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TOUGH+ v1.5 Core Code

TOUGH+ v1.5 is a numerical code for the simulation of multi-phase, multi-component flow and transport of mass and heat through porous and fractured media, and represents the third update of the code since its first release [Moridis et al., 2008]. TOUGH+ is a successor to the TOUGH2 [Pruess et al., 1991; 2012] family of codes for multi-component, multiphase fluid and heat flow developed at the Lawrence Berkeley National Laboratory. It is written in standard FORTRAN 95/2003, and can be run on any computational platform (workstations, PC, Macintosh). TOUGH+ v1.5 employs dynamic memory allocation, thus minimizing storage requirements. It has a completely modular structure, follows the tenets of Object-Oriented Programming (OOP), and involves the advanced features of FORTRAN 95/2003, i.e., modules, derived data types, the use of pointers, lists and trees, data encapsulation, defined operators and assignments, operator extension and overloading, use of generic procedures, and maximum use of the powerful intrinsic vector and matrix processing operations. TOUGH+ v1.5 is the core code for its family of applications, i.e., the part of the code that is common to all its applications. It provides a description of the underlying physics and thermodynamics of non-isothermal flow, of the mathematical and numerical approaches, as well as a detailed explanation of the general (common to all applications) input requirements, options, capabilities and output specifications. The core code cannot run by itself: it needs to be coupled with the code for the specific TOUGH+ application option that describes a particular type of problem. The additional input requirements specific to a particular TOUGH+ application options and related illustrative examples can be found in the corresponding User's Manual.

Moridis, GeorgeJ↗

Systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change

Background: Long non-coding RNA (lncRNA) is a class of non-coding RNA with important regulatory roles in biological process of organisms. The systematic comparison of lncRNAs with protein coding mRNAs in population expression and their response to environmental change are still poorly understood. Here we identified 17,610 lncRNAs and calculated their expression levels based on RNA-seq of 80 individuals of Miscanthus lutarioriparius from two environments, the nearly native habitats and transplanted field, respectively. Results: LncRNAs had significantly higher expression diversity and lower expression frequency in population than protein coding mRNAs in both environments, which suggested that lncRNAs may experience more relaxed selection or divergent evolution in population compared with protein coding RNAs. In addition, the increase of expression diversity for lncRNAs was always significantly higher and the magnitude of fold change of expression in new stress environment was significantly larger than protein-coding mRNAs. These results suggested that lncRNAs may be more sensitive to environmental change than protein-coding mRNAs. Analysis of environment-robust and environment-specific lncRNA-mRNA co-expression network between two environments revealed the characterization of lncRNAs in response to environmental change. Furthermore, candidate lncRNAs contributing to water use efficiency (WUE) identified based on the WUE-lncRNA-mRNA co-expression network suggested the roles of lncRNAs in response to environmental change. Conclusion: Our study provided a comprehensive understanding of expression characterization of lncRNAs in population for M. lutarioriparius under field condition, which would be useful to explore the roles of lncRNAs and could accelerate the process of adaptation in new environment for many plants.

Expression diversity↗

(U) Ristra Next Generation Code Report

LANL’s Weapons Physics management (ADX) and ASC program office have defined a strategy for exascale-class application codes that follows two supportive, and mutually risk-mitigating paths: evolution for established codes (with a strong pedigree within the user community) based upon existing programming paradigms (MPI+X); and Ristra (formerly known as NGC), a high-risk/high-reward push for a next-generation multi-physics, multi-scale simulation toolkit based on emerging advanced programming systems (with an initial focus on data-flow task-based models exemplified by Legion [5]). Development along these paths is supported by the ATDM, IC, and CSSE elements of the ASC program, with the resulting codes forming a common ecosystem, and with algorithm and code exchange between them anticipated. Furthermore, solution of some of the more challenging problems of the future will require a federation of codes working together, using established-pedigree codes in partnership with new capabilities as they come on line. The role of Ristra as the high-risk/high-reward path for LANL’s codes is fully consistent with its role in the Advanced Technology Development and Mitigation (ATDM) sub-program of ASC (see Appendix C), in particular its emphasis on evolving ASC capabilities through novel programming models and data management technologies.

97 MATHEMATICS AND COMPUTING↗

DOE OE Energy Storage Systems Safety Roadmap Focus on Proposed Changes to the ICC International Codes Special Briefing Paper — Unofficial Hearing Results April 2018

The goal of the DOE OE ESS Safety Roadmap1 is to foster confidence in the safety and reliability of energy storage systems (ESSs). Three interrelated objectives support the realization of that goal: research, codes and standards, and communication/coordination. The objective focused on codes and standards is - To apply research and development (R&D) to support efforts that are focused on ensuring that codes and standards are available to enable the safe implementation of ESSs in a comprehensive, non-discriminatory and science-based manner. The purpose of this special briefing paper is to support the above objective by providing information about current and upcoming efforts being conducted by U.S. standards developing organizations, specifically code changes associated with the 2018 Group A International Codes (I-Codes) of the International Code Council (ICC) that are relevant to ESSs.

25 ENERGY STORAGE↗

Relativistic Modeling Capabilities in Perseus Extended MHD Simulation Code for HED Plasmas

This project is submitted in response to DE-FOA-0001153, and will be carried out by Dr. Charles Seyler and Dr. Nathaniel Hamlin as post doc under the direction of Professor Seyler. The objectives are to enable PERSEUS to self-consistently model relativistic high-energy-density (HED) laboratory and astrophysical phenomena. Electrons and ions in a plasma are generally modeled either as fluids using a two-fluid code, like PERSEUS, or as particles using a Particle-In- Cell (PIC) code. Nonrelativistic PERSEUS solves the two-fluid equations, formulated in terms of a generalized Ohm’s law (GOL), so as to model about nine orders of magnitude in density variation using a local semi-implicit method. Relativistic PERSEUS preserves this structure and therefore retains these advantageous properties, enabling it to model a broader range of relativistic HED phenomena than previous codes. We have also overcome a major technical challenge associated with solving a relativistic system of equations relating conserved quantities (momentum, energy, etc.) to primitive variables (density, velocity, and pressure). We have thus far developed a relativistic version of PERSEUS and demonstrated that it recovers expected nonrelativistic results. We are currently using relativistic PERSEUS to model two HED phenomena, namely laser-plasma interactions and X-pinches, both of which show spectroscopic evidence of relativistic electrons. In an X-pinch, a section of wire carrying sufficiently large current forms a plasma column that pinches down to a point-like source, generating X-rays for use in radiographic imaging. Laser-plasma interactions have been simulated using PIC codes, and we use their results as a benchmark for comparison. However, neither PIC codes nor existing two-fluid schemes can simulate X-pinches, due to the broad range of densities which have thus far made such a simulation computationally prohibitive. In both laser-plasma interaction and Xpinch simulations, we have observed relativistic phenomena that PERSEUS could not previously model. This includes relativistic channeling of a laser into an over-dense deuterium gas (i.e. induced transparency), consistent with PIC simulation results, along with energetic electrons and ions following an X-pinch and likely accompanied by strong X-ray emission, consistent with experimental observations of energetic X-rays. This proposal includes our latest simulation results. We will improve computational efficiency with techniques that allow the use of a less refined numerical grid. This will enable extensions to three-dimensional geometries. We will improve modeling of laser-plasma interactions and X-pinches, including radiative transport processes, in order to improve comparisons with PIC simulations and experimental diagnostics. We will also model power loss through electrode surface plasmas in magnetically insulated transmission lines (MITLs). We will model relativistic astrophysical phenomena in both astrophysical and HED regimes, which could shed light on the validity of laboratory astrophysics for certain problems. These phenomena are currently modeled using PIC codes and existing relativistic two-fluid codes, neither of which can model the range of length scales of which relativistic PERSEUS is capable. There is strong potential for this project to have a broad impact on both the astrophysical and laboratory plasma communities. In the laboratory community, our work is applicable to those concerned with laser-plasma interactions such as laser-driven fusion, and those in the dense Z pinch community concerned with X-pinches and electrode surface plasmas. An improved understanding of the mechanisms of hard (i.e. high-energy) X-ray generation will likely make important contributions toward the use of X-pinches for radiography through the harnessing or mitigation of hard X-rays, depending on the application. The modeling of electrode surface plasmas, including vacuum electron flow, will improve our understanding of power loss to various loads.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

SCALE Lattice Physics Code Assessments of Accident Tolerant Fuel

This report highlights accident-tolerant fuel (ATF) code assessment activities performed under Project NRCHQ- 60-17-T-0017, Lattice Physics Enhancements and Assessment. ATF covers a broad range of advanced fuel and clad designs for light water reactors (LWRs) to enhance performance under several accident conditions. Several ATF concepts are anticipated to be deployed as lead test rods (LTRs) or lead test assemblies (LTAs) within the next five years. The purpose of this work is to assess the predictive capabilities of NRC neutronics codes that underpin various licensing calculations. ATF designs use different fuel and clad materials compared to standard UO 2 fuel and zirconium-alloy claddings (hereafter UO 2 -Zry). These new materials and geometrical designs need to be assessed to quantify the impact of nuclear data uncertainties on quantities of interest (QOIs) in licensing calculations and the impact of modeling approximations which may be valid for UO 2 -Zry but not for ATF. This report outlines a systematic approach for ATF neutronics code assessment which includes sensitivity and uncertainty (S/U) analysis of nuclear data, identification of experimental benchmark and gaps for code validation, investigation of modeling approximations, and code-to-code comparisons of calculated QOIs against high-fidelity reference continuous energy (CE) Monte Carlo (MC) calculations. This report focuses on the assessment of the SCALE/Polaris lattice physics code for reactor safety analysis. Polaris lattice physics calculations generate few group (FG) cross sections for PARCS full-core calculations. (Full-core analysis, spent fuel analysis, and severe accident analysis will be performed in future work.) The selected ATF concepts for this report include Cr 2 O 3 and Al 2 O 3 -Cr 2 O 3 -doped UO 2 fuel, U 3 Si 2 fuel, FeCrAl cladding, SiC cladding, and Cr-coated cladding.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OE Energy Storage Systems Safety Roadmap Focus on Codes and Standards - July 2017

The goal of the DOE OE ESS Safety Roadmap1 is to foster confidence in the safety and reliability of energy storage systems. There are three interrelated objectives to support the realization of that goal: research, codes and standards and communication/coordination. The objective focused on codes and standards is To apply research and development to support efforts that are focused on ensuring that codes and standards are available to enable the safe implementation of energy storage systems in a comprehensive, non-discriminatory and science-based manner. The following activities are intended to support that objective and realization of the goal: a. Review and assess codes and standards which affect the design, installation, and operation of ESS systems. b. Identify gaps in knowledge that require research and analysis that can serve as a basis for criteria in those codes and standards. c. Identify areas in codes and standards that are potentially in need of revision or enhancement and can benefit from activities conducted under research and development. d. Develop input for new or revisions to existing codes and standards through individual stakeholders, facilitated task forces, or through laboratory staff supporting these efforts. The purpose of this document is to support the above activities by providing information on current and upcoming efforts being conducted by U.S. standards developing organizations (SDOs) and other entities that are focused on energy storage system safety.

25 ENERGY STORAGE↗

DOE OE Energy Storage Systems Safety Roadmap Focus on Codes and Standards - February 2018

The goal of the DOE OE ESS Safety Roadmap1 is to foster confidence in the safety and reliability of energy storage systems. There are three interrelated objectives to support the realization of that goal: research, codes and standards and communication/coordination. The objective focused on codes and standards is: To apply research and development to support efforts that are focused on ensuring that codes and standards are available to enable the safe implementation of energy storage systems in a comprehensive, non-discriminatory and science-based manner. The following activities support that objective and realization of the goal: a. Review and assess codes and standards which affect the design, installation, and operation of ESS systems. b. Identify gaps in knowledge that require research and analysis that can serve as a basis for criteria in those codes and standards. c. Identify areas in codes and standards that are potentially in need of revision or enhancement and can benefit from activities conducted under research and development. d. Develop input for new or revisions to existing codes and standards through individual stakeholders, facilitated task forces, or through laboratory staff supporting these efforts. The purpose of this document is to support the above activities by providing information on current and upcoming efforts being conducted by U.S. standards developing organizations (SDOs) and other entities that are focused on energy storage system safety.

25 ENERGY STORAGE↗

(U) Radiation Hydrodynamics in the Ristra Project’s Symphony code: Initial release

One of the recent focuses in the next-generation code (NGC/Ristra)project at LANL is to develop a cell-centered Lagrangian radiation-hydrodynamics code under FleCSI framework. The FleCSI frame-work provides a unified data and execution model in order to insulate production code development from the uncertainty of evolving runtimeand architectures. We have developed the code, Symphony, which in-corporates the hydrodynamics code, FleCSALE, and the radiation transport code, Puno.This memo is intended to describe the coupling of radiation and hydrodynamics within the Ristra Project’s code Symphony.

97 MATHEMATICS AND COMPUTING↗

MCNP ® Code Version 6.3.0 Theory & User Manual

This document acts as a repository of knowledge for the Monte Carlo N-Particle (MCNP) transport computer code. It is maintained alongside the source code and attempts to introduce new users and re-familiarize experienced users with the theory and practices of using the MCNP code for the wide range of particle transport analyses that it is appropriate for. The latest version of the MCNP code, version 6.3.0, provides the Monte Carlo particle transport community with the latest feature developments and bug fixes in the MCNP code. The MCNP code version 6.0 and later is also known as the MCNP6 code.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

3D modeling of the Staged Z-pinch with the FLASH code

The Staged Z-pinch (SZP) fusion concept is a magneto-inertial compression scheme developed by Magneto-Inertial Fusion Technologies, Inc. (MIFTI), in which small amounts of fusion fuel are brought to fusion-relevant conditions by passing multi-million amperes strong current through a cylindrical shell of high atomic number material. One- and two-dimensional modeling performed by MIFTI with the MACH2 code, suggests that net fusion energy gain can be achieved when currents in the 10 million amperes range compress a 50%-50% mixture of deuterium and tritium gas. In this project we enhance and use the FLASH code to execute high-fidelity, simulations of various SZP configurations, a collaboration between the Flash Center for Computational Science at the University of Rochester and the Laboratory for Laser Energetics, and MIFTI. FLASH is a high-performance computing, multi-physics, radiation magnetohydrodynamic (MHD) code with extended physics capabilities, which is developed at the Flash Center. The goal of this project is to assess the shell/fuel stability of the pinch to two- and three-dimensional MHD instabilities and to utilize FLASH’s extended physics capabilities to understand how extended-MHD effects impact implosion dynamics and plasma conditions at stagnation. The project is a natural extension of an ongoing collaborative effort between MIFTI and the Flash Center through the U.S. DOE Advanced Research Projects Agency-Energy (ARPA-E) BETHE program and can provide MIFTI with simulation capabilities that are currently beyond their reach with MACH2. Ultimately, MIFTI wants FLASH to become one of their simulation workhorses for reliable, high-fidelity SZP platform design. During the project, the Flash Center team developed a suite of in one- and two-dimensional FLASH simulations to model different variants of the SZP platform, performed code-to-code comparisons with MACH2, and used the FLASH code to design and model SZP experiments like the Double Eagle experiments that MIFTI recently performed. Also, the Flash Center team developed the capabilities of FLASH to be able to do three-dimensional simulations of pulsed-power experiments with the code for the first time. Two publications from this effort are currently under review and two more are in preparation. MIFTI has also committed to the use of FLASH for future SZP simulation efforts.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

(U) A Code System for Cross-Section Uncertainty Propagation for PARTISN

A rudimentary code system has been developed for propagating neutron cross-section uncertainties to response uncertainties using the PARTISN multigroup discrete-ordinates neutron transport code. The code system uses the first-order sandwich rule with sensitivities computed using SENSMG and covariances computed using NJOY. Databases of reaction cross sections and covariances using ENDF/B-VIII.0 data in the LANL standard 30-group structure have been precalculated. The final uncertainty in a k eff example problem compares well with the result from TOFFEE, a similar code that propagates neutron cross-section uncertainties to response uncertainties using the MCNP6 Monte Carlo neutron transport code. Presently, neither code system propagates uncertainties in $\overline{v}$, $\overline{μ}$, or χ, and neither code system propagates nuclide-nuclide covariances

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Differentiable Multiphysics Codes: A Breakthrough Technology for Simulation and Computing

This document summarizes the findings of a strategic planning exercise commissioned by the Weapons Simulation and Computing, Computational Physics (WSC/CP) program at the Lawrence Livermore National Laboratory (LLNL) in FY24. During the year, the committee met with multiple stakeholder communities to gather input, opinions, suggestions and concerns which have been incorporated throughout this document. The key findings from this exercise are summarized: • The development of multiphysics modelling and simulation (mod/sim) codes and software technologies, their deployment on exascale compute platforms, and their broad adoption across the NNSA is a major success of the Advanced Simulation and Computing (ASC) program and the Exascale Computing Project (ECP). Sustained investment in these core technologies is essential. • Today’s state of the art involves running ensembles of O(100K) simulations to perform uncertainty quantification (UQ) and design studies using multiple statistical methods such as Bayesian optimization to understand sensitivities of our models and explore parameterized design spaces. Even with exascale computing, we are practically limited to O(10) parameters in these studies since the number of simulations required to sample the space scales exponentially with the number of design parameters. • The data from these simulation ensembles is increasingly being used to train machine learned (ML) surrogates (or reduced order models, ROMs) which can then be used for optimization or real time design exploration. However, the trained surrogates are still limited in the number of parameters they can represent due to the sampling limitations previously noted. • Augmenting our suite of integrated multiphysics simulation codes, both current and emerging, with the ability to compute gradients (solution derivatives) of arbitrary simulation outputs with respect to (some or all) simulation inputs would be a breakthrough technology, opening the door to a new era of efficient and automated inverse design based on verified and validated mod/sim capabilities. • This capability, which we refer to as differentiable multiphysics codes (DMCs), would revolutionize both UQ and optimization studies by breaking the curse of dimensionality that presently limits our “gradient-free” ensemble based computing approach. A similar breakthrough occurred in the AI/ML community once the ability to compute gradients of arbitrary loss functions using back-propagation became commonplace. Gradient information from the multiphysics codes can also be used to dramatically improve the efficiency and scale of training of ML/ROM surrogates for rapid assessments. • Achieving this in our suite of codes will be a grand challenge, similar to the amount of effort that was required to transition from CPU to GPU computing. It will require buy-in from the entire WSC/CP program and beyond, including all integrated codes, physics and engineering models, third-party library dependencies and performance portability abstractions. It will also require investment in research and development of numerical methods for computing adjoints of coupled physics across multiple adaptively refined moving meshes and of stochastic (Monte Carlo) and mesh free (SPH) methods. • New software and numerical techniques, largely pioneered by the AI/ML community, make this feasible. Chief among these is automatic differentiation (AD), the ability to employ AD at point-wise locations in a physics calculation (instead of traditional black-box approaches) and the ability to perform “back-propagation in time” (or reverse mode AD) for non-linear partial differential equations (PDEs). Fundamentally, the conclusion of this strategic planning exercise is that the time is right to undertake a large scale effort in WSC, centered on the existing integrated codes, to continue the natural evolution of mod/sim in the age of AI/ML. Instead of attempting to replace mod/sim with purely data driven AI/ML models, we believe the key to success is to integrate AI/ML by building on top of the decades of hard-won knowledge and the verified/validated multiphysics modelling capability that is the hallmark of the ASC program.

97 MATHEMATICS AND COMPUTING↗

Methodology to Establish Performance Targets for Building Energy Codes

This report explains the underlying development of the U.S. NZE building sector performance targets reported in Federal Register Notice XX. This document also includes NZE performance targets for U.S. states, which were developed following the same procedures used to develop the national values. These national and state targets are intended to support the establishment and attainment of NZE goals over time. Where residential and commercial building energy code compliance mechanisms apply to new buildings and major renovations and dictate performance requirements, these targets reflect the recommended, minimum levels of performance. Appendix A provides the performance values and targets by U.S. state for residential and commercial buildings. These include each state’s adopted energy code performance, current published MEC performance value, and a nominal NZE code compliance performance target. The current code and NZE values can be compared to the state adopted code value to indicate the level of advancement needed to move towards recommended NZE building performance levels. Additional supplemental resources are available to support states and local governments ready to move from setting NZE policy goals to adopting NZE codes. More information about these resources and the actions states can take to achieve NZE buildings with energy codes are provided in the body of this document.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Aligning Ukrainian Building Energy Codes with the EPBD

The aim of this report is to support Ukraine in revising its building energy codes in line with regulations laid out by the Energy Performance in Buildings Directive (EPBD). The main objectives are to i) provide valuable information to help Ukraine align its building energy codes with EPBD requirements, ii) advance the capacity of key stakeholders in Ukraine to develop new regulations based on robust technical methodologies and analysis, iii) summarize building energy codes best practices using examples from the EU and elsewhere, and iv) recommend steps Ukraine can take to improve its building energy code regulations and implementation. This report summarizes EPBD requirements for new buildings, and buildings undergoing major renovations, related to cost-optimal and Nearly Zero Energy Building (NZEB) requirements. This report highlights Ukraine’s progress in aligning it’s building energy codes with the aforementioned requirements and best practices regarding those requirements from the EU and internationally. Based on best practices and Ukraine’s current progress on requirements, recommendations are presented. A brief overview of the EPBD and building energy codes in Ukraine is also provided. Implementation related to building energy codes is touched upon as well. Potential next steps for Ukraine are outlined based on provided recommendations.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

An Educational Guide for 2D Stellar Structure Calculations of Rapidly Rotating Stars using the ESTER code

The Evolution STEllaire en Rotation (ESTER) code is the first 2D stellar structure code to be made open-source and freely available to the astronomy and astrophysics community. An important and novel advancement of this code is that it can reproduce the distorted shape and observable signatures (e.g., gravity darkening) of rapidly rotating stars. ESTER also calculates the steady-state large-scale flows within the star, namely their differential rotation and associated meridional circulation. In this report, we explore and document the physics implemented within version 1.1.0rc2 of the ESTER code, in a way that complements published descriptions. We illustrate this physics by plotting how stellar structure parameters vary through stellar interiors at a range of latitudes and at different angular velocities. We investigate how the thin convective envelopes of intermediate mass stars vary with latitude when rapidly rotating, becoming deeper and thicker near the equator. Simple comparisons of ESTER model predictions (e.g., central temperature and density, luminosity) with the output from the Modules for Experiments in Stellar Astrophysics (MESA) code [Paxton et al., 2010] shows generally good agreement. Additional comparisons provide important benchmarking and verification for ESTER as a comparatively young code. Finally, we provide a guide for installing and running the code on our local university cluster, aimed at helping students to begin work.

79 ASTRONOMY AND ASTROPHYSICS↗

MCNP® Code Version 6.3.2 Theory & User Manual (Rev. 1)

This document acts as a repository of knowledge for the Monte Carlo N-Particle (MCNP) transport computer code. It is maintained alongside the source code and attempts to introduce new users and re-familiarize experienced users with the theory and practices of using the MCNP code for the wide range of particle transport analyses that it is appropriate for. The latest version of the MCNP code, version 6.3.2, provides the Monte Carlo particle transport community with the latest feature developments and bug fixes in the MCNP code. The MCNP code version 6.0 and later is also known as the MCNP6 code.

42 ENGINEERING↗

Permutation codes for sources.

Source encoding techniques based on permutation codes are investigated. For a broad class of distortion measures it is shown that optimum encoding of a source permutation code is easy to instrument even for very long block lengths. Also, the nonparametric nature of permutation encoding is well suited to situations involving unknown source statistics. For the squared-error distortion measure a procedure for generating good permutation codes of a given rate and block length is described. The performance of such codes for a memoryless Gaussian source is compared both with the rate-distortion function bound and with the performance of various quantization schemes. The comparison reveals that permutation codes are asymptotically ideal for small rates and perform as well as the best entropy-coded quantizers presently known for intermediate rates. They can be made to compare favorably at high rates, too, provided the coding delay associated with extremely long block lengths is tolerable.

Berger, T.↗