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DOE OSTI2019

Improving Ligand Geometry in Protein Data Bank Structures Computationally

Information about the three‐dimensional structures of complex biological molecules is an indispensable research tool for many fields of study, including biology, chemistry, pharmacology, and computer science. The Protein Data Bank (PDB) is an public digital archive providing access to structures of nucleic acids, proteins, and large macromolecular machines determined experimentally by X‐ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and 3‐dimensional electron microscopy (3DEM). PDB structures undergo validation for structural plausibility upon their deposition into the PDB using the program Mogul, which cross references each deposited structure against similar data in the Cambridge Structural Database (CSD). Ligands associated with PDB structures are a common source of structural inaccuracy. In this study, a programmatic pipeline was developed to determine if ligand geometric accuracy could be improved using known computational tools. Ligands with dubious geometry were identified through a Python mining code. A sample set of the identified structures was remodeled into minimum energy conformations using the molecular dynamics program AMBER and then fit to the original experimental density maps using the molecular modeling program Coot. The refined models were compared to the original models in the PDB as well as to similar structures in the CSD using the deposition statistical validation server. Preliminary results suggest that the pipeline effectively identifies and improves ligand structures that possess inaccurate geometry. This method can be used to evaluate and improve the accuracy of specific ligands in structures both archived and pending deposition. Support or Funding Information This work was supported by an NSF REU and the RCSB PDB [NSF (DBI‐1338415), NIH, and DOE.] This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Miller, Beck↗

DOE OSTI2015

NJOY21: Making NJOY Suitable for the 21. Century - 14409

NJOY has a long history of nuclear data processing. NJOY began as a successor to MINX (Multigroup Interpretation of Nuclear X-Sections), a Los Alamos code and was first publicly released in the summer of 1977. The initial version included modules such as RECONR for resonance reconstruction on a union energy grid, BROADR for Doppler broadening plus a new Multigroup averaging program, GROUPR and an associated output module, DTR. Soon thereafter the HEATR, ERRORR, and THERMR modules were added to NJOY. By the mid 1980's, NJOY had a worldwide user community. The current version of NJOY2012 was released in December 2012. NJOY2012 builds on the success of more than 45 years of nuclear data processing at Los Alamos National Laboratory. NJOY2012 was rewritten using Fortran 90/95, utilizing among other things the concepts of public and private variables, eliminating common blocks in lieu of Fortran modules and taking advantage of allocatable arrays. A new version of NJOY is being developed at Los Alamos National Laboratory; NJOY21: NJOY for the 21. Century. NJOY21 uses modern programming standards of quality, reliability, and maintainability. It is being designed from the ground up to utilize modern methods of interacting with computer codes by providing an interactive and scripting (e.g., Python) interface. This will allow scientists the ability to more easily work with the results of the various steps in the processing of nuclear data. NJOY21 will continue the legacy of NJOY by providing a trusted and verified processing code that is fast, flexible, easy to use and customize and capable of handling both modern and established nuclear data formats. This paper introduces NJOY21 by first relating the history of NJOY; the majority of the paper will discuss NJOY21. NJOY21 will take advantage of the many decades of nuclear data processing experience that is contained in NJOY2012 and previous versions of NJOY and extend the capabilities and convenience of processing nuclear data. We will discuss how NJOY21 will remain backwards compatible with NJOY2012 - i.e., how current NJOY2012 input decks will continue to work with NJOY21. We will also discuss the verification and validation of the NJOY21 code base. Finally we will discuss new features in NJOY21 that do not exist in NJOY2012. These features include changes in how a scientist can interact with NJOY to process and verify and validate nuclear data; and the ability to read and write new nuclear data formats. (authors)

42 ENGINEERING↗

NASA NTRS1998

Charon Message-Passing Toolkit for Scientific Computations

The Charon toolkit for piecemeal development of high-efficiency parallel programs for scientific computing is described. The portable toolkit, callable from C and Fortran, provides flexible domain decompositions and high-level distributed constructs for easy translation of serial legacy code or design to distributed environments. Gradual tuning can subsequently be applied to obtain high performance, possibly by using explicit message passing. Charon also features general structured communications that support stencil-based computations with complex recurrences. Through the separation of partitioning and distribution, the toolkit can also be used for blocking of uni-processor code, and for debugging of parallel algorithms on serial machines. An elaborate review of recent parallelization aids is presented to highlight the need for a toolkit like Charon. Some performance results of parallelizing the NAS Parallel Benchmark SP program using Charon are given, showing good scalability.

VanderWijngaart, Rob F.↗

NASA NTRS1998

Charon Message-Passing Toolkit for Scientific Computations

VanderWijngarrt, Rob F.↗

DOE OSTI2023

Recent MCNP® Code Developments and Improvements for Nuclear Energy Applications [Slides]

The MCNP® code is a general-purpose radiation transport code developed at LANL over the past 46+ years. This code is capable of modeling the fundamental physics of particles as they move through and interact with materials. It is used in many LANL and worldwide radiation transport applications (see next slide) for example in the Fundamental nuclear physics and data experiments at LANSCE.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1994

Preconditioned implicit solvers for the Navier-Stokes equations on distributed-memory machines

The GMRES method is parallelized, and combined with local preconditioning to construct an implicit parallel solver to obtain steady-state solutions for the Navier-Stokes equations of fluid flow on distributed-memory machines. The new implicit parallel solver is designed to preserve the convergence rate of the equivalent 'serial' solver. A static domain-decomposition is used to partition the computational domain amongst the available processing nodes of the parallel machine. The SPMD (Single-Program Multiple-Data) programming model is combined with message-passing tools to develop the parallel code on a 32-node Intel Hypercube and a 512-node Intel Delta machine. The implicit parallel solver is validated for internal and external flow problems, and is found to compare identically with flow solutions obtained on a Cray Y-MP/8. A peak computational speed of 2300 MFlops/sec has been achieved on 512 nodes of the Intel Delta machine,k for a problem size of 1024 K equations (256 K grid points).

Ajmani, Kumud↗

NASA NTRS2009

Findings from the Supersonic Qualification Program of the Mars Science Laboratory Parachute System

In 2012, the Mars Science Laboratory Mission (MSL) will deploy NASA's largest extra-terrestrial parachute, a technology integral to the safe landing of its advanced robotic explorer on the surface. The supersonic parachute system is a mortar deployed 21.5 m disk-gap-band (DGB) parachute, identical in geometric scaling to the Viking era DGB parachutes of the 1970's. The MSL parachute deployment conditions are Mach 2.3 at a dynamic pressure of 750 Pa. The Viking Balloon Launched Decelerator Test (BLDT) successfully demonstrated a maximum of 700 Pa at Mach 2.2 for a 16.1 m DGB parachute in its AV4 flight. All previous Mars deployments have derived their supersonic qualification from the Viking BLDT test series, preventing the need for full scale high altitude supersonic testing. The qualification programs for Mars Pathfinder, Mars Exploration Rover, and Phoenix Scout Missions were all limited to subsonic structural qualification, with supersonic performance and survivability bounded by the BLDT qualification. The MSL parachute, at the edge of the supersonic heritage deployment space and 33% larger than the Viking parachute, accepts a certain degree of risk without addressing the supersonic environment in which it will deploy. In addition, MSL will spend up to 10 seconds above Mach 1.5, an aerodynamic regime that is associated with a known parachute instability characterized by significant canopy projected area fluctuation and dynamic drag variation. This aerodynamic instability, referred to as "area oscillations" by the parachute community has drag performance, inflation stability, and structural implications, introducing risk to mission success if not quantified for the MSL parachute system. To minimize this risk and as an alternative to a prohibitively expensive high altitude test program, a multi-phase qualification program using computation simulation validated by subscale test was developed and implemented for MSL. The first phase consisted of 2% of fullscale supersonic wind tunnel testing of a rigid DGB parachute with entry-vehicle to validate two high fidelity computational fluid dynamics (CFD) tools. The computer codes utilized Large Eddy Simulation and Detached Eddy Simulation numerical approaches to accurately capture the turbulent wake of the entry vehicle and its coupling to the parachute bow-shock. The second phase was the development of fluid structure interaction (FSI) computational tools to predict parachute response to the supersonic flow field. The FSI development included the integration of the CFD from the first phase with a finite element structural model of the parachute membrane and cable elements. In this phase, a 4% of full-scale supersonic flexible parachute test program was conducted to provide validation data to the FSI code and an empirical dataset of the MSL parachute in a flight-like environment. The final phase is FSI simulations of the full-scale MSL parachute in a Mars type deployment. Findings from this program will be presented in terms of code development and validation, empirical findings from the supersonic testing, and drag performance during supersonic operation.

EDL↗

NASA NTRS1982

Prediction of sound radiation from different practical jet engine inlets

Computer codes which were based upon a special integral representation of the external solutions of the Helmholtz equation were upgraded so that they would yield accurate results for the acoustic radiation patterns in the field surrounding an axisymmetric body for nondimensional wave numbers, based on duct radius, of up to twenty. The accuracy of these computer programs was checked by the use of the point source method for the generation of exact solutions and then by comparison with the results of other experimental and theoretical studies. These computer codes were used in a parametric study of the dependence of the radiated sound field on input modal distribution, wave number, and inlet lip shape. The results of this study show that: (1) as the wave number (i.e., cut off ratio) is increased for a given input modal distribution that the acoustic radiation peak moves towards the inlet centerline and becomes more compact (i.e., narrows); (2) as the input mode number is increased for a given cut off ratio the acoustic radiation peak moves away from the inlet centerline and becomes more compact.

Meyer, W. L.↗

NASA NTRS1990

Networks for image acquisition, processing and display

The human visual system comprises layers of networks which sample, process, and code images. Understanding these networks is a valuable means of understanding human vision and of designing autonomous vision systems based on network processing. Ames Research Center has an ongoing program to develop computational models of such networks. The models predict human performance in detection of targets and in discrimination of displayed information. In addition, the models are artificial vision systems sharing properties with biological vision that has been tuned by evolution for high performance. Properties include variable density sampling, noise immunity, multi-resolution coding, and fault-tolerance. The research stresses analysis of noise in visual networks, including sampling, photon, and processing unit noises. Specific accomplishments include: models of sampling array growth with variable density and irregularity comparable to that of the retinal cone mosaic; noise models of networks with signal-dependent and independent noise; models of network connection development for preserving spatial registration and interpolation; multi-resolution encoding models based on hexagonal arrays (HOP transform); and mathematical procedures for simplifying analysis of large networks.

Ahumada, Albert J., Jr.↗

DOE OSTI2022

High-Temperature Gas-Cooled Reactor Research Survey and Overview: Preliminary Data Platform Construction for the Nuclear Energy University Program

Since the U.S. Department of Energy Office of Nuclear Energy initiated the Nuclear Energy University Program (NEUP) in 2009, there are 29 NEUP projects focusing on high-temperature gas-cooled reactor (HTGR) research up to July 2022. The resultant research product, either experimental or computational, were published as final NEUP reports, journal articles and conference proceedings. However, these federally funded products have been scattered and sometimes cannot be easily accessed. To improve access to this valuable HTGR validation data and optimize the return on the significant investment made by the Department of Energy, the Advanced Reactor Technologies (ART) Gas-Cooled Reactor (GCR) program started a survey of completed and ongoing HTGR NEUP projects to develop a public-access database specific for HTGRs applications that can be used to retrieve computational fluid dynamics and system code validation data. This effort will help guide future NEUP-funded research, define new state of the ART Phenomena Identification and Ranking Table (PIRT), and promote the usage of this data in the codes validation matrices. This report provides an overview of the NEUP-funded HTGR-related research projects from Fiscal Year (FY) 2009–2021 and identifies validation knowledge gaps still existing in HTGR thermal-fluid research. A preliminary data platform has been developed for the 29 NEUP projects investigating HTGR thermal hydraulics, including their final reports as well as the available scientific publications. As an ultimate goal for this work, the ART-GCR program will create a central database at Idaho National Laboratory to identify, organize, and store these datasets generated by experimental investigations or computational models, experimental facility descriptions, and publicly-available academic products from the HTGR-related NEUP projects and provide future guidance for the storage and transmission of important project documentations for later NEUP projects as well.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2020

Towards Generic Parallel Programming in Computer Science Education with Kokkos

Parallel patterns, views, and spaces are promising abstractions to capture the programmer's intent as well as the contextual information that can be used by an underlying runtime to efficiently map software to parallel hardware. These abstractions can be valuable in cases where an algorithm must accommodate requirements of code and performance portability across hardware architectures and vendor programming models. Kokkos is a parallel programming model for host- and accelerator architectures that relies on these abstractions and targets these requirements. It consists of a pure C++ interface, a specification, and a programming library. The programming library exposes patterns and types and maps them to an underlying abstract machine model. The abstract machine model offers a generic view of parallel hardware. While Kokkos is gaining popularity in large-scale HPC applications at some DOE laboratories, we believe that the implemented concepts are of interest to a broader audience including academia as they may contribute to a generic, vendor, and architecture-independent education of parallel programming. In this work, we give an insight into the design considerations of this programming model and list important abstractions. Further, we document best practices obtained from giving virtual classes on Kokkos and give pointers to resources that the reader may consider valuable for a lecture on generic parallel programming for students with preexisting knowledge on this matter.

Ciesko, Jan↗

NASA NTRS1999

Improvements to the Unstructured Mesh Generator MESH3D

The AIRPLANE process starts with an aircraft geometry stored in a CAD system. The surface is modeled with a mesh of triangles and then the flow solver produces pressures at surface points which may be integrated to find forces and moments. The biggest advantage is that the grid generation bottleneck of the CFD process is eliminated when an unstructured tetrahedral mesh is used. MESH3D is the key to turning around the first analysis of a CAD geometry in days instead of weeks. The flow solver part of AIRPLANE has proven to be robust and accurate over a decade of use at NASA. It has been extensively validated with experimental data and compares well with other Euler flow solvers. AIRPLANE has been applied to all the HSR geometries treated at Ames over the course of the HSR program in order to verify the accuracy of other flow solvers. The unstructured approach makes handling complete and complex geometries very simple because only the surface of the aircraft needs to be discretized, i.e. covered with triangles. The volume mesh is created automatically by MESH3D. AIRPLANE runs well on multiple platforms. Vectorization on the Cray Y-MP is reasonable for a code that uses indirect addressing. Massively parallel computers such as the IBM SP2, SGI Origin 2000, and the Cray T3E have been used with an MPI version of the flow solver and the code scales very well on these systems. AIRPLANE can run on a desktop computer as well. AIRPLANE has a future. The unstructured technologies developed as part of the HSR program are now targeting high Reynolds number viscous flow simulation. The pacing item in this effort is Navier-Stokes mesh generation.

Thomas, Scott D.↗

NASA NTRS1975

Computer program design specifications for the Balloon-borne Ultraviolet Stellar Spectrometer (BUSS) science data decommutation program (BAPS48)

The Balloon-Borne Ultraviolet Stellar Spectrometer (BUSS) Science Data Docummutation Program (BAPS48) is a pulse code modulation docummutation program that will format the BUSS science data contained on a one inch PCM tracking tape into a seven track serial bit stream formatted digital tape.

Rodriguez, R. M.↗

DOE OSTI2017

Initial CEED API (CEED-MS10)

Key components of CEED software development involve fast finite element operator storage and evaluation, architecture optimizations, performant algorithms for all orders, global kernels for finite element operators, efficient use of the memory sub-system, optimal data locality and motion, enhanced scalability and parallelism, and fast tensor contractions. As ultimate goals of the project, CEED is exploring and identifying the best algorithms for the full range of discretizations and applying algorithmic and software development to support ECP applications’ needs. In this milestone, we initiated the development and implementation of a common CEED API consisting of two main components: low-level and high-level APIs. We accomplished the goal of having the low-level component ready for the release of CEED v1.0 in the next quarter, see CEED-MS13. In this report we also provide a highlight from CEED’s integration with the MARBL app and the corresponding Laghos miniapp. A main theme in this work has been the systematic transition of advanced algorithms, developed and tested in Laghos, to the large-scale multi-physics settings of the MARBL code. The low-level CEED API provides a set of FE kernels and components for writing new low-level kernels. Examples include: vector and sparse linear algebra, element matrix assembly over a batch of elements, partial assembly and action for efficient high-order operators like mass, diffusion, advection, etc. The main goal of the low-level API is to establish the basis for the high-level API. Also, identifying such low-level kernels and providing a reference implementation for them serves as the basis for collaboration with vendors and STs. Another goal for the low-level API is to make it easy for applications with their own discretization infrastructure, who do not want to switch directly to using the high-level CEED API, to still evaluate and use the core operations provided by the low-level API. One of the challenges with high-order methods is that a global sparse matrix is no longer a good representation of a high-order linear operator, both with respect to the FLOPs needed for its evaluation, as well as the memory transfer needed for a matvec. Thus, another important question we tried to address while developing the low-level API is: is it possible to abstract out in a natural and efficient way the different implementations and data structures that arise when dealing with various computational device types: CPUs, GPUs, etc. Fully answering this question is beyond the scope of this particular milestone, since that requires longer time as we develop and expand the devices we support. The future high-level API will be the frontend provided by CEED consisting of high-level abstractions such as meshes, finite element spaces and solutions, bilinear forms, solvers, etc. At this high-level, an important aspect of the API will be to provide a uniform abstraction layer for writing code in a portable manner. To achieve that, we plan to utilize the MPI programming model combined with a device abstraction layer (DAL) for finite element computations that we will develop. The DAL will serve as the bridge between the low- and the high-level APIs, allowing a variety of programming models to be used for the low-level kernel implementations. The software artifacts delivered as part of this milestone include an initial CEED API software implementation (libCEED) provided through the CEED website, http://ceed.exascaleproject.org and the CEED GitHub organization, http://github.com/ceed. In addition to details and results from the above R&D efforts, in this document we are also reporting on other project-wide activities performed in Q1 of FY18, including: the Nek5000 v17.0 MFEM v3.3.2 and PETSc v3.8 releases, collaborations with ECP/ST and SciDAC projects, the inaugural Nek5000 hackathon and various outreach activities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Evaluation of Physical Security Risk for Potential Implementation of FLEX using Dynamic Simulation Methods

The requirements for United States nuclear power plants to maintain a large onsite physical security force contribute to their large operational costs. The cost of maintaining the current physical security posture is approximately 10% of the overall operation and maintenance budget for commercial nuclear power plants. The goal of the Light Water Reactor Sustainability Program Physical Security Pathway is to develop tools, methods, and technologies and provide the technical basis for an optimized physical security posture. This pathway will analyze and minimize the conservatisms built into current security postures in order to reduce security costs while still ensuring adequate security and operational safety. The research performed at Idaho National Laboratory within this pathway has successfully developed a dynamic force-on-force (FOF) modeling framework using various computer simulation tools and integrated them with the dynamic assessment Event Modeling Risk Assessment using Linked Diagrams (EMRALD) tool. This document provides an overview of lessons learned in applying a dynamic computational framework that links results from a commercially available FOF simulation tool, a commercially available thermal-hydraulic tool, and EMRALD to an operating commercial nuclear power plant. This process of including plant procedures and multiple analysis results is being called Modeling and Analysis for Safety Security using Dynamic EMRALD Framework. Previous reports described how a user could integrate their plant-specific FOF models with the dynamic simulation tool EMRALD, model operator actions, integrate with probabilistic risk assessment tools, such as Computer Aided Fault Tree Analysis System or Systems Analysis Programs for Hands-on Integrated Reliability Evaluations, and with thermal-hydraulic tools, such as RELAP-5. Previous reports applied various combinations of available simulations codes with EMRALD using generic plant models to demonstrate how to perform the analysis. This report documents the results of applying the dynamic computational framework to an actual nuclear facility using their security scenarios and timelines. The purpose of this study was to verify that results achieved using generic models are similar to actual plant results and to refine our guidance of the use of the framework. Such an assessment enables further analysis, such as what-if scenarios and staff-reduction evaluation, thereby optimizing physical security at plants. NOTE: The work performed in this report is based on a generic EMRALD model with actual plant data used for the analysis. However, only the generic model and general results of the analysis are in the report. No plant’s sensitive information is discussed in this report. The discussion shows examples of insights that can be obtained from the MASS-DEF methodology.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NASA NTRS1992

Users manual for program SSFREQ intermediate mode stability curves: Developed for use on a PC computer

The piping in a liquid rocket can assume complex configurations due to multiple tanks, multiple engines, and structures that must be piped around. The capability to handle some of these complex configurations have been incorporated into the SSFREQ code. The capability to modify the input on line has been implemented. The configurations allowed include multiple tanks, multiple engines, the splitting of a pipe into equal segments going to different (or the same) engines. This program will handle the following type elements: straight pipes, bends, inline accumulators, tuned stub accumulators, Helmholtz resonators, parallel resonators, pumps, split pipes, multiple tanks, and multiple engines.

Armstrong, Wilbur C.↗

DOE OSTI2023

An Overview of UME: Unstructured Mesh Explorations [Slides]

What is UME? UME extracts an important computational kernel from a large computational physics application, which is based on an unstructured mesh representation. The memory layout, indexing, data management, and communication patterns are as close to the original application as possible. The original application is a long-lived Fortran program, with ~750K source lines of code (sloc). UME is a C++17 implementation of a zone gradient operator, with about ~3K sloc.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2012

Spent fuel pool storage calculations using the ISOCRIT burnup credit tool

In order to conservatively apply burnup credit in spent fuel pool criticality safety analyses, Westinghouse has developed a software tool, ISOCRIT, for generating depletion isotopics. This tool is used to create isotopics data based on specific reactor input parameters, such as design basis assembly type; bounding power/burnup profiles; reactor specific moderator temperature profiles; pellet percent theoretical density; burnable absorbers, axial blanket regions, and bounding ppm boron concentration. ISOCRIT generates burnup dependent isotopics using PARAGON; Westinghouse's state-of-the-art and licensed lattice physics code. Generation of isotopics and passing the data to the subsequent 3D KENO calculations are performed in an automated fashion, thus reducing the chance for human error. Furthermore, ISOCRIT provides the means for responding to any customer request regarding re-analysis due to changed parameters (e.g., power uprate, exit temperature changes, etc.) with a quick turnaround.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗