near large-eddy-resolving (250-m grid spacing) 3D simulations of a hail-producing supercell. It is shown that the three-moment ice configuration controls size sorting in a physically based way and leads to an improved capacity to simulate large, heavily rimed ice (hail), including mean and maximum sizes and reflectivity, and thus an overall improvement in the representation of ice-phase particles in the P3 scheme.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Convective and Turbulent Motions in Nonprecipitating Cu. Part II: LES Simulated Cloud Represented by a Starting Plume

The dynamic structure of a small trade wind cumulus (Cu) is analyzed using a novel approach. Cu developing in a shear-free environment is simulated by 10-m-resolution LES model with spectral bin microphysics. The aim is to clarify the dynamical nature of cloud updraft zone (CUZ) including entrainment and mixing in growing Cu. The validity of concept stating that a cloud at developing state can be represented by a parcel or a jet is tested. To investigate dynamical entrainment in CUZ performed by motions with scales larger than the turbulence scales, the modeled fields of air velocity were filtered by wavelet filter that separated convective motions from turbulent ones. Two types of objects in developing cloud were investigated: small volume ascending at maximal velocity (point parcel) and CUZ. It was found that the point parcel representing the upper part of cloud core is adiabatic. The motion of the air in this parcel ascending from cloud base determines cloud-top height. The top-hat (i.e., averaged) values of updraft velocity and adiabatic fraction in CUZ are substantially lower than those in the point parcel. Evaluation of the terms in the dynamical equation typically used in 1D cloud parcel models show that this equation can be applied for calculation of vertical velocities at the developing stage of small Cu, at least up to the heights of the inversion layer. Dynamically, the CUZ of developing cloud resembles the starting plume with the tail of nonstationary jet. Both the top-hat vertical velocity and buoyancy acceleration linearly increase with the height, at least up to the inversion layer. An important finding is that lateral entrainment of convective (nonturbulent) nature has a little effect on the top-hat CUZ velocity and cannot explain the vertical changes of conservative variables qt and θl. In contrast, entrained air lifting inside CUZ substantially decreases top-hat liquid water content and its adiabatic fraction. Possible reasons of these effects are discussed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

“Gray Zone” Simulations Using a Three-Dimensional Planetary Boundary Layer Parameterization in the Weather Research and Forecasting Model

Abstract Generating accurate weather forecasts of planetary boundary layer (PBL) properties is challenging in many geographical regions, oftentimes due to complex topography or horizontal variability in, for example, land characteristics. While recent advances in high-performance computing platforms have led to an increase in the spatial resolution of numerical weather prediction (NWP) models, the horizontal gridcell spacing (Δ x ) of many regional-scale NWP models currently fall within or are beginning to approach the gray zone (i.e., Δ x ≈ 100–1000 m). At these gridcell spacings, three-dimensional (3D) effects are important, as the most energetic turbulent eddies are neither fully parameterized (as in traditional mesoscale simulations) nor fully resolved [as in traditional large-eddy simulations (LES)]. In light of this modeling challenge, we have implemented a 3D PBL parameterization for high-resolution mesoscale simulations using the Weather Research and Forecasting Model. The PBL scheme, which is based on the algebraic model developed by Mellor and Yamada, accounts for the 3D effects of turbulence by calculating explicitly the momentum, heat, and moisture flux divergences in addition to the turbulent kinetic energy. In this study, we present results from idealized simulations in the gray zone that illustrate the benefit of using a fully consistent turbulence closure framework under convective conditions. While the 3D PBL scheme reproduces the evolution of convective features more appropriately than the traditional 1D PBL scheme, we highlight the need to improve the turbulent length scale formulation. Significance Statement The spatial resolution of weather models continues to increase at a rapid rate in accordance with the enhancement of computing power. As a result, smaller-scale atmospheric features become more explicitly resolved. However, most numerical models still ignore the impact of horizontal weather variations on boundary layer flows, which becomes more important at these smaller spatial scales. To address this issue, we have implemented a new modeling approach, using fundamental principles, which accounts for horizontal variability. Our results show that including three-dimensional effects of turbulence is necessary to achieve realistic boundary layer characteristics. This novel technique may be useful for many applications including complex terrain flows, pollutant dispersion, and surface–atmosphere interaction studies.

Juliano, Timothy W.↗

DOE OSTI2023

Thermodynamic analysis of heat transfer reduction in spark ignition using thermal barrier coatings

This work uses a 0D thermodynamic engine model coupled to a 1D surface temperature solver to study the potential of low thermal inertia thermal barrier coatings (TBCs) on combustion chamber surfaces to increase the efficiency of spark ignition engines. Under ideal conditions, coating the piston crown, head, and valve faces with a TBC with a thermal inertia of 640 J/m 2 K s 1/2 resulted in less than a 1% relative improvement in efficiency. Despite using a low thermal inertia coating to avoid open cycle charge heating, the reduction in closed cycle heat transfer, which is the pathway to increasing efficiency, increased knock propensity. Therefore, any efficiency gain through closed cycle heat transfer reduction in spark ignition is offset by the need to retard spark timing to counter knock. An exergy analysis of completely blocking heat transfer for a 10 crank-angle degree window showed that on a low compression engine, like those used for stoichiometric gasoline spark ignition, the maximum efficiency gain achievable was limited compared to a higher compression ratio engine. Furthermore, the high gas temperatures of stoichiometric operation mean that even state-of-the-art TBCs cannot elevate surface temperatures enough purely through temperature swing to achieve a significant reduction in heat transfer near top dead center, where work availability is highest. Overall, these results indicate that low thermal inertia TBCs are ill-suited for achieving an efficiency benefit in spark ignition through a heat transfer reduction pathway. Instead spark ignition TBC research should explore ways to use low thermal inertia TBCs to achieve open cycle charge cooling to reduce knock propensity.

Engineering↗

DOE OSTI2024

Recent progress in realizing novel one-dimensional polymorphs via nanotube encapsulation

Encapsulation of various materials inside nanotubes has emerged as an effective method in nanotechnology that facilitates the formation of novel one-dimensional (1D) structures and enhances their functionality. Because of the effects of geometrical confinement and electronic interactions with host nanotubes, encapsulated materials often exhibit low-dimensional polymorphic structures that differ from their bulk forms. These polymorphs exhibit unique properties, including altered electrical, optical, and magnetic behaviors, making them promising candidates for applications in electronics, energy storage, spintronics, and quantum devices. This review explores recent advancements in the encapsulation of a wide range of materials such as organic molecules, elemental substances, metal halides, metal chalcogenides, and other complex compounds. In particular, we focus on novel polymorphs formed through the geometrical confinement effect within the nanotubes. The atomic structure, other key properties, and potential applications of these encapsulated materials are discussed, highlighting the impact of nanotube encapsulation on their functionalities.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

The effects of well damage and completion designs on geoelectrical responses in mature wellbore environments

Well integrity is one of the major concerns in long-term geologic storage sites due to the potential risk of well leakage and groundwater contamination. Evaluating changes in electrical responses due to energized steel-cased wells has the potential to quantify and predict possible wellbore failures because any kind of breakage or corrosion along highly conductive well casings will have an impact on the distribution of the subsurface electrical potential. However, realistic wellbore-geoelectrical models that can fully capture fine-scale details of well completion design and the state of well damage at the field scale require extensive computational effort, or they can even be intractable to simulate. To overcome this computational burden while still keeping the model realistic, we have used the hierarchical finite-element method that represents electrical conductivity at each dimensional component (1D edges, 2D planes, and 3D cells) of a tetrahedral mesh. This allows well completion designs with real-life geometric scales and well systems with realistic, detailed, progressive corrosion and damage in our models. We have developed a comparison of possible discretization approaches of a multicasing completion design in the finite-element model. The effects of the surface casing and the coupling between concentric well casings as well as the effects of the degree and the location of well damage on the electrical responses are also examined. As a result, we analyze real surface electric field data to detect wellbore integrity failure associated with damage.

58 GEOSCIENCES↗

DOE OSTI2021

Integrating deep neural networks with full-waveform inversion: Reparameterization, regularization, and uncertainty quantification

Full-waveform inversion (FWI) is an accurate imaging approach for modeling the velocity structure by minimizing the misfit between recorded and predicted seismic waveforms. However, the strong nonlinearity of FWI resulting from fitting oscillatory waveforms can trap the optimization in local minima. We have adopted a neural-network-based full-waveform inversion (NNFWI) method that integrates deep neural networks with FWI by representing the velocity model with a generative neural network. Neural networks can naturally introduce spatial correlations as regularization to the generated velocity model, which suppresses noise in the gradients and mitigates local minima. Furthermore, the velocity model generated by neural networks is input to the same partial differential equation (PDE) solvers used in conventional FWI. The gradients of the neural networks and PDEs are calculated using automatic differentiation, which back propagates gradients through the acoustic PDEs and neural network layers to update the weights of the generative neural network. Experiments on 1D velocity models, the Marmousi model, and the 2004 BP model determine that NNFWI can mitigate local minima, especially for imaging high-contrast features such as salt bodies, and it significantly improves the inversion in the presence of noise. Adding dropout layers to the neural network model also allows analyzing the uncertainty of the inversion results through Monte Carlo dropout. NNFWI opens a new pathway to combine deep learning and FWI for exploiting the characteristics of deep neural networks and the high accuracy of PDE solvers. Because NNFWI does not require extra training data and optimization loops, it provides an attractive and straightforward alternative to conventional FWI.

58 GEOSCIENCES↗

DOE OSTI2025

Continuous surface-to-distributed acoustic sensor snapshots explain reactivation of individual natural fractures during an unconventional reservoir stimulation

ABSTRACT Fiber-optic sensing technologies allow petroleum engineering teams to detect hydraulic fracture interaction with boreholes during unconventional reservoir stimulation. In combination with high-repeatability seismic sources, the same distributed acoustic sensors (DASs) enable vertical seismic profiling (VSP) of the fracture evolution away from the boreholes. We discovered clear signatures of seismic scattering on activated fractures during nine days of continuous seismic monitoring of the fracturing stages at the Austin Chalk/Eagle Ford Field Laboratory. The present study applies a novel approach for quantitative analysis of the scattering events in terms of the evolution of the geometry and elastic stiffness of individual fractures. Our characterization strategy sequentially refines the fracture models: from a stack of 1D soft layers to 3D rectangular inclusions. First, we estimate the number of fracture locations and reflectivity using a modified sparse-spike deconvolution of the stacked VSP traces. The fracture set consists of five fractures spaced by 15–30 m with a reflectivity of approximately 1%. Then, we develop a scattering integral method to refine these estimates along with an inversion of the fracture top and bottom for each monitoring vintage. We find that, initially, some of the fractures are located above the monitoring fiber with the height of approximately 100 m. Then we integrate the seismic interpretation with the low-frequency DAS and pressure and microseismic monitoring to reconstruct the activation process of the fractures. Most likely, some of the natural fractures slowly grew downward to the monitoring fiber as a result of fluid injections in the stimulated well. This led to bright strain anomalies but did not trigger seismicity. The top of the fractures remained almost constant and were limited by a lithologic boundary/stress barrier. To our knowledge, this is the first time VSP data enabled tracking of the fracture evolution with such high spatial and temporal resolution, which was previously only available for crosswell surveys and at a much smaller scale.

Glubokovskikh, Stanislav↗

DOE OSTI2020

Characterization of elastic mechanical properties of Tuscaloosa Marine Shale from well logs using the vertical transversely isotropic model

To avoid steep declines in the Tuscaloosa Marine Shale (TMS) production, wells are fracture-stimulated to release the hydrocarbons trapped in the matrix of the formation. An accurate estimation of Young’s modulus and Poisson’s ratio is essential for hydraulic fracture propagation. In addition, ignoring the highly heterogeneous and anisotropic character of TMS can lead to erroneous stress values, which subsequently affect hydraulic fracture width estimates and the overall hydraulic fracturing process. We have developed an empirical 1D geomechanical model that takes into account VTI anisotropy, and it is used to characterize the elastic mechanical properties of TMS in two wells. In the analyzed formation, the vertical Poisson’s ratio is less than the horizontal Poisson’s ratio, which suggests the necessity of an alternative to the ANNIE equations. The stiffness coefficients [Formula: see text] and [Formula: see text] were estimated using the relationships developed from the ultrasonic core data available for the two TMS. Further, correlations between the static and dynamic properties from laboratory tests were used to improve the minimum horizontal stress calculation. We compare VTI Young’s moduli, Poisson’s ratios, and minimum horizontal stress with the isotropic solution. VTI modeling improves the estimation of the elastic mechanical properties. The isotropic solution underestimates the minimum horizontal stress in the formation. Moreover, it was shown that the 20 ft shale interval below the TMS base is characterized by a low Young’s modulus (the vertical Young’s modulus is equal to 20 GPa, whereas the horizontal Young’s modulus is equal to 40 GPa) and may be a frac barrier.

Geochemistry & Geophysics↗