Results for “Software Construction” — Page 54

DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS1991

Telerobotic rovers for extraterrestrial construction

The topics are presented in viewgraph form and include the following: fundamental concepts; advantages of modularity; modular robot; robot design; motor control system; simple manipulator; 4 degree of freedom manipulator; intermodule communication; network layout; positioning system--IR-TROP; IR TROP system design; testbed layout; modularized control; and centralized control. The objectives are the following: to design small modular robots; to test robotic cooperation and teleoperation; to develop modular control software; to develop intermodule communication network; to develop high accuracy positioning system; and to explore distributed algorithms for coordination.

Grasso, Chris↗

DOE OSTI2025

Software Validation Work With The ZPPR-15 Data

The analysis activities for fast reactors involve using many different pieces of software that are relied upon for their predictive capabilities. For this software to be considered reliable, documented proof that the predictions of the software are accurate is required. In this manuscript, the validation work that covers some of the Argonne software used in fast reactor design activities is discussed and displayed. This validation work includes neutron and gamma flux distributions, reaction rate distributions, and reactivity worth. In an ideal world, a reactor development program would have access to a comprehensive set of experimental facilities to help inform the design aspects of the reactor itself. While thermal-hydraulics experiments, and to a limited degree mechanical experiments, can be carried out today for validation needs, neutronics related experimental facilities are rather impractical because of the lack of experimental facilities. Given the desired time table for construction of new reactors, the reconstitution or creation of new neutronic experimental facilities is untenable and thus those reactor development programs must rely upon any available experimental measurements that are qualitatively similar to the design. While a methodology has been proposed to assess the similarity between the past experimental measurements and the reactor itself, that aspect is beyond the scope of this manuscript. In this manuscript, the focus is entirely placed on the analysis results for a series of experiments carried out at the ZPPR facility in Idaho in the mid-1980s. In this regard, this manuscript only shows the validation of the stated neutronics software for specific loadings of the ZPPR reactor. Because of the fuel form, its proposed enrichment, and the material content of the reactor core, the ZPPR-15 experiments were identified as potential validation data for the reactor. The ZPPR-15 experiments were intended as mockups of a 330 MWe Integral Fast Reactor program which was a follow on program to the Clinch River Breeder Reactor. In the ZPPR-15 series of experiments, measurements of the neutron spectrum, control rod worth, sodium void worth, foil reaction rate distributions, Doppler worth of heated samples, gamma dose, and axial expansion worth were all carried out and published. In many cases, these reactivity coefficients are good candidates to validate the reactivity coefficient calculation scheme used by the analysis software and included in the safety analysis activities of fast reactor development projects today. This manuscript discusses the modeling methodology and accuracy of the calculated experimental results using the LANL software MCNP and the ANL software package ARC (Argonne Reactor Codes). As will be shown, for many of the experimental measurements, the two software packages are found to be good predictive analysis tools for those experiments. In other cases, problems with the analysis methodology or underlying cross section data are exposed which indicates where predictive analysis is not as reliable. Finally, in some of the measurements the conclusion is reached that the experimental measurement cannot be reproduced with the analysis software as it is simply too difficult.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2026

Software Validation Work With The ZPPR-15 Data

The analysis activities for fast reactors involve using many different pieces of software that are relied upon for their predictive capabilities. For this software to be considered reliable, documented proof that the predictions of the software are accurate is required. In this manuscript, the validation work that covers some of the Argonne software used in fast reactor design activities is discussed and displayed. This validation work includes neutron and gamma flux distributions, reaction rate distributions, and reactivity worth. In an ideal world, a reactor development program would have access to a comprehensive set of experimental facilities to help inform the design aspects of the reactor itself. While thermal-hydraulics experiments, and to a limited degree mechanical experiments, can be carried out today for validation needs, neutronics related experimental facilities are rather impractical because of the lack of experimental facilities. Given the desired time table for construction of new reactors, the reconstitution or creation of new neutronic experimental facilities is untenable and thus those reactor development programs must rely upon any available experimental measurements that are qualitatively similar to the design. While a methodology has been proposed to assess the similarity between the past experimental measurements and the reactor itself, that aspect is beyond the scope of this manuscript. In this manuscript, the focus is entirely placed on the analysis results for a series of experiments carried out at the ZPPR facility in Idaho in the mid-1980s. In this regard, this manuscript only shows the validation of the stated neutronics software for specific loadings of the ZPPR reactor. Because of the fuel form, its proposed enrichment, and the material content of the reactor core, the ZPPR-15 experiments were identified as potential validation data for the reactor. The ZPPR-15 experiments were intended as mockups of a 330 MWe Integral Fast Reactor program which was a follow on program to the Clinch River Breeder Reactor. In the ZPPR-15 series of experiments, measurements of the neutron spectrum, control rod worth, sodium void worth, foil reaction rate distributions, Doppler worth of heated samples, gamma dose, and axial expansion worth were all carried out and published. In many cases, these reactivity coefficients are good candidates to validate the reactivity coefficient calculation scheme used by the analysis software and included in the safety analysis activities of fast reactor development projects today. This manuscript discusses the modeling methodology and accuracy of the calculated experimental results using the LANL software MCNP and the ANL software package ARC (Argonne Reactor Codes). As will be shown, for many of the experimental measurements, the two software packages are found to be good predictive analysis tools for those experiments. In other cases, problems with the analysis methodology or underlying cross section data are exposed which indicates where predictive analysis is not as reliable. Finally, in some of the measurements the conclusion is reached that the experimental measurement cannot be reproduced with the analysis software as it is simply too difficult.

Aliberti, Gerardo↗

DOE OSTI2014

ARCHER{sub RT} – A GPU-based and photon-electron coupled Monte Carlo dose computing engine for radiation therapy: Software development and application to helical tomotherapy

Purpose: Using the graphical processing units (GPU) hardware technology, an extremely fast Monte Carlo (MC) code ARCHER{sub RT} is developed for radiation dose calculations in radiation therapy. This paper describes the detailed software development and testing for three clinical TomoTherapy® cases: the prostate, lung, and head and neck. Methods: To obtain clinically relevant dose distributions, phase space files (PSFs) created from optimized radiation therapy treatment plan fluence maps were used as the input to ARCHER{sub RT}. Patient-specific phantoms were constructed from patient CT images. Batch simulations were employed to facilitate the time-consuming task of loading large PSFs, and to improve the estimation of statistical uncertainty. Furthermore, two different Woodcock tracking algorithms were implemented and their relative performance was compared. The dose curves of an Elekta accelerator PSF incident on a homogeneous water phantom were benchmarked against DOSXYZnrc. For each of the treatment cases, dose volume histograms and isodose maps were produced from ARCHER{sub RT} and the general-purpose code, GEANT4. The gamma index analysis was performed to evaluate the similarity of voxel doses obtained from these two codes. The hardware accelerators used in this study are one NVIDIA K20 GPU, one NVIDIA K40 GPU, and six NVIDIA M2090 GPUs. In addition, to make a fairer comparison of the CPU and GPU performance, a multithreaded CPU code was developed using OpenMP and tested on an Intel E5-2620 CPU. Results: For the water phantom, the depth dose curve and dose profiles from ARCHER{sub RT} agree well with DOSXYZnrc. For clinical cases, results from ARCHER{sub RT} are compared with those from GEANT4 and good agreement is observed. Gamma index test is performed for voxels whose dose is greater than 10% of maximum dose. For 2%/2mm criteria, the passing rates for the prostate, lung case, and head and neck cases are 99.7%, 98.5%, and 97.2%, respectively. Due to specific architecture of GPU, modified Woodcock tracking algorithm performed inferior to the original one. ARCHER{sub RT} achieves a fast speed for PSF-based dose calculations. With a single M2090 card, the simulations cost about 60, 50, 80 s for three cases, respectively, with the 1% statistical error in the PTV. Using the latest K40 card, the simulations are 1.7–1.8 times faster. More impressively, six M2090 cards could finish the simulations in 8.9–13.4 s. For comparison, the same simulations on Intel E5-2620 (12 hyperthreading) cost about 500–800 s. Conclusions: ARCHER{sub RT} was developed successfully to perform fast and accurate MC dose calculation for radiotherapy using PSFs and patient CT phantoms.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1987

Open control/display system for a telerobotics work station

A working Advanced Space Cockpit was developed that integrated advanced control and display devices into a state-of-the-art multimicroprocessor hardware configuration, using window graphics and running under an object-oriented, multitasking real-time operating system environment. This Open Control/Display System supports the idea that the operator should be able to interactively monitor, select, control, and display information about many payloads aboard the Space Station using sets of I/O devices with a single, software-reconfigurable workstation. This is done while maintaining system consistency, yet the system is completely open to accept new additions and advances in hardware and software. The Advanced Space Cockpit, linked to Grumman's Hybrid Computing Facility and Large Amplitude Space Simulator (LASS), was used to test the Open Control/Display System via full-scale simulation of the following tasks: telerobotic truss assembly, RCS and thermal bus servicing, CMG changeout, RMS constrained motion and space constructible radiator assembly, HPA coordinated control, and OMV docking and tumbling satellite retrieval. The proposed man-machine interface standard discussed has evolved through many iterations of the tasks, and is based on feedback from NASA and Air Force personnel who performed those tasks in the LASS.

Keslowitz, Saul↗

NASA NTRS1990

Cost-effective use of liquid nitrogen in cryogenic wind tunnels, phase 2

Cryogenic seal tests were performed and Rulon A was selected for the subject nutating positive displacement expander. A four-chamber expander was designed and fabricated. A nitrogen reliquefier flow system was also designed and constructed for testing the cold expander. Initial tests were unsatisfactory because of high internal friction attributed to nutating Rulon inlet and outlet valve plates. Replacement of the nutating valves with cam-actuated poppet valves improved performance. However, no net nitrogen reliquefaction was achieved due to high internal friction. Computer software was developed for accurate calculation of nitrogen reliquefaction from a system such as that proposed. These calculations indicated that practical reliquefaction rates of 15 to 19 percent could be obtained. Due to mechanical problems, the nutating expander did not demonstrate its feasibility nor that of the system. It was concluded that redesign and testing of a smaller nutating expander was required to prove concept feasibility.

Mcintosh, Glen E.↗

NASA NTRS1991

The development of a program analysis environment for Ada: Reverse engineering tools for Ada

The Graphical Representations of Algorithms, Structures, and Processes for Ada (GRASP/Ada) has successfully created and prototyped a new algorithm level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and thus improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype (Version 1) was designed and implemented using FLEX and BISON running under the Virtual Memory System (VMS) on a VAX 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. In Phase 3 of the project, the prototype was prepared for limited distribution (GRASP/Ada Version 3.0) to facilitate evaluation. The user interface was extensively reworked. The current prototype provides the capability for the user to generate CSD from Ada source code in a reverse engineering mode with a level of flexibility suitable for practical application.

Cross, James H., II↗

NASA NTRS1994

CLIPS++: Embedding CLIPS into C++

This paper describes a set of C++ extensions to the CLIPS language and their embodiment in CLIPS++. These extensions and the implementation approach of CLIPS++ provide a new level of embeddability with C and C++. These extensions are a C++ include statement and a defcontainer construct; (include (c++-header-file.h)) and (defcontainer (c++-type)). The include construct allows C++ functions to be embedded in both the LHS and RHS of CLIPS rules. The header file in an include construct is the same header file the programmer uses for his/her own C++ code, independent of CLIPS. The defcontainer construct allows the inference engine to treat C++ class instances as CLIPS deftemplate facts. Consequently existing C++ class libraries may be transparently imported into CLIPS. These C++ types may use advanced features like inheritance, virtual functions, and templates. The implementation has been tested with several class libraries, including Rogue Wave Software's Tools.h++, GNU's libg++, and USL's C++ Standard Components. The execution speed of CLIPS++ has been determined to be 5 to 700 times the execution speed of CLIPS 6.0 (10 to 20X typical).

Obermeyer, Lance↗

NASA NTRS1995

Computing Interactions Of Free-Space Radiation With Matter

High Charge and Energy Transport (HZETRN) computer program computationally efficient, user-friendly package of software adressing problem of transport of, and shielding against, radiation in free space. Designed as "black box" for design engineers not concerned with physics of underlying atomic and nuclear radiation processes in free-space environment, but rather primarily interested in obtaining fast and accurate dosimetric information for design and construction of modules and devices for use in free space. Computational efficiency achieved by unique algorithm based on deterministic approach to solution of Boltzmann equation rather than computationally intensive statistical Monte Carlo method. Written in FORTRAN.

Wilson, J. W.↗

NASA NTRS1980

Environmental Analysis

Burns & McDonnell Engineering's environmental control study is assisted by NASA's Computer Software Management and Information Center's programs in environmental analyses. Company is engaged primarily in design of such facilities as electrical utilities, industrial plants, wastewater treatment systems, dams and reservoirs and aviation installations. Company also conducts environmental engineering analyses and advises clients as to the environmental considerations of a particular construction project. Company makes use of many COSMIC computer programs which have allowed substantial savings.

Source record↗

NASA NTRS2008

Small-Body Extensions for the Satellite Orbit Analysis Program (SOAP)

An extension to the SOAP software allows users to work with tri-axial ellipsoid-based representations of planetary bodies, primarily for working with small, natural satellites, asteroids, and comets. SOAP is a widely used tool for the visualization and analysis of space missions. The small body extension provides the same visualization and analysis constructs for use with small bodies. These constructs allow the user to characterize satellite path and instrument cover information for small bodies in both 3D display and numerical output formats. Tri-axial ellipsoids are geometric shapes the diameters of which are different in each of three principal x, y, and z dimensions. This construct provides a better approximation than using spheres or oblate spheroids (ellipsoids comprising two common equatorial diameters as a distinct polar diameter). However, the tri-axial ellipsoid is considerably more difficult to work with from a modeling perspective. In addition, the SOAP small-body extensions allow the user to actually employ a plate model for highly irregular surfaces. Both tri-axial ellipsoids and plate models can be assigned to coordinate frames, thus allowing for the modeling of arbitrary changes to body orientation. A variety of features have been extended to support tri-axial ellipsoids, including the computation and display of the spacecraft sub-orbital point, ground trace, instrument footprints, and swathes. Displays of 3D instrument volumes can be shown interacting with the ellipsoids. Longitude/latitude grids, contour plots, and texture maps can be displayed on the ellipsoids using a variety of projections. The distance along an arbitrary line of sight can be computed between the spacecraft and the ellipsoid, and the coordinates of that intersection can be plotted as a function of time. The small-body extension supports the same visual and analytical constructs that are supported for spheres and oblate spheroids in SOAP making the implementation of the more complex algorithms largely transparent to the user.

Carnright, Robert↗

NASA NTRS2000

Thermal Analysis of ISS Service Module Active TCS

ISS Service Module mission must begin in July 2000. The verification of design thermal requirements is mostly due to thermal analysis. The thermal analysis is enough difficult problem because of large number of ISS configurations that had to be investigated and various orbital environments. Besides the ISS structure has articulating parts such as solar arrays and radiators. The presence of articulating parts greatly increases computation times and requires accurate approach to organization of calculations. The varying geometry needs us to calculate the view factors several times during the orbit, while in static geometry case we need do it only once. In this paper we consider the thermal mathematical model of SM that includes the TCS and construction thermal models and discuss the results of calculations for ISS configurations 1R and 9Al. The analysis is based on solving the nodal heat balance equations for ISS structure by Kutta-Merson method and analytical solutions of heat transfer equations for TCS units. The computations were performed using thermal software TERM [1,2] that will be briefly described.

Altov, Vladimir V.↗

NASA NTRS1987

Parallel software support for computational structural mechanics

The application of the parallel programming methodology known as the Force was conducted. Two application issues were addressed. The first involves the efficiency of the implementation and its completeness in terms of satisfying the needs of other researchers implementing parallel algorithms. Support for, and interaction with, other Computational Structural Mechanics (CSM) researchers using the Force was the main issue, but some independent investigation of the Barrier construct, which is extremely important to overall performance, was also undertaken. Another efficiency issue which was addressed was that of relaxing the strong synchronization condition imposed on the self-scheduled parallel DO loop. The Force was extended by the addition of logical conditions to the cases of a parallel case construct and by the inclusion of a self-scheduled version of this construct. The second issue involved applying the Force to the parallelization of finite element codes such as those found in the NICE/SPAR testbed system. One of the more difficult problems encountered is the determination of what information in COMMON blocks is actually used outside of a subroutine and when a subroutine uses a COMMON block merely as scratch storage for internal temporary results.

Jordan, Harry F.↗

NASA NTRS1997

On Designing Lightweight Threads for Substrate Software

Existing user-level thread packages employ a 'black box' design approach, where the implementation of the threads is hidden from the user. While this approach is often sufficient for application-level programmers, it hides critical design decisions that system-level programmers must be able to change in order to provide efficient service for high-level systems. By applying the principles of Open Implementation Analysis and Design, we construct a new user-level threads package that supports common thread abstractions and a well-defined meta-interface for altering the behavior of these abstractions. As a result, system-level programmers will have the advantages of using high-level thread abstractions without having to sacrifice performance, flexibility or portability.

Haines, Matthew↗

DOE OSTI2019

COMBIgor: Data-Analysis Package for Combinatorial Materials Science

Combinatorial experiments involve synthesis of sample libraries with lateral composition gradients requiring spatially-resolved characterization of structure and properties. Here, due to maturation of combinatorial methods and their successful application in many fields, the modern combinatorial laboratory produces diverse and complex data sets requiring advanced analysis and visualization techniques. In order to utilize these large data sets to uncover new knowledge, the combinatorial scientist must engage in data science. For data science tasks, most laboratories adopt common-purpose data management and visualization software. However, processing and cross-correlating data from various measurement tools is no small task for such generic programs. Here we describe COMBIgor, a purpose-built open-source software package written in the commercial Igor Pro environment, designed to offer a systematic approach to loading, storing, processing, and visualizing combinatorial data sets. It includes (1) methods for loading and storing data sets from combinatorial libraries, (2) routines for streamlined data processing, and (3) data analysis and visualization features to construct figures. Most importantly, COMBIgor is designed to be easily customized by a laboratory, group, or individual in order to integrate additional instruments and data-processing algorithms. Utilizing the capabilities of COMBIgor can significantly reduce the burden of data management on the combinatorial scientist.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Optimizing CMS build infrastructure via Apache Mesos

The Offline Software of the CMS Experiment at the Large Hadron Collider (LHC) at CERN consists of 6M lines of in-house code, developed over a decade by nearly 1000 physicists, as well as a comparable amount of general use open-source code. A critical ingredient to the success of the construction and early operation of the WLCG was the convergence, around the year 2000, on the use of a homogeneous environment of commodity x86-64 processors and Linux.Apache Mesos is a cluster manager that provides efficient resource isolation and sharing across distributed applications, or frameworks. It can run Hadoop, Jenkins, Spark, Aurora, and other applications on a dynamically shared pool of nodes. Lastly, we present how we migrated our continuous integration system to schedule jobs on a relatively small Apache Mesos enabled cluster and how this resulted in better resource usage, higher peak performance and lower latency thanks to the dynamic scheduling capabilities of Mesos.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Cabana: A Performance Portable Library for Particle-Based Simulations

Particle-based simulations are ubiquitous throughout many fields of computational science and engineering, spanning the atomistic level with molecular dynamics (MD), to mesoscale particle-in-cell (PIC) simulations for solid mechanics, device-scale modeling with PIC methods for plasma physics, and massive N-body cosmology simulations of galaxy structures, with many other methods in between (Hockney & Eastwood, 1989). While these methods use particles to represent significantly different entities with completely different physical models, many low-level details are shared including performant algorithms for short- and/or long-range particle interactions, multi-node particle communication patterns, and other data management tasks such as particle sorting and neighbor list construction. Cabana is a performance portable library for particle-based simulations, developed as part of the Co-Design Center for Particle Applications (CoPA) within the Exascale Computing Project (ECP) (Alexander et al., 2020). The CoPA project and its full development scope, including ECP partner applications, algorithm development, and similar software libraries for quantum MD, is described in (Mniszewski et al., 2021). Cabana uses the Kokkos library for on-node parallelism (Edwards et al., 2014; Trott et al., 2022), enabling simulation on multi-core CPU and GPU architectures, and MPI for GPU-aware, multi-node communication. Cabana provides particle simulation capabilities on almost all current Kokkos backends, including serial execution, OpenMP (including OpenMP-Target for GPUs), CUDA (NVIDIA GPUs), HIP (AMD GPUs), and SYCL (Intel GPUs), providing a clear path for the coming generation of accelerator-based exascale hardware. Cabana builds on Kokkos by providing new particle data structures and particle algorithms resulting in a similar execution policy-based, node-level programming model that is intended to be used in addition to the core Kokkos library within an application. Cabana is designed as an application and physics agnostic, but particle-specific toolkit which can either be used to generate a new application, or to be used as needed in existing applications at various levels of invasiveness including through interfaces that wrap user memory in existing data structures.

97 MATHEMATICS AND COMPUTING↗