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Manuscript model outputs, model source code, and figure scripts: The role of geomorphology in mediating biomass allocation impacts on salt-marsh resilience and carbon accumulation

This data package provides model source code (C++), model outputs, and figure generation scripts (R) needed to reproduce the following manuscript: Bruns, Nicholas E., Genevieve L. Noyce, and Matthew L. Kirwan. "The Role of Geomorphology in Mediating Biomass Allocation Impacts on Salt-Marsh Resilience and Carbon Accumulation." Estuarine, Coastal and Shelf Science 327 (December 2025): 109549. https://doi.org/10.1016/j.ecss.2025.109549. This manuscript investigates how geomorphology mediates the impact of biomass allocation shifts on salt marsh persistence and carbon (C) sequestration under sea level rise. We use a 1-D soil-column model (Kirwan and Mudd 2012) to perform experiments across a range of static root:shoot ratios (RSR = 1-4) spanning observed values. The model explicitly simulates interactions between tidal inundation, productivity, inorganic sediment deposition, and organic matter accumulation. Experiments determine whether geomorphic feedbacks amplify, dampen, or leave unchanged the ecosystem response to biomass allocation shifts. A first experiment uses constant sea level rise (2.5 mm/yr) to examine equilibrium dynamics and their influence on carbon accumulation rates across different suspended sediment concentrations (SSC). A second set of experiments calculates threshold sea level rise rates for marsh drowning across RSR and SSC combinations. Final experiments apply accelerating sea level rise scenarios (2000-2200) derived from NOAA projections (Sweet et al. 2022) to generate an envelope of expected responses, quantifying the importance of biomass allocation shifts on marsh carbon accumulation and persistence. All experiments are repeated across SSC ranging from 5-50 mg/L to investigate how these interactions vary in micro-tidal marshes with different sediment supplies. Package contents: * README.txt with detailed description of package contents and instructions for reproducing manuscript figures and model outputs * R scripts for generating all manuscript figures * C++ baseline model code from Kirwan and Mudd (2012) * C++ source code for 4 experimental model variants used in the manuscript, extending above baseline code * Model input files (.csv, .txt) including sea level rise scenarios * Model output files (.txt) used in manuscript analyses Temporal coverage: Model simulations span years 1900-2200, with accelerating sea level rise scenarios for 2000-2200. Key variables: Root:shoot ratio, suspended sediment concentration, carbon accumulation rate, vertical accretion rate, marsh elevation, inundation depth, threshold sea level rise rate.

54 ENVIRONMENTAL SCIENCES

Multiphysics modeling of accelerators through code integration

This work aims to improve the ability of particle accelerator researchers to develop high-performance accelerator cavity designs by creating an overall multiphysics framework that integrates and couples existing application codes. This framework will allow accelerator researchers to build multiphysics models that will optimize cavity design, improve understanding of whole-device performance, and reduce the development and fabrication costs of accelerator research. We utilize the open-source VizSchema data standard as an intermediate data structure interface layer to standardize interfaces between individual application codes. VizScema is extensively documented online, and plugins for VizSchema are available for popular visualization packages, including VisIt and ParaView. Currently, the work focuses on coupling the EM field solver COMSOL and the electron gun code MICHELLE to allow COMSOL field-solve results to be seamlessly used by MICHELLE for particle-solve. Later work will extend this integration to include other fields, particles, and thermodynamics simulation codes.

43 PARTICLE ACCELERATORS

Adopting Code Verification Methodology Based on Model Form

Code verification is an essential part of credibility analysis for computational models. It assesses whether the mathematical model is implemented correctly into the code and whether the numerical methods behave consistently, and is done before solution verification and validation. Robust guidance for code verification exists in the literature. However, there is no known, concise guide for selecting the approach based on the model form that also presents an overview of the common elements. This document was written to address this gap as an accessible reference for beginning a code-verification effort.

97 MATHEMATICS AND COMPUTING

Adapting Code Verification Methodology to Model Form

Code verification is an essential part of credibility analysis for computational models. It assesses whether the mathematical model is implemented correctly into the code and whether the numerical methods behave consistently, and is done before solution verification and validation. Robust guidance for code verification exists in the literature. However, there is no known, concise guide for selecting the approach based on the model form that also presents an overview of the common elements. This document was written to address this gap as an accessible reference for beginning a code-verification effort.

97 MATHEMATICS AND COMPUTING

New charged-particle transport computational capability: the SIT code An L-4 milestone

We have developed a new high-fidelity code for direct transport of charged particles using the simple integral transport method. The code can be coupled to the outputs of any hydrodynamical simulation code in 1-D, 2-D or 3-D. In this report we summarize the formalism involved in treating complex transport problems. We present physical examples wherein we have used the code to calculate the transport of alpha particles. Future work is planned to study the sensitivity of hydrodynamical mix to charged-particle radiochemistry and reaction-in-flight neutrons for the complex inertial confinement fusion problems encountered at NIF and at the Z-machine.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA

ASME Code change proposal to implement new universal high temperature constitutive models for Section III, Division 5

This report completes work on a universal high temperature constitutive model suitable for use with the ASME Boiler & Pressure Vessel Code Section III, Division 5 rules for the design by inelastic analysis of Class A nuclear reactor components. The goals of this work are to provide a simple model form that adequately captures the high temperature response of materials and can be applied to any future Code material. Additionally, the report describes an automated process for calibrating a model against test data. The idea is to simplify the effort required to generate a constitutive model for an arbitrary material, provided test data is available. This will accelerate the process of qualifying new Code materials in the future. In addition, the report provides calibrated models and detailed validation comparisons to test data for five currently-qualified or soon-to-be qualified materials: 316H, Grade 91, Alloy 800H, Alloy 617, and Alloy 709. The report surveys the available data for the remaining two ASME Class Materials --- 2.25Cr-1Mo and 304H --- concluding that there is enough data data to generate a model for 2.25Cr-1Mo steel provided some additional sources of non-public data can be included in the test database, but that a dedicated cyclic test campaign would be needed for 304H. Supplemental material includes the full text of an ASME Code change proposal to incorporate the models for the four currently-qualified Class A material, detailed validation comparisons to test data for the five material models, and input files for reference implementations of the constitutive models in the NEML and NEML2 modeling frameworks.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Software Quality Assurance for the MOOSE-Based Open-Source Multiphysics Code Cardinal - An Expanded CI Testing Suite

Cardinal is a wrapping of the GPU-oriented spectral element Computational Fluid Dynamics (CFD) code NekRS and the Monte Carlo particle transport code OpenMC within the Multiphysics Object-Oriented Simulation Environment (MOOSE). Cardinal provides high-resolution thermal-hydraulics and/or radiation transport feedback to MOOSE multiphysics simulations. Multiphysics feedback is implemented in a geometry-agnostic manner which eliminates the need for rigid one-to-one mappings. A generic data transfer implementation also allows NekRS and OpenMC to couple to any MOOSE application, enabling a broad set of multiphysics capabilities. Cardinal simulations can also leverage combinations of MPI, OpenMP, and GPU resources. Cardinal continuous development and improvement efforts have led to the software being considered as a high-fidelity design and licensing tool for key areas of nuclear reactor relevant physics, including neutron transport, fluid flow, heat transfer, and mechanical processes. The fast development and expansion of the software from a pure R&D framework towards its application in the nuclear industry and regulation require a focus on developing, enhancing and, maintaining Cardinal’s software quality through strict adherence to a Software Quality Assurance (SQA) framework and SQA program. To facilitate compliance with SQA standards, the Cardinal SQA Program has been initiated during Fiscal Year 2023 (FY23). During the development of the Cardinal SQA Program, multiple gaps have been identified. These gaps are primarily related to model verification and code pedigree as they relate to the use of Cardinal as a safety analysis tool. These gaps have been captured in a report published in 2023. A second report highlighted the progress made during Fiscal Year 2024 (FY24) and described Argonne’s effort to document and integrate software verification within Cardinal’s software development process. This report documents a snapshot of the verification test cases currently available for Cardinal and NekRS in their assimilation into a Continuous Integration (CI) platform. Following the CI practice permits the integrating of source code changes frequently and ensuring that the integrated codebase clears the verification testing for the software. It should be noted that the SQA program itself, including the program plans, procedures, configuration management, and testing strategies, need to be developed in a future step of this task.

22 GENERAL STUDIES OF NUCLEAR REACTORS

Evaluation of LLM-Generated Kokkos Code Using Compile-Time and Run-Time Testing

Due to the growing use of large language models (LLMs) by developers and researchers, it has become essential to reliably evaluate their ability to generate code that uses specialized libraries. We explore the use of compile-time and run-time evaluation of LLM-generated Kokkos code through extending the methods used by OpenAI with the HumanEval dataset. Our evaluation framework is based on the first 40 prompts from the Kokkos138 dataset. We start by discussing two different forms of LLM prompting, using entirely plain English or providing pseudocode for added context. These two methods are used to generate Kokkos code with the Llama-3.1-8B-Instruct and CodeQwen1.5-7B-Chat models. We found that both forms of prompting led to high failure rates and difficulties with reliably parsing LLM-generated code, while prompts with pseudocode for context generally led to improved results on more complicated tests.

97 MATHEMATICS AND COMPUTING

Staged Z-Pinch Modeling with Hydra and Chicago Codes (CRADA Final Report)

This was a collaborative effort between Lawrence Livermore National Security, LLC (“Contractor”), as manager and operator of Lawrence Livermore National Laboratory (“LLNL”) and Magneto Inertial Fusion Technologies, Inc. ("MIFTI" or "Participant"), to develop staged Z-pinch (SZP) modeling with HYDRA and CHICAGO codes. The contractor performed numerical simulations of the SZP to reproduce and validate Participant’s MACH2 simulations. Contractor used the state-of-the-art, radiation-magneto-hydrodynamic code HYDRA, as well as the hybrid particle-in-cell code CHICAGO. This work helped assess the physical and numerical uncertainties associated with the simulations and the overall fusion scheme. HYDRA is a well-established and validated code. This work has helped to independently assess the SZP concept to give confidence to the Participant and to the broader fusion community.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Leveraging MARVEL and SPHERE to Demonstrate NEAMS Thermal Hydraulics Codes

The Single Primary Heat Extraction and Removal Emulator (SPHERE) and Microreactor Applications Research Validation and Evaluation (MARVEL) were utilized to demonstrate thermal hydraulics codes of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. A recent long-duration test of a sodium heat pipe conducted at the SPHERE facility was utilized for the validation of the heat pipe code Sockeye. The first 10 hours of operation featured a startup of the heat pipe from room temperature; this portion was modeled with Sockeye and compared to the experimental data. Measurements included several thermocouple measurements across the length of the heat pipe surface. Two of Sockeye’s heat pipe models were applied to experiment, as well as several models of the cooling at the condenser end of the heat pipe. Sockeye results gave a decent match to the experimental data, with notable discrepancy in the condenser section, where experimental data indicated a significant inactive length of the heat pipe. The MARVEL microreactor was modeled through a coupled simulation of System Analysis Module (SAM) and SubChannel Module (SCM). This multiscale coupled simulation was performed as an exercise to demonstrate the compatibility and applicability of these codes for thermal-hydraulic analysis of microreactors. The coupling between the SCM and SAM codes for multiscale modeling of MARVEL, was achieved through a domain overlapping approach. In this example a transient SAM simulation provided boundary conditions to SCM, and SCM provided pressure drop to SAM.

97 - MATHEMATICS AND COMPUTING

Deflagration to Detonation Transition Update: XDDT Code Modularization

A legacy FORTRAN 77 implementation of the Baer–Nunziato two-phase mixture theory for deflagration-to-detonation transition (DDT) in reactive granular materials—hereafter the XDDT (eXplosive DDT) code—has been modularized to Fortran 90 with modular structure, external input files, and adaptive mesh capability. During validation, two code defects were identified and corrected: an inconsistency in the nodal solid pressure evaluation and a nonphysical burn-front tracking criterion. The ignition criterion was also corrected to use the granular surface temperature from the interface heat transfer model, matching the original Baer implementation. An initial attempt to validate against Figure 3 of the original Baer and Nunziato (1986) paper revealed that the code’s detonation velocity on a 201-node mesh (5.5 km/s) was approximately 21% below the expected Chapman–Jouguet value for 70% TMD HMX (∼7 km/s). Validation was redirected to the piston-driven DDT experiments of McAfee et al. (1989), Shot B-9036, for which well-characterized ionization-pin data are available. With the compaction-burn coefficient calibrated to 𝐶 𝛼 = 75, the XDDT code reproduces the DDT transition time to within 0.4% and produces a steady-state detonation velocity within 4% of the McAfee experimental value of 6.36 km/s. The burn model was generalized to support pressure-dependent exponents, enabling application to nitrocellulose-based ball propellants (TS3659) with a cube-root pressure dependence. Validation against the Sandusky/Baer PDC82 piston-impact experiment yielded a reactive wave velocity of 2.3–2.8 km/s, in good agreement with the experimental value of ∼2.2 km/s, and wave coalescence within 5% of the experimental timing. The mathematical model, input parameter requirements, and a roadmap for extending XDDT to PETN with an autocatalytic burn model are presented.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF

Entity—Hardware-agnostic Particle-in-cell Code for Plasma Astrophysics. I. Curvilinear Special Relativistic Module

Entity is a new-generation, fully open-source particle-in-cell (PIC) code developed to overcome key limitations in astrophysical plasma modeling, particularly the extreme separation of scales and the performance challenges associated with evolving, GPU-centric computing infrastructures. It achieves hardware-agnostic performance portability across various GPU and CPU architectures using the Kokkos library. Crucially, Entity maintains a high standard for usability, clarity, and customizability, offering a robust and easy-to-use framework for developing new algorithms and grid geometries, which allows extensive control without requiring edits to the core source code. This paper details the core general-coordinate special relativistic module. Entity is the first PIC code designed to solve the Vlasov–Maxwell system in general coordinates, enabling a coordinate-agnostic framework that provides the foundational structure for straightforward extension to arbitrary coordinate geometries. The core methodology achieves numerical stability by solving particle equations of motion in the global orthonormal Cartesian basis, despite using generalized coordinates like Cartesian, axisymmetric spherical, and quasi-spherical grids. Charge conservation is ensured via a specialized current deposition technique using conformal currents. The code exhibits robust scalability and performance portability on major GPU platforms (AMD MI250X, NVIDIA A100, and Intel Max Series), with the 3D particle pusher and the current deposition operating efficiently at about 2 ns per particle per time step. Functionality is validated through a comprehensive suite of standard Cartesian plasma tests and the accurate modeling of relativistic magnetospheres in curvilinear axisymmetric geometries.

Hakobyan, Hayk [Flatiron Institute, New York, NY (

Data Driven Commercial Building Energy Code Compliance and Technology Inventory for New York City

Building Performance Standards (BPS) are gaining national traction. A BPS will require new processes in the design, construction, and operation of buildings that take the occupants into account and enable predictive analysis to ensure compliance with current and future GHG emissions caps. In New York City, most buildings over 25,000 square feet will be regulated by a BPS starting in 2024, regardless of whether it is new construction permitted under current energy codes or an existing building. This research is one of the first to begin the evaluation of a long-term series of building policies in the context of an open data ecosystem, in cooperation with city agencies. Existing building policies enacted in NYC have ranged from building energy benchmarking and labeling to energy audits to the regulation of GHG emission in buildings. Through the development of a dataset related to building technologies and energy consumption, this project can help to evaluate if meaningful conclusions can be drawn for the data that has been largely self-reported in compliance with city regulations. This project will also provide lessons learned from a deep dive into these types of datasets to provide best practices for municipalities or states seeking to embark on policies like those enacted in NYC. In addition, a Building Automation System (BAS) Stretch Standard of Care (SSOC) for owners, designers, and building operators will enable the measurement and predictive analysis of energy consumption and GHG emissions at the plant, system, or component level, in anticipation of regulated GHG limits on buildings based on energy use. The SSOC is expected to be suitable for use on a national level. The primary feature of an SSOC is a standardized format for a set of BAS points that can be used to control and to gather data from individual plants, systems, or components that are related to building energy consumption. This project examined how measurements compare to prescriptive or simulation-based energy code targets, finding little correlation between predictive 8760-hour energy modeling and actual energy consumption for a small sample (n=27) of buildings constructed after 2015. Other analysis found that, while large multifamily housing (MFH) buildings showed a general trend similar to predicted reductions in energy use from the implementation of model commercial energy codes, this trend was not evident in the office, K-12 school, and hotel use groups in NYC. No upward or downward trends in energy consumption were found when buildings were grouped by size. Energy audit data were analyzed and it appears that there is bias by audit company on measures recommended to clients. Further research should be performed to cross-analyze this with other attributes, such as building size, vintage, and number of stories. Analysis found that for 281 buildings that were permitted and completed after 2015 and had submitted benchmarking data in 2022, between 81% and 96% (by use group) were found to be in compliance with the 2024 to 2029 NYC BPS emission caps, and between 55% and 89% were in compliance with the 2030-2034 caps. This work is beneficial to the public in helping policymakers and building stakeholders better understand the wide-ranging implications of a BPS.

29 ENERGY PLANNING, POLICY, AND ECONOMY

Electric Readiness in Residential Energy Code: Technical Brief

This technical brief provides requirements for electric readiness that could be incorporated into model residential energy codes. It provides background on the basis and benefits of the provisions, and model code language that can be plugged into the IECC or adapted into other energy codes. This brief has been updated to reflect changes in the 2024 IECC.

2021 IECC

Highly-detailed neutronic and thermal-hydraulic coupled calculations for OPAL reactor using diverse codes and approaches

The industry-standard approach for designing and operating research reactors cores relies on well-established methodologies that consider uncoupled neutronic calculations and a subchannel analysis of the Thermal-Hydraulic (TH) associated problem. Advancements in computing power and codes allow detailed Multiphysics approaches to be implemented, thereby reducing conservatism. In this study, a comparative analysis of results from diverse detailed neutronic-TH coupled core approaches is developed. To address a realistic application case, the comparison is made for a reported critical configuration from the Open Pool Australian Lightwater research reactor (OPAL) at Hot Full Power (HFP) and low burnup. Both cell-core and stochastic methodologies for neutronics are evaluated, whereas two different subchannel codes are considered for TH. In conclusion, the convergence of the coupled schemes, and the consistency of the main parameters are discussed, showing the compatibility of the alternative methods and their ability to offer critical insights not captured by standard practices.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS

MCNP® Code Version 6.3.1: Build Guide (Rev. 1)

This is a build guide for the MCNP® code, version 6.3.1, that expands upon the README.md included with the source code. It covers compilers, dependencies, building, testing, and installing the code in one of its supported configurations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Buffer-IPyC separation process in TRISO fuel particles simulated with Bison code

During High Temperature Gas-cooled Reactor (HTGR) operation, tristructural isotropic (TRISO) coated-particle fuel undergoes irradiation-induced changes in morphology and thermomechanical properties. Experimental results from the Advanced Gas Reactor (AGR) Fuel Development and Qualification Program show, among other things, the mechanism of gap formation between the buffer and inner pyrolytic carbon (IPyC) layers, which could be explored further via computational simulations using the Bison code. Two simulation models were developed, the debonding restricted model, where no gap formation between buffer and IPyC layers is permitted, and the debonding enabled model, where the gap between those layers is created. The inputs of the simulated models are based on the irradiation conditions from the AGR-1 experiment. The research included simulations on spherical and aspherical fuel types. Under the specific temperatures and fluences of the AGR-1 irradiation experiment, and the Bison simulations, it was concluded that the most common scenario is a gap formation along the buffer-IPyC interface, while the least possible scenario is the situation where there is no gap formation at the buffer-IPyC junction. The computational results confirmed that the sphericity of the fuel influences the thickness of the gap that occurs at the buffer-IPyC junction, in a way that with increasing aspect ratio the gap thickness increases. The results obtained for spherical and aspherical fuel are nearly identical. Finally, performed simulations match conclusions observed from the AGR-1 experiment, which as such shows that the Bison code is a good computational method for simulating the TRISO fuel. Future simulations will include the validation of performed research and comparison of the results between Bison and PARFUME codes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS

Benchmarking of massively parallel phase-field codes for directional solidification

We present a detailed benchmark comparing two state-of-the-art phase-field implementations for simulating alloy solidification under experimentally relevant conditions. The study investigates the directional solidification of Al-3wt%Cu under high-velocity solidification conditions and SCN-0.46wt% camphor under microgravity conditions from National Aeronautics and Space Administration (NASA) DECLIC-DSI-R experiments. Both codes, one employing finite-difference discretization with uniform mesh and GPU-acceleration (GPU-PF) and the other one employing finite-element discretization with adaptive-mesh and CPU-parallelization (PRISMS-PF), solve the same quantitative phase-field formulation that incorporates an anti-trapping current for the solidification of dilute alloys. We evaluate the predictions of each code for dendritic morphology, primary spacing, and tip dynamics in both 2D and 3D, as well as their numerical convergence and computational performance. While existing benchmark problems have primarily focused on simplified or small-scale simulations, they do not reflect the computational and modeling challenges posed by employing experimentally relevant time and length scales. Our results provide a practical framework for assessing phase-field code performance as well as validating and facilitating their application in integrated computational materials engineering (ICME) workflows that require integration with realistic experimental data.

36 MATERIALS SCIENCE