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At least 19 records

Augmenting Molecular Graphs with Geometries via Machine Learning Interatomic Potentials

Accurate molecular property predictions require 3D geometries, which are typically obtained using expensive methods such as density functional theory (DFT). Here, we attempt to obtain molecular geometries by relying solely on machine learning interatomic potential (MLIP) models. To this end, we first curate a large-scale molecular relaxation dataset comprising 3.5 million molecules and 300 million snapshots. Then MLIP pre-trained models are trained with supervised learning to predict energy and forces given 3D molecular structures. Once trained, we show that the pre-trained models can be used in different ways to obtain geometries either explicitly or implicitly. First, it can be used to obtain approximate low-energy 3D geometries via geometry optimization. While these geometries do not consistently reach DFT-level chemical accuracy or convergence, they can still improve downstream performance compared to non-relaxed structures. To mitigate potential biases and enhance downstream predictions, we introduce geometry fine-tuning based on the relaxed 3D geometries. Second, the pre-trained models can be directly fine-tuned for property prediction when ground truth 3D geometries are available. Our results demonstrate that MLIP pre-trained models trained on relaxation data can learn transferable molecular representations to improve downstream molecular property prediction and can provide practically valuable but approximate molecular geometries that benefit property predictions. Our code is publicly available at: https://github.com/divelab/AIRS/.

Fu, Cong [Texas A & M Univ., College Station, TX (

Two-phase flow numerical analysis of electrode geometry for alkaline water electrolyzers

Hydrogen is a promising component of a future energy-secure and efficient economy, but its competitiveness depends on reducing production costs. One strategy is to operate alkaline water electrolyzers at higher current densities to increase output. However, this intensifies performance losses due to gas bubble accumulation, which blocks transport pathways and deactivates electrochemically active surfaces. Enhancing bubble evacuation through electrode design is therefore essential. Previous studies have explored various approaches — such as modifying surface morphology, applying sonication or pressure modulation, and introducing surfactants — but these efforts have addressed a limited range of conditions due to the complexity of two-phase flow and electrode geometries. Experiments have also largely been focused on either cell level improvements, which lack the information necessary to isolate each contributing factor, or on modified geometries that are not relevant to practical cell operation. From a modeling perspective, conventional Eulerian multiphase models do not track the complex gas–liquid interfacial dynamics and often neglect surface tension and contact angle effects, reducing their predictive accuracy. To provide insights on the effects of different electrode geometries on the performance of alklaine water electrolyzers this work employs an immersed boundary volume-of-fluid method to simulate bubble behavior in 3D porous electrodes. Multiple base electrode geometries, typically used in practice, with varying porosity are evaluated under a constant surface gas generation rate. Simulation data is analyzed to quantify electrode gas coverage, bubble size dynamics and other relevant metrics. Results show that porosity strongly influences bubble accumulation on electrode surfaces, with higher porosity reducing gas coverage, and its not strictly dependent on the electrode geometry. However, the electrode’s base geometry significantly affects gas accumulation at the separator gap, independent of porosity. A foam electrode geometry resulted in the lowest gas coverage of all electrodes with a median volumetric gas coverage of 11%, but at the cost of a 70% reduction in active area compared with the largest surface area electrode, while gyroid electrodes showed the best trade-off between gas coverage, particularly at the separator surface, and electrochemically active area. In conclusion, the results highlight the need for holistic electrode design strategies.

Alkaline

Assessing the viability of a new subsize tensile specimen geometry for evaluation of structural nuclear and additively manufactured materials

The use of subsize specimens in nuclear materials testing has been a subject of ongoing interest due to radiation safety concerns and resource conservation needs. It is also of interest in additive manufacturing (AM), also known as 3D-printing, as subsize specimens can more accurately represent the behavior of the small, intricate geometries often produced using AM. A novel, extremely small geometry, called the Subsize Teeny (SST) was recently developed and is of interest for implementation. Given its extraordinarily small size and the complexities associated with subsize specimen testing, adequate vetting of this geometry is necessary to ensure data quality. Here, a variety of unirradiated nuclear structural materials were tested in the SST geometry and compared against the well-established SSJ3 geometry. In addition, two case studies implementing the SST as a screening geometry for AM materials were also conducted. The question of SST viability was found to be highly nuanced and will often be dependent on the context or application in question. It was determined, however, that the SST is a largely invalid geometry for exceptionally coarse-grained materials or in cases where the physical defect volume equals or exceeds 0.1 % or where the specimen machining parameters result in significant surface alterations. On the other hand, it was determined that the SST may be employed with confidence if the test material is nearly or totally free of physical defects, isotropic, demonstrates homogeneous plastic deformation, and possesses a fine-grained, nearly or totally homogeneous microstructure with at least twelve slip systems.

Additive manufacturing

The role of focusing geometry in MeV x-ray production from petawatt laser–solid interaction

Relativistic laser–plasma interactions provide a compact and flexible route to generating bright, ultrashort pulses of MeV x rays, with applications in high-energy density science, nuclear physics, and radiography. Despite extensive study of intensity scaling in laser-driven electron acceleration, the role of focusing geometry and focal-volume effects in MeV radiation production remains insufficiently understood. Here, we present experimental and kinetic simulation results from the Texas Petawatt Laser (120 J, 140 fs) in which the focusing geometry (f/3 or f/1.5) is varied, while the laser energy and pulse duration are fixed. Experimentally, the f/3 geometry produces approximately three times more MeV radiation than the f/1.5 geometry, despite its twofold lower nominal vacuum intensity. This result is based on the time-integrated radiation per unit solid angle, as measured along the diagnostic line of sight. Three-dimensional particle-in-cell simulations reproduce this trend when a modest (10s of μm) effective focal plane shift is introduced, demonstrating that relativistic laser–plasma coupling is highly sensitive to focal geometry in the presence of a preplasma. This behavior is consistent with differences in interaction length and effective intensity at the critical surface between the two configurations. The sensitivity of the tightly focused f/1.5 configuration ($z_R ≈$⁠ 5 μ m) reflects the combined influence of thermal lensing and an extended preplasma, while the f/3 geometry (⁠$z_R ≈$ 80 μ m) remains comparatively robust. These results demonstrate a breakdown of conventional intensity scaling and identify focusing geometry as a critical control parameter for MeV electron and x-ray generation at petawatt powers. Implications for laser–plasma-based radiographic facilities are also discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

An efficient second-order adaptive procedure for inserting CAD geometries into hexahedral meshes using volume fractions

Here, this paper is concerned with inserting three-dimensional computer-aided design (CAD) geometries into meshes composed of hexahedral elements using a volume fraction representation. An adaptive procedure for doing so is presented. The procedure consists of two steps. The first step performs spatial acceleration using a k-d tree. The second step involves subdividing individual hexahedra in an adaptive mesh refinement (AMR)-like fashion and approximating the CAD geometry linearly (as a plane) at the finest subdivision. The procedure requires only two geometric queries from a CAD kernel: determining whether or not a queried spatial coordinate is inside or outside the CAD geometry and determining the closest point on the CAD geometry’s surface from a given spatial coordinate. We prove that the procedure is second-order accurate for sufficiently smooth geometries and sufficiently refined background meshes. We demonstrate the expected order of accuracy is achieved with several verification tests and illustrate the procedure’s effectiveness for several exemplar CAD geometries.

Adaptive

Enabling the broader adoption of fusion simulation on complex geometry

This project addressed a key barrier to advanced fusion and nuclear simulation: the difficulty of performing high-fidelity Monte Carlo neutronics directly on complex, real-world CAD geometry. Traditional workflows require engineers to rebuild CAD models as simplified constructive solid geometry, a time-consuming and error-prone process that limits design iteration and broader adoption of simulation tools. The goal of this Phase I SBIR was to make CAD-based neutronics practical, accessible, and robust for industrial and research users. During the project, Coreform significantly enhanced the Direct Accelerated Geometry Monte Carlo (DAGMC) workflow and fully integrated it into Coreform Cubit as a first-class capability. Major achievements include optimized material assignment and surface meshing workflows, substantial performance improvements to geometry imprinting and preparation, native export of DAGMC models, and new visualization tools to support OpenMC source definition and lost-particle debugging. Coreform also expanded Cubit’s capabilities as a full OpenMC preprocessor, including the ability to convert OpenMC constructive solid geometry models back into CAD for visualization, multiphysics coupling, and debugging. In collaboration with Argonne National Laboratory, the project delivered comprehensive new DAGMC documentation and training materials, transforming DAGMC from a research-oriented tool into a production-ready workflow. Results were disseminated through tutorials, conference training, and multiple well-attended webinars demonstrating integrated CAD-based neutronics and multiphysics workflows. Overall, this project demonstrated that high-fidelity Monte Carlo simulations can be performed directly on complex CAD geometry, reducing setup time, improving usability, and enabling faster, more informed design decisions for fusion and nuclear energy systems.

42 ENGINEERING

Geometry-aware framework for deep energy method: An application to structural mechanics with hyperelastic materials

Here, in this work, we introduce a novel physics-informed framework named the Geometry-Aware Deep Energy Method (GADEM) for solving structural mechanics problems on different geometries. As the weak form of the physical system equation (or the energy-based approach) has demonstrated clear advantages compared to the strong form for solving solid mechanics problems, GADEM employs the weak form and aims to infer the solution on multiple shapes of geometries. Integrating a geometry-aware framework into an energy-based method results in an effective physics-informed deep learning model in terms of accuracy and computational cost. Different ways to represent the geometric information and to encode the geometric latent vectors are investigated in this work. We introduce a loss function of GADEM which is minimized based on the potential energy of all considered geometries. An adaptive learning method is also employed for the sampling of collocation points to enhance the performance of GADEM. We present some applications of GADEM to solve solid mechanics problems, including a loading simulation of a toy tire involving contact mechanics and large deformation hyperelasticity. The numerical results of this work demonstrate the remarkable capability of GADEM to infer the solution on various and new shapes of geometries using only one trained model.

97 MATHEMATICS AND COMPUTING

Numerical simulation of asteroid geometry variance on airburst threat

For an atmospheric airburst the primary source of concern when assessing uncertainty is the size and velocity. Determining these properties provides the basis for threat assessment, as the total energy of the asteroid may then be estimated, and the threat investigated thoroughly. Even with clarity as to how much energy an asteroid may deposit, a great deal of uncertainty still exists for the actual energy deposition process. One such source of uncertainty is the geometry of the incoming asteroid. The geometry of an asteroid will alter the stress distribution during entry, which adds uncertainty to when fracture will occur. Here, in this study, we use Smoothed Particle Hydrodynamics to model the atmospheric airburst of Tunguska-scale asteroids with varying geometric profiles, including a sphere, ellipsoid, binary and superellipsoid. Each asteroid is modeled as a homogenous structure with strength. We assess uncertainty through a series of planar 2D simulation cases for each geometry, comparing the source of stochasticity across geometries. A single 3D airburst simulation for each geometry is also analyzed. Additionally, the 3D cases are compared to the highly uncertain Tunguska event, predicting variance in burst height across geometries, but all bounded by theoretical burst heights proposed for Tunguska.

Airburst

Nanocrystal Geometry Governs Phase Transformation Pathways in Palladium Hydride

Pathways and structural dynamics of phase transformations impact performance of materials in energy and information storage technologies. Palladium hydride (PdH x ) nanocrystals are an ideal model system for studying solute-induced phase transformations, where elastic energy from lattice mismatch between α-PdH x and β-PdH x phases is often considered a key to determining the transformation pathways. α/β-PdH x interfacial elastic energy is affected by the confined geometry of a nanocrystal. However, how nanocrystal geometry influences phase transformation pathways is largely unknown. Using in situ liquid phase transmission electron microscopy, we directly visualize hydrogenation in Pd nanocrystals with two geometries, a nanocube and a hexagonal nanoplate. Both follow similar sequences of an initially curved nucleus, interface flattening, and reverse-stage nucleation; however, their evolving α/β-PdH x interfaces exhibit geometry-dependent crystallographic alignments. In nanocubes, {100}-aligned configurations conform to static elastic energy ordering, representing a pathway that maintains a local mechanical equilibrium, whereas nanoplates display both {110}- and {211}-aligned interfaces. Theoretical simulations show that geometry determines the accessibility of alternative phase transformation pathways as the system is driven far from equilibrium during hydrogenation. In conclusion, these findings identify geometry as a fundamental parameter for directing phase transformation pathways, offering design principles for accessing atypical configurations and improving properties of intercalation-based devices.

Lee, Daewon [Lawrence Berkeley National Laboratory

Geometry and size dependent microstructure and crack formation in Rene 41 superalloy fabricated by laser powder bed fusion

This study provides a systematic investigation into the size and geometry-dependent microstructural evolution and cracking susceptibility of LPBF-fabricated Rene 41. By coupling experimental microstructural analysis with thermal modeling, this research uniquely identifies the relationship between geometry-specific thermal histories, carbide coarsening, and liquation cracking. Four different geometries with varying thickness were fabricated with the identical process parameters. It was found that the grain size and morphology are not affected by the part size. However, the thinner parts exhibited coarser sub-grain structures compared to the thicker ones. The crack formation was observed for the parts with cross-sections smaller than 1 mm, whereas thicker parts had high density without any defects. Further, the cracks were observed in the interdendritic regions, suggesting that liquation cracking was the active micro-crack formation mechanism. The detailed microstructural analysis combined with a thermal finite element analysis proved that the heat extraction efficiency was lower for thinner parts causing a lower cooling rate and coarser carbides, making them more susceptible to constitutional liquation. Microhardness measurements were conducted for each geometry and correlated with the observed microstructural variations. The findings highlight the critical need for geometry-specific optimization of LPBF process parameters to mitigate cracking and achieve microstructural uniformity, offering valuable insights into the fabrication of complex, high-performance aerospace components.

36 MATERIALS SCIENCE

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.

Amber

Using AMReX's Embedded Boundaries to Support MFIX-Exa’s Geometry Capabilities

MFIX-Exa is an AMReX-based application used for the simulation of chemically reacting multiphase flows inside reactors. The reactor geometry is mostly a combination of primitive shapes such as cylinders, cubes and spheres of varying dimensions connected together with potentially a lot of dead space between them. Additionally, the reactors may have particle-laden jets introduced at different parts of their geometry to enhance reactant mixing. This talk presents how MFIX-Exa uses OpenSCAD’s csg format to allow users to define the embedded boundary (EB) geometry and how it supports specifying inflow through certain sections of the EB. The talk will describe how MFIX-Exa leverages the EB features of grid-pruning, restart files and redistribution. Finally, the talk goes over some capabilities which are currently not available in MFIX-Exa but planned for the future, such as moving parts of the reactor geometry.

embedded boundaries

Thermomechanics coupling to Monte Carlo particle transport on unstructured mesh geometries using Cardinal

Geometry deformation due to thermal expansion influences neutron transport in many systems. Studying this phenomenon involves coupling models for neutronics, thermal hydraulics, and solid mechanics. To enable high fidelity modeling of these coupled physics, new capabilities were introduced in Cardinal, coupling OpenMC Monte Carlo particle transport models with MOOSE thermomechanical physics on unstructured moving-mesh geometries. In this work, we present a fully open-source capability leveraging on-the-fly mesh skinning to automatically regenerate OpenMC geometry, which allows multiphysics feedback from temperature, density, and geometry changes. The new capability is verified using an analytic benchmark slab problem, which couples S 2 neutron transport with thermal conduction, convective boundary conditions, Doppler-broadened cross sections, and nonlinear thermal expansion effects along the heated slab. Cardinal reproduces the analytic solutions for the neutron flux, heating, k eff , and temperature with demonstrated convergence in various error terms including mesh resolution and cross section temperature library spacing. For the nominal benchmark conditions and with a fine mesh, maximum relative errors for neutron flux, temperature, and heating are lower than 1%, while errors in integral quantities such as k eff and slab length are within 1 pcm and 48 µm, respectively. This work (i) presents a new numerical approach to thermomechanics coupling with OpenMC models, (ii) is the first (to our knowledge) to utilize a mechanical partial differential equation (PDE) solution to solve the (Griesheimer and Kooreman, 2022) analytic benchmark, and (iii) develops this verified capability within an open-source package.

97 - MATHEMATICS AND COMPUTING

Consistent solutions of the radiation diffusion equation in spherical and cylindrical geometries

We have extended the radiation diffusion model of Hammer and Rosen [Phys. Plasmas 10, 1829 (2003)] to diverging spherical and cylindrical geometries. The effect of curvilinear geometry on the supersonic, expanding wavefront increases as the internal radius of a spherical or cylindrical shell approaches zero. Small spherical geometries are important for modeling systems at the size scale of inertial confinement fusion capsules, at these scales existing quasi-analytic models for planar geometry significantly disagree with the results of simulation. With this method, the benefits of rapid iteration can be applied to common spherical systems at much smaller length scales. We present comparisons between numerical diffusion solutions and the analytic model to give ranges of applicability for the model.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Modeling Multi-View Impedance-Based Cross-Geometry SOH Estimator for Li-ion Batteries

Abstract: Accurately estimating battery’s State of Health (SOH) remains challenging when models must generalize across cell designs and operating conditions. Most Electrochemical Impedance Spectroscopy (EIS)-based approaches either (i) hand-engineer a few Nyquist-plot features for shallow models—fast but does not generalize across geometries—or (ii) learn directly from Nyquist plots with deep networks, which removes manual feature extraction, yet still limited to a single plot type. As a result, cross-geometry robustness and deployability on constrained Internet of Things (IoT) devices remain open problems. We propose a compact Convolutional Neural Network (CNN) (∼ 10k parameters) that takes multi-representation EIS inputs—Nyquist (real/imaginary) and phase–magnitude (|Z|/ϕ) stacked as four channels, so the model can learn complementary degradation signatures while remaining small enough for fast inference. We build a dataset from cyclic aging of two geometries (LG INR18650MJ1 cylindrical cells and LIR2032 coin cells), acquire EIS every ten cycles from 10 kHz to 10 mHz (10 points/decade), and evaluate with leave-one-cell-out testing strategy. We further study fusion vs. single-representation inputs and assess feasibility for on-device deployment (e.g., NVIDIA Jetson device). The results show that training on multiple EIS representations improves SOH estimation accuracy and cross-geometry generalization compared to single-representation models, which uses only Nyquist or phase–magnitude plots. This design targets accurate, generalizable SOH prediction without manual feature engineering while enabling practical real-time use.

Bakr, Ahmed [The University of Alabama (UA)]

A Block-Structured Adaptive Mesh Framework to Solve Radiation Transfer Equation in Irregular Embedded Geometries

Radiation transport arises in various scientific, industrial, and medical fields, and understanding its effect in applications is needed to make accurate predictions, safety assessments and performance optimizations. Solving the Radiation Transport Equation (RTE) is challenging due to its integro-differential nature, which involves both differential and integral terms. The differential term describes the change in radiation intensity due to absorption and emission, while the integral term accounts for scattering. The accurate modeling of radiation is further complicated in many applications due to the complex, irregular geometries. Various methods exist for solving the RTE, including the zonal, Monte Carlo, spherical harmonics, discrete ordinates, and finite volume methods. Traditional mesh-based approaches, which rely on structured or unstructured meshes, struggle with irregular geometries due to: a) the difficulty of conforming structured grids to irregular domains, b) challenges in enforcing boundary conditions correctly, and c) the additional computational cost of unstructured mesh methods. This work presents a second-order accurate method for solving the RTE in irregular geometries. The radiation intensity is discretized using the finite-volume method in both spatial and angular directions on regular Cartesian grid blocks. Leveraging the block-structured adaptive mesh refinement (AMR) framework provided by AMReX, our method refines the grid locally to reduce spatial discretization error, ensuring a converged numerical solution while minimizing computational costs elsewhere. A two-stage deferred correction approach is employed: First, a first-order discretization on grid blocks is solved using an algebraic multigrid method in HYPRE. Second, a correction term is applied explicitly to achieve second-order accuracy. The correction term is calculated by approximating the radiation flux on cell faces using a Total Variation Diminishing (TVD) scheme. This approach ensures quick convergence of the multigrid method while preserving higher-order accuracy of the numerical solution. Irregular geometries are resolved as embedded boundaries (EB), resulting in both cut cells and regular cells. In cut cells, we modify the fluxes using face fractions and incorporate additional contributions from EB boundary conditions. To ensure higher-order convergence near the EB interface, the correction term is modified by interpolating the radiation intensity to fictitious ghost points. The implementation takes advantage of modern supercomputers by leveraging AMReX’sMPI/X parallelization strategy where X can be MPI or a GPU accelerator including CUDA, HIP and DPC++. We validate our solver using classical test cases, both with and without EB, demonstrating accuracy and efficiency. Additionally, we analyze the impact of adaptive mesh refinement on solution accuracy and computational cost, highlighting the advantages of our approach for high-resolution radiation transport simulations.

computational fluid dynamics (CFD)

Understanding Geometry and Microstructure Interactions In LPBF By Linking Lab Scale Studies To Real Part Case Examples

The mechanical properties derived from simple tensile tests are uniquely important in the design and qualification of load bearing metallic components. The tensile properties in standards for wrought metallic materials are generally accessible for design and simulation engineers, but this is not the case for additively manufactured metals. This work investigates the influence of tensile specimen geometry on the mechanical properties of laser powder bed fusion (LPBF) additively manufactured Ti-6Al-4V, particularly in relation to properties measured from specimens excised from an exemplar part. A comprehensive analysis was conducted across various specimen geometries, considering factors such as thermal history, cross-sectional area, shape, and surface roughness. Key findings reveal that sample size, particularly cross-sectional area, significantly affects reported tensile properties, with ASTM E8 flat and round specimens exhibiting differences in elastic modulus (13%), yield strength (17%), ultimate tensile strength (UTS) (14%), and elongation to failure (11%). Additionally, surface roughness was found to have a limited impact on ASTM round geometries, but it becomes critical in thin-walled and small high-throughput samples. The ASTM flat samples closely matched the properties of samples excised from the exemplar part, underscoring the necessity of testing witness samples that accurately represent end-use conditions. Furthermore, mechanical properties of samples built within the stitch zone of the exemplar part demonstrated reduced ductility, highlighting the importance of laser alignment and qualification in multi-laser additive manufacturing processes. Overall, this study emphasizes the need for careful consideration of specimen geometry and testing conditions to ensure accurate reporting of mechanical properties in LPBF Ti-6Al-4V.

36 MATERIALS SCIENCE