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All sources NASA NTRS DOE OSTI

DOE OSTI2021

Implementation of higher-order velocity mapping between marker particles and grid in the particle-in-cell code XGC

The global total-f gyrokinetic particle-in-cell code XGC, used to study transport in magnetic fusion plasmas or to couple with a core gyrokinetic code while functioning as an edge gyrokinetic code, implements a 5-dimensional (5D) continuum grid to perform the dissipative operations, such as plasma collisions, or to exchange the particle distribution function information with a core code. To transfer the distribution function between marker particles and a rectangular 2D velocity-space grid, XGC employs a bilinear mapping. The conservation of particle density and momentum is accurate enough in this bilinear operation, but the error in the particle energy conservation can become undesirably large and cause non-negligible numerical heating in a steep edge pedestal. In the present work we update XGC to use a novel mapping technique, based on the calculation of a pseudo-inverse, to exactly preserve moments up to the order of the discretization space. We describe the details of the implementation and we demonstrate the reduced interpolation error for a tokamak test plasma by using 1st- and 2nd-order elements with the pseudo-inverse method and comparing to the bilinear mapping.

Fusion Plasma↗

DOE OSTI2026

INtegrated Fluid & paRticles simulatioN cOde (INF&RNO) v1.0

INF&RNO (INtegrated Fluid & paRticle simulation cOde) is a 2D cylindrical (r-z) code to model the interaction of short laser pulse(s) with an underdense plasma. The code is based on an envelope model for the laser field, and the action of the laser on the plasma is modeled with the time-averaged ponderomotive force approximation. The code features an improved laser envelope solver which enables an accurate description of the laser pulse evolution deep into depletion even at a reasonably low resolution.

Benedetti, Carlo [Lawrence Berkeley National Labor↗

DOE OSTI2021

Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

Abstract Background Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. Results We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10 −3 ), and combined dataset (p = 1.1 × 10 −4 ). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10 −35 , loss-of-function p = 2.26 × 10 −13 ) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10 −6 , OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. Conclusions In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Superdense coding interleaved with forward error correction

Superdense coding promises increased classical capacity and communication security but this advantage may be undermined by noise in the quantum channel. We present a numerical study of how forward error correction (FEC) applied to the encoded classical message can be used to mitigate against quantum channel noise. By studying the bit error rate under different FEC codes, we identify the unique role that burst errors play in superdense coding, and we show how these can be mitigated against by interleaving the FEC codewords prior to transmission. As a result, we conclude that classical FEC with interleaving is a useful method to improve the performance in near-term demonstrations of superdense coding.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

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↗

DOE OSTI2024

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↗

DOE OSTI2021

Nyx: A Massively Parallel AMR Code for Computational Cosmology

Nyx is a highly parallel, adaptive mesh, finite-volume N-body compressible hydrodynamics solver for cosmological simulations. It has been used to simulate different cosmological scenarios with a recent focus on the intergalactic medium and Lyman alpha forest. Together, Nyx, the compressible astrophysical simulation code, Castro, and the low Mach number code MAESTROeX, make up the AMReX-Astrophysics Suite of open-source, adaptive mesh, performance-portable astrophysical simulation codes. Other examples of cosmological simulation research codes include Enzo, Enzo-P/Cello, RAMSES, ART, FLASH, Cholla, as well as Gadget, Gasoline, Arepo, Gizmo, and SWIFT.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2012

Early-stage quantitative risk assessment to support development of codes and standard requirements for indoor fueling of hydrogen vehicles

Sandia National Laboratories is developing the technical basis for assessing the risk of hydro gen infrastructure for use in the development of relevant codes and standards. The development of codes and standards is an important step in ensuring the safe design and operation of the hydrogen fuel cell infrastructure. Codes and standards organizations are increasingly using risk-informed processes to establish code requirements.

Groth, Katrina M.↗

DOE OSTI2013

CBP Toolbox Version 2.0: Code Integration Enhancements

This report describes enhancements made to code integration aspects of the Cementitious Barriers Project (CBP) Toolbox as a result of development work performed at the Savannah River National Laboratory (SRNL) in collaboration with Vanderbilt University (VU) in the first half of fiscal year 2013. Code integration refers to the interfacing to standalone CBP partner codes, used to analyze the performance of cementitious materials, with the CBP Software Toolbox. The most significant enhancements are: 1) Improved graphical display of model results. 2) Improved error analysis and reporting. 3) Increase in the default maximum model mesh size from 301 to 501 nodes. 4) The ability to set the LeachXS/Orchestra simulation times through the GoldSim interface. These code interface enhancements have been included in a new release (Version 2.0) of the CBP Toolbox.

36 MATERIALS SCIENCE↗

DOE OSTI2013

Verification and Validation of High-Fidelity Multi-Physics Simulation Codes for Advanced Nuclear Reactors (Year 2)

The project objective is to verify and validate a suite of high-fidelity multi-physics simulation methods and codes developed during the previous I-NERI projects, against Monte Carlo solutions and experimental measurements for LWR and VHTR cores. Using benchmark problems developed during the previous year, ANL and KAERI continued to work on verifying the neutronics code DeCART and associated cross section libraries. Initial progress was also made on validating the code against experimental data. KAERI focused on verifying the DeCART code against numerical benchmark problems such as a PMR200 2-D pin cell/core and a HTTR 2-D block/core as well as improving DeCART capabilities such as the cross-section library group structure optimization, the fundamental and generalized adjoint equation solver, cylindrical boundary treatment, improved ray tracing, and implementing the direct resonance integral table method for resonance treatment. Verification test results for the updated capabilities showed substantial improvements in the estimation of eigenvalue and reaction rates.

Lee, C. H.↗

DOE OSTI2014

User's Manual for the RealGasBrine v1.0 Option of TOUGH+ v1.5: A Code for the Simulation of System Behavior in Gas-Bearing Geologic Media

REALGASBRINE v1.0 is a numerical code that for the simulation of the behavior of gas-bearing porous and/fractured geologic media. It is an option of TOUGH+ v1.5 [Moridis, 2014], a successor to the TOUGH2 [Pruess et al., 1999] family of codes for multi-component, multiphase fluid and heat flow developed at the Lawrence Berkeley National Laboratory. REALGASBRINE v1.0 needs the TOUGH+ v1.5 core code in order to compile and execute. It is written in standard FORTRAN 95/2003, and can be run on any computational platform (workstation, PC, Macintosh) for which such compilers are available. REALGASBRINE v1.0 describes the non-isothermal two- (for pure water) or three-phase (for brine) flow of an aqueous phase and a real gas mixture in a gas-bearing medium, with a particular focus in ultra-tight (such as tight-sand and shale gas) systems. Up to 12 individual real gases can be tracked, and salt can precipitate as solid halite. The capabilities of the code include coupled flow and thermal effects, real gas behavior, Darcy and non-Darcy flow, several isotherm options of gas sorption onto the grains of the porous media, complex fracture descriptions, gas solubility into water, and geomechanical effects on flow properties. REALGASBRINE v1.0 allows the study of flow and transport of fluids and heat over a wide range of time frames and spatial scales not only in gas reservoirs, but also in any problem involving the flow of gases in geologic media, including the geologic storage of greenhouse gas mixtures, the behavior of geothermal reservoirs with multi-component condensable (H 2 O and CO 2 ) and non-condensable gas mixtures, the transport of water and released H 2 in nuclear waste storage applications, etc.

15 GEOTHERMAL ENERGY↗

DOE OSTI2014

AGR-2 safety test predictions using the PARFUME code

This report documents calculations performed to predict failure probability of TRISO-coated fuel particles and diffusion of fission products through these particles during safety tests following the second irradiation test of the Advanced Gas Reactor program (AGR-2). The calculations include the modeling of the AGR-2 irradiation that occurred from June 2010 to October 2013 in the Advanced Test Reactor (ATR) and the modeling of a safety testing phase to support safety tests planned at Oak Ridge National Laboratory and at Idaho National Laboratory (INL) for a selection of AGR-2 compacts. The heat-up of AGR-2 compacts is a critical component of the AGR-2 fuel performance evaluation, and its objectives are to identify the effect of accident test temperature, burnup, and irradiation temperature on the performance of the fuel at elevated temperature. Safety testing of compacts will be followed by detailed examinations of the fuel particles to further evaluate fission product retention and behavior of the kernel and coatings. The modeling was performed using the particle fuel model computer code PARFUME developed at INL. PARFUME is an advanced gas-cooled reactor fuel performance modeling and analysis code (Miller 2009). It has been developed as an integrated mechanistic code that evaluates the thermal, mechanical, and physico-chemical behavior of fuel particles during irradiation to determine the failure probability of a population of fuel particles given the particle-to-particle statistical variations in physical dimensions and material properties that arise from the fuel fabrication process, accounting for all viable mechanisms that can lead to particle failure. The code also determines the diffusion of fission products from the fuel through the particle coating layers, and through the fuel matrix to the coolant boundary. The subsequent release of fission products is calculated at the compact level (release of fission products from the compact). PARFUME calculates the release fraction as the ratio of the number of atoms released from the compact to the amount produced in the compact fuel kernels and through uranium contamination. These safety test predictions aim at giving guidance for the upcoming safety tests to be conducted at ORNL and INL. The AGR-2 compacts modeled in this study belong to the four U.S. capsules of the AGR-2 irradiation test train. For each capsule, the compacts with the lowest and highest burnups were selected to provide a prediction envelope. The objective of this document is to present results of calculations and analyses made by PARFUME on these selected AGR-2 compacts. These results include: • Fuel failure probability • Palladium penetration • Fractional release of fission products Details associated with completion of these calculations are provided in the remainder of this document: the AGR-2 Safety Testing plan is briefly introduced in Section 2, PARFUME modeling is outlined in Section 3, results are described in Section 4, conclusions are given in Section 5, and references are listed in Section 6.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2015

Code Disentanglement: Initial Plan

The first step to making more ambitious changes in the EAP code base is to disentangle the code into a set of independent, levelized packages. We define a package as a collection of code, most often across a set of files, that provides a defined set of functionality; a package a) can be built and tested as an entity and b) fits within an overall levelization design. Each package contributes one or more libraries, or an application that uses the other libraries. A package set is levelized if the relationships between packages form a directed, acyclic graph and each package uses only packages at lower levels of the diagram (in Fortran this relationship is often describable by the use relationship between modules). Independent packages permit independent- and therefore parallel|development. The packages form separable units for the purposes of development and testing. This is a proven path for enabling finer-grained changes to a complex code.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Safety, codes and standards for hydrogen installations. Metrics development and benchmarking

Automakers and fuel providers have made public commitments to commercialize light duty fuel cell electric vehicles and fueling infrastructure in select US regions beginning in 2014. The development, implementation, and advancement of meaningful codes and standards is critical to enable the effective deployment of clean and efficient fuel cell and hydrogen solutions in the energy technology marketplace. Metrics pertaining to the development and implementation of safety knowledge, codes, and standards are important to communicate progress and inform future R&D investments. This document describes the development and benchmarking of metrics specific to the development of hydrogen specific codes relevant for hydrogen refueling stations. These metrics will be most useful as the hydrogen fuel market transitions from pre-commercial to early-commercial phases. The target regions in California will serve as benchmarking case studies to quantify the success of past investments in research and development supporting safety codes and standards R&D.

08 HYDROGEN↗

DOE OSTI2015

Advanced Imaging Optics Utilizing Wavefront Coding

Image processing offers a potential to simplify an optical system by shifting some of the imaging burden from lenses to the more cost effective electronics. Wavefront coding using a cubic phase plate combined with image processing can extend the system's depth of focus, reducing many of the focus-related aberrations as well as material related chromatic aberrations. However, the optimal design process and physical limitations of wavefront coding systems with respect to first-order optical parameters and noise are not well documented. We examined image quality of simulated and experimental wavefront coded images before and after reconstruction in the presence of noise. Challenges in the implementation of cubic phase in an optical system are discussed. In particular, we found that limitations must be placed on system noise, aperture, field of view and bandwidth to develop a robust wavefront coded system.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Sandia National Laboratories Environmental Fluid Dynamics Code: Marine Hydrokinetic Module User’s Manual

This document describes the marine hydrokinetic (MHK) input file and subroutines for the Sandia National Laboratories Environmental Fluid Dynamics Code (SNL-EFDC), which is a combined hydrodynamic, sediment transport, and water quality model based on the Environmental Fluid Dynamics Code (EFDC) developed by John Hamrick, formerly sponsored by the U.S. Environmental Protection Agency, and now maintained by Tetra Tech, Inc. SNL-EFDC has been previously enhanced with the incorporation of the SEDZLJ sediment dynamics model developed by Ziegler, Lick, and Jones. SNL-EFDC has also been upgraded to more accurately simulate algae growth with specific application to optimizing biomass in an open-channel raceway for biofuels production. A detailed description of the input file containing data describing the MHK device/array is provided, along with a description of the MHK FORTRAN routine. Both a theoretical description of the MHK dynamics as incorporated into SNL-EFDC and an explanation of the source code are provided. This user manual is meant to be used in conjunction with the original EFDC and sediment dynamics SNL-EFDC manuals. Through this document, the authors provide information for users who wish to model the effects of an MHK device (or array of devices) on a flow system with EFDC and who also seek a clear understanding of the source code, which is available from staff in the Water Power Technologies Department at Sandia National Laboratories, Albuquerque, New Mexico.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Methodology for Evaluating Cost-effectiveness of Commercial Energy Code Changes

This document lays out the U.S. Department of Energy’s (DOE’s) method for evaluating the cost-effectiveness of energy code proposals and editions. The evaluation is applied to provisions or editions of the American Society of Heating, Refrigerating and Air-Conditioning Engineers (ASHRAE) Standard 90.1 and the International Energy Conservation Code (IECC). The method follows standard life-cycle cost (LCC) economic analysis procedures. Cost-effectiveness evaluation requires three steps: 1) evaluating the energy and energy cost savings of code changes, 2) evaluating the incremental and replacement costs related to the changes, and 3) determining the cost-effectiveness of energy code changes based on those costs and savings over time.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2015

Report on FY15 Alloy 617 Code Rules Development

Due to its strength at very high temperatures, up to 950°C (1742°F), Alloy 617 is the reference construction material for structural components that operate at or near the outlet temperature of the very high temperature gas-cooled reactors. However, the current rules in the ASME Section III, Division 5 Subsection HB, Subpart B for the evaluation of strain limits and creep-fatigue damage using simplified methods based on elastic analysis have been deemed inappropriate for Alloy 617 at temperatures above 650°C (1200°F) (Corum and Brass, Proceedings of ASME 1991 Pressure Vessels and Piping Conference, PVP-Vol. 215, p.147, ASME, NY, 1991). The rationale for this exclusion is that at higher temperatures it is not feasible to decouple plasticity and creep, which is the basis for the current simplified rules. This temperature, 650°C (1200°F), is well below the temperature range of interest for this material for the high temperature gas-cooled reactors and the very high temperature gas-cooled reactors. The only current alternative is, thus, a full inelastic analysis requiring sophisticated material models that have not yet been formulated and verified. To address these issues, proposed code rules have been developed which are based on the use of elastic-perfectly plastic (EPP) analysis methods applicable to very high temperatures. The proposed rules for strain limits and creep-fatigue evaluation were initially documented in the technical literature (Carter, Jetter and Sham, Proceedings of ASME 2012 Pressure Vessels and Piping Conference, papers PVP 2012 28082 and PVP 2012 28083, ASME, NY, 2012), and have been recently revised to incorporate comments and simplify their application. Background documents have been developed for these two code cases to support the ASME Code committee approval process. These background documents for the EPP strain limits and creep-fatigue code cases are documented in this report.

36 MATERIALS SCIENCE↗