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DOE OSTI2015

Alpha particles diffusion due to charge changes

Alpha particles diffusion due to charge changes in a magnetized plasma is studied. Analytical calculations and numerical simulations are employed to show that this process can be very important in the pedestal-edge-SOL regions. This is the first study that presents clear evidence of the importance of atomic processes on the diffusion of alpha particles. A simple 1D model that includes inelastic collisions with plasma species, “cold” neutrals, and partially ionized species was employed. The code, which follows the exact particle orbits and includes the effect of inelastic collisions via a Monte Carlo type random process, runs on a graphic processor unit (GPU). The analytical and numerical results show excellent agreement when a uniform background (plasma and cold species) is assumed. The simulations also show that the gradients in the density of the plasma and cold species, which are large and opposite in the edge region, produce an inward flux of alpha particles. Calculations of the alpha particles flux reaching the walls or divertor plates should include these processes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2013

HipGISAXS : a high-performance computing code for simulating grazing-incidence X-ray scattering data

This article describes the development of a flexible grazing-incidence small-angle X-ray scattering (GISAXS) simulation code in the framework of the distorted wave Born approximation that effectively utilizes the parallel processing power provided by graphics processors and multicore processors. The code, entitled High-Performance GISAXS , computes the GISAXS image for any given superposition of user-defined custom shapes or morphologies in a material and for various grazing-incidence angles and sample orientations. These capabilities permit treatment of a wide range of possible sample structures, including multilayered polymer films and nanoparticles on top of or embedded in a substrate or polymer film layers. In cases where the material displays regions of significant refractive index contrast, an algorithm has been implemented to perform a slicing of the sample and compute the averaged refractive index profile to be used as the reference geometry of the unperturbed system. A number of case studies are presented, which demonstrate good agreement with the experimental data for a variety of polymer and hybrid polymer/nanoparticle composite materials. The parallelized simulation code is well suited for addressing the analysis efforts required by the increasing amounts of GISAXS data being produced by high-speed detectors and ultrafast light sources.

Chemistry↗

DOE OSTI2012

Fast DRR generation for 2D to 3D registration on GPUs

Purpose: The generation of digitally reconstructed radiographs (DRRs) is the most time consuming step on the CPU in intensity based two-dimensional x-ray to three-dimensional (CT or 3D rotational x-ray) medical image registration, which has application in several image guided interventions. This work presents optimized DRR rendering on graphical processor units (GPUs) and compares performance achievable on four commercially available devices. Methods: A ray-cast based DRR rendering was implemented for a 512 Multiplication-Sign 512 Multiplication-Sign 72 CT volume. The block size parameter was optimized for four different GPUs for a region of interest (ROI) of 400 Multiplication-Sign 225 pixels with different sampling ratios (1.1%-9.1% and 100%). Performance was statistically evaluated and compared for the four GPUs. The method and the block size dependence were validated on the latest GPU for several parameter settings with a public gold standard dataset (512 Multiplication-Sign 512 Multiplication-Sign 825 CT) for registration purposes. Results: Depending on the GPU, the full ROI is rendered in 2.7-5.2 ms. If sampling ratio of 1.1%-9.1% is applied, execution time is in the range of 0.3-7.3 ms. On all GPUs, the mean of the execution time increased linearly with respect to the number of pixels if sampling was used. Conclusions: The presented results outperform other results from the literature. This indicates that automatic 2D to 3D registration, which typically requires a couple of hundred DRR renderings to converge, can be performed quasi on-line, in less than a second or depending on the application and hardware in less than a couple of seconds. Accordingly, a whole new field of applications is opened for image guided interventions, where the registration is continuously performed to match the real-time x-ray.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2013

Combining prior day contours to improve automated prostate segmentation

Purpose: To improve the accuracy of automatically segmented prostate, rectum, and bladder contours required for online adaptive therapy. The contouring accuracy on the current image guidance [image guided radiation therapy (IGRT)] scan is improved by combining contours from earlier IGRT scans via the simultaneous truth and performance level estimation (STAPLE) algorithm. Methods: Six IGRT prostate patients treated with daily kilo-voltage (kV) cone-beam CT (CBCT) had their original plan CT and nine CBCTs contoured by the same physician. Three types of automated contours were produced for analysis. (1) Plan: By deformably registering the plan CT to each CBCT and then using the resulting deformation field to morph the plan contours to match the CBCT anatomy. (2) Previous: The contour set drawn by the physician on the previous day CBCT is similarly deformed to match the current CBCT anatomy. (3) STAPLE: The contours drawn by the physician, on each prior CBCT and the plan CT, are deformed to match the CBCT anatomy to produce multiple contour sets. These sets are combined using the STAPLE algorithm into one optimal set. Results: Compared to plan and previous, STAPLE improved the average Dice's coefficient (DC) with the original physician drawn CBCT contours to a DC as follows: Bladder: 0.81 {+-} 0.13, 0.91 {+-} 0.06, and 0.92 {+-} 0.06; Prostate: 0.75 {+-} 0.08, 0.82 {+-} 0.05, and 0.84 {+-} 0.05; and Rectum: 0.79 {+-} 0.06, 0.81 {+-} 0.06, and 0.85 {+-} 0.04, respectively. The STAPLE results are within intraobserver consistency, determined by the physician blindly recontouring a subset of CBCTs. Comparing plans recalculated using the physician and STAPLE contours showed an average disagreement less than 1% for prostate D98 and mean dose, and 5% and 3% for bladder and rectum mean dose, respectively. One scan takes an average of 19 s to contour. Using five scans plus STAPLE takes less than 110 s on a 288 core graphics processor unit. Conclusions: Combining the plan and all prior days via the STAPLE algorithm to produce treatment day contours is superior to the current standard of deforming only the plan contours to the daily CBCT. STAPLE also improves the precision, with a substantial decrease in standard deviation, a key for adaptive therapy. Geometrically and dosimetrically accurate contours can be automatically generated with STAPLE on prostate region kV CBCT in a time scale suitable for online adaptive therapy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

SU-G-TeP1-15: Toward a Novel GPU Accelerated Deterministic Solution to the Linear Boltzmann Transport Equation

Purpose: To develop a Graphic Processor Unit (GPU) accelerated deterministic solution to the Linear Boltzmann Transport Equation (LBTE) for accurate dose calculations in radiotherapy (RT). A deterministic solution yields the potential for major speed improvements due to the sparse matrix-vector and vector-vector multiplications and would thus be of benefit to RT. Methods: In order to leverage the massively parallel architecture of GPUs, the first order LBTE was reformulated as a second order self-adjoint equation using the Least Squares Finite Element Method (LSFEM). This produces a symmetric positive-definite matrix which is efficiently solved using a parallelized conjugate gradient (CG) solver. The LSFEM formalism is applied in space, discrete ordinates is applied in angle, and the Multigroup method is applied in energy. The final linear system of equations produced is tightly coupled in space and angle. Our code written in CUDA-C was benchmarked on an Nvidia GeForce TITAN-X GPU against an Intel i7-6700K CPU. A spatial mesh of 30,950 tetrahedral elements was used with an S4 angular approximation. Results: To avoid repeating a full computationally intensive finite element matrix assembly at each Multigroup energy, a novel mapping algorithm was developed which minimized the operations required at each energy. Additionally, a parallelized memory mapping for the kronecker product between the sparse spatial and angular matrices, including Dirichlet boundary conditions, was created. Atomicity is preserved by graph-coloring overlapping nodes into separate kernel launches. The one-time mapping calculations for matrix assembly, kronecker product, and boundary condition application took 452±1ms on GPU. Matrix assembly for 16 energy groups took 556±3s on CPU, and 358±2ms on GPU using the mappings developed. The CG solver took 93±1s on CPU, and 468±2ms on GPU. Conclusion: Three computationally intensive subroutines in deterministically solving the LBTE have been formulated on GPU, resulting in two orders of magnitude speedup. Funding support from Natural Sciences and Engineering Research Council and Alberta Innovates Health Solutions. Dr. Fallone is a co-founder and CEO of MagnetTx Oncology Solutions (under discussions to license Alberta bi-planar linac MR for commercialization).

60 APPLIED LIFE SCIENCES↗

DOE OSTI2012

Modern approaches for the theoretical description of multiparticle scattering and nuclear reactions

A review of novel approaches to solution of multiparticle scattering problems in the area above three-body breakup together with the review of new computational technologies which provide very effective and ultrafast realization of the novel approaches with ordinary PC are given. The novel direction presented here is based on two key points: a new formulation of the quantum scattering theory in a discrete Hilbert space of stationary wave packets and the massive-parallel solution of the resulted matrix equations with usage of ultrafast graphic processors (the so called GPU-computations). For the reader's convenience, a short review of the modern GPU calculations for the medicine, physics, military applications etc. is presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

Model of a Thin Current Sheet in the Earth’s Magnetotail with a Kinetic Description of Magnetized Electrons

Steady-state two-dimensional thin current sheets (TCSs) in collisionless space plasma, similar to the current sheet of the near-Earth magnetotail, are considered. The magnetic field of the sheet is orthogonal to the current and has a nonzero normal component, the electrons are magnetized, and the ions are unmagnetized. To solve the problem of kinetic description of electrons in such current sheets in a general form, they are described by the Vlasov equation in the drift approximation, the general solution to which is found in the form of a function of three independent integrals of the system of drift motion equations. An important case is considered in which the electron guiding centers obey a Maxwell–Boltzmann distribution in a stationary electromagnetic field. The obtained results make it possible to create one- and two-dimensional numerical− analytical models of current sheets in which unmagnetized ions are described by the Vlasov equation, which should be solved numerically, whereas the contribution of magnetized electrons is taken into account analytically. To numerically solve the time-independent Vlasov equation, a new method is proposed that allows one to perform the bulk of computations by using graphic processors. On the basis of the new theory, a one-dimensional numerical−analytical model of a steady-state TCS in the near-Earth magnetotail is presented, TCS configurations are calculated, and the role of electrostatic effects and electron pressure anisotropy is analyzed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

HipGISAXS

Implementation of a flexible Grazing Incidence Small-Angle Scattering (GISAXS). Simulation code based on the Distorted Wave Born Approximation (DWBA) theory that effectively utilizes the parallel processing power provided by graphic processors and multicore processors. This constitutes a handy tool for experimentalists facing a massive flux of data, allowing them to accurately simulate the GISAXS process and analyze the produced data. The software computes the diffraction image for any given super position of custom shapes or morphologies in a user-defined region of the reciprocal space for all possible grazing incidence angles and in-plane sample rotations. This flexibility then allows to easily tackle a wide range of possible sample structures such as nanoparticles o top of or embedded in a substrate or a multilayered structure. In cases where the sample displays regions of significant refractive index contrast, an algorithm has been implemented to perform a slicing of the sample along the vertical direction and compute the averaging refractive index profile to be used as the reference geometry of the unpertubed system. Preliminary tests show good agreement with experimental data for a variety of commonly encountered nanostructures.

Xiaoye, Sherry Li↗

DOE OSTI2012

Final Reports from the Los Alamos National Laboratory Computational Physics Student Summer Workshop

The two primary purposes of LANL’s Computational Physics Student Summer Workshop are (1) To educate graduate and exceptional undergraduate students in the challenges and applications of computational physics of interest to LANL, and (2) Entice their interest toward those challenges. Computational physics is emerging as a discipline in its own right, combining expertise in mathematics, physics, and computer science. The mathematical aspects focus on numerical methods for solving equations on the computer as well as developing test problems with analytical solutions. The physics aspects are very broad, ranging from low-temperature material modeling to extremely high temperature plasma physics, radiation transport and neutron transport. The computer science issues are concerned with matching numerical algorithms to emerging architectures and maintaining the quality of extremely large codes built to achieve multi-physics calculations. Although graduate programs associated with computational physics are emerging, it is apparent that the pool of U.S. citizens in this multidisciplinary field is relatively small and is typically not focused on the aspects that are of primary interest to LANL. Furthermore, more structured foundations for LANL interaction with universities in computational physics is needed; currently interactions rely almost solely on individuals’ personalities and personal contacts. Thus a tertiary purpose of the Summer Workshop is to build an educational network of LANL researchers, university professors, and emerging students to advance the field and LANL’s involvement in it. This was the second year for the Summer Workshop. Like the previous year, the workshop’s goals were achieved by bringing into LANL a select group of students recruited from across the United States and immersing them for ten weeks in lectures and interesting research projects. The lectures provided an overview of the computational physics topics of interest this year along with some detailed instruction while the projects gave the students a positive experience accomplishing technical goals. Each team consisted of two students working under one or more mentors from LANL on specific research projects associated with predefined topics. This year, the topics were on verification of simulations in plasma and radiation-hydrodynamics codes, hypervelocity material deformation, plasma physics, graphical processor unit (“GPU”) programming, multi-material mixing, turbulence modeling, computational material science, and electromagnetic pulse simulations. The students’ growth was furthered by their participation on teams where their teammates were sometimes of different academic rank. It also developed them by requiring them to produce written and oral reports that they presented to peers, mentors, and management.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2013

Searches for neutrino oscillations in the MiniBooNE experiment: neutrino and antineutrino occurrence analysis of the electron; Búsquedas de oscilaciones de neutrinos en el experimento MiniBooNE: análisis de aparición de neutrinos y antineutrinos del electrón

In this work we implemented the electron neutrino and antineutrino appearance oscillation analyses of the MiniBooNE experiment using the data publicly released by the Collaboration. The calculations were made with algorithms in C++ as well as in graphic processors using CUDA. We performed the analyses corresponding to the publications of 2007 and 2009 in neutrino mode, 2010 in antineutrino mode, and 2013 in neutrino and antineutrino modes, and constructed the confidence intervals in the oscillations parameter space for each case. The contours calculated in this work are indistinguishable from those reported by the MiniBooNE Collaboration when the frequentist corrections of Feldman and Cousins are not taken into account. After implementing these corrections small differences with respect to the official contours appear in the low signal regions, which are ascribed to the fake experiment generation method employed here, and that require further investigation. The best fit probabilities and null point, as the observed event excesses show small variations with respect to those reported in the publications, arising from a difference in the definition of the signal region employed here and forced by the format of the released data, and are consistent within errors. This work was carried out independently to the MiniBooNE Collaboration, and its results are not official. Antes que nada quiero agradecer a mi asesor el Dr. Alexis Aguilar Arévalo, con quien he estado trabajando desde mi servicio social, hace varios años ya. Con él he aprendido una gran variedad de temas: mis primeros programas serios fueron con su guía; principalmente de él adapté mi estilo de redacción de código, me enseñó más física experimental y estadística que lo que aprendí en toda la carrera; formando en mi lo que significa ser un buen experimentalista, mi perspectiva de la física de partículas elementales no podría ser tan amplia como lo es si no fuera por él; enseñándome la historia de los descubrimientos, así como las técnicas experimentales para hacerlos y la teoría que los explica. Mucho trabajo me costó, pero el conocimiento tan amplio que tengo sobre los neutrinos, experimental y teórico, se debe a la enorme paciencia de mi asesor. Mucho le agradezco haberme mandado a Fermilab, en donde fui parte de un activo y amable grupo de trabajo, en donde aprendí una forma distinta de hacer ciencia: mucho más colaborativa. Le agradezco su perfeccionismo y apoyo constante en todos estos años, sin los cuales no hubiera logrado enorgullecerme de esta tesis tanto como lo estoy ahora. Para mi es un rol a seguir, mostrándome la clase de físico en que me quiero convertir. Sobre todo le agradezco su amistad, gracias Alexis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1983

Graphics enhanced computer emulation for improved timing-race and fault tolerance control system analysis

A computer simulation system has been developed for the Space Shuttle's advanced Centaur liquid fuel booster rocket, in order to conduct systems safety verification and flight operations training. This simulation utility is designed to analyze functional system behavior by integrating control avionics with mechanical and fluid elements, and is able to emulate any system operation, from simple relay logic to complex VLSI components, with wire-by-wire detail. A novel graphics data entry system offers a pseudo-wire wrap data base that can be easily updated. Visual subsystem operations can be selected and displayed in color on a six-monitor graphics processor. System timing and fault verification analyses are conducted by injecting component fault modes and min/max timing delays, and then observing system operation through a red line monitor.

Szatkowski, G. P.↗

NASA NTRS1983

AIDDE the Ames Interactive Dynamic Display Editor

This paper describes the design and development of the Ames Interactive Dynamic Display Editor language (AIDDE). AIDDE and its associated tools are a software system that facilitates the interactive creation and use of real-time displays. For the present purposes, real-time displays are pictures on a CRT that change over time to reflect the state of a system. A graphics tree describes a display. Display dynamics are specified by attaching expressions to the tree. Offline, AIDDE is used to draw displays, define display dynamics, and generate host computer source code and a representation of the tree convenient for use in a graphics device. At run time, the compiled host code passes the results of the expressions to a graphics device to modify the tree. The graphics processor repeatedly traverses the tree to draw a changing display on the CRT. Several real-time displays have been implemented using AIDDE with good results.

Globus, A.↗

NASA NTRS1985

LAMPS software and mesoscale prediction studies

The full-physics version of the LAMPS model has been implemented on the Perkin-Elmer computer. In Addition, LAMPS graphics processors have been rewritten to the run on the Perkin-Elmer and they are currently undergoing final testing. Numerical experiments investigating the impact of convective parameterized latent heat release on the evolution of a precipitating storm have been performed and the results are currently being evaluated. Curent efforts include the continued evaluation of the impact of initial conditions on LAMPS model results. This work will help define measurement requirements for future research field projects as well as for observations in support of operational forecasts. Also, the impact of parameterized latent heat on the evolution of precipitating systems is continuing. This research is in support of NASA's proposed Earth Observation Mission (EOM).

Perkey, D. J.↗

NASA NTRS1990

A personal computer-based, multitasking data acquisition system

A multitasking, data acquisition system was written to simultaneously collect meteorological radar and telemetry data from two sources. This system is based on the personal computer architecture. Data is collected via two asynchronous serial ports and is deposited to disk. The system is written in both the C programming language and assembler. It consists of three parts: a multitasking kernel for data collection, a shell with pull down windows as user interface, and a graphics processor for editing data and creating coded messages. An explanation of both system principles and program structure is presented.

Bailey, Steven A.↗

NASA NTRS1990

A package for 3-D unstructured grid generation, finite-element flow solution and flow field visualization

A set of computer programs for 3-D unstructured grid generation, fluid flow calculations, and flow field visualization was developed. The grid generation program, called VGRID3D, generates grids over complex configurations using the advancing front method. In this method, the point and element generation is accomplished simultaneously, VPLOT3D is an interactive, menudriven pre- and post-processor graphics program for interpolation and display of unstructured grid data. The flow solver, VFLOW3D, is an Euler equation solver based on an explicit, two-step, Taylor-Galerkin algorithm which uses the Flux Corrected Transport (FCT) concept for a wriggle-free solution. Using these programs, increasingly complex 3-D configurations of interest to aerospace community were gridded including a complete Space Transportation System comprised of the space-shuttle orbitor, the solid-rocket boosters, and the external tank. Flow solutions were obtained on various configurations in subsonic, transonic, and supersonic flow regimes.

Parikh, Paresh↗

NASA NTRS1991

Virtual reality applications to automated rendezvous and capture

Virtual Reality (VR) is a rapidly developing Human/Computer Interface (HCI) technology. The evolution of high-speed graphics processors and development of specialized anthropomorphic user interface devices, that more fully involve the human senses, have enabled VR technology. Recently, the maturity of this technology has reached a level where it can be used as a tool in a variety of applications. This paper provides an overview of: VR technology, VR activities at Marshall Space Flight Center (MSFC), applications of VR to Automated Rendezvous and Capture (AR&C), and identifies areas of VR technology that requires further development.

Hale, Joseph↗

NASA NTRS2008

Aspects of Synthetic Vision Display Systems and the Best Practices of the NASA's SVS Project

NASA s Synthetic Vision Systems (SVS) Project conducted research aimed at eliminating visibility-induced errors and low visibility conditions as causal factors in civil aircraft accidents while enabling the operational benefits of clear day flight operations regardless of actual outside visibility. SVS takes advantage of many enabling technologies to achieve this capability including, for example, the Global Positioning System (GPS), data links, radar, imaging sensors, geospatial databases, advanced display media and three dimensional video graphics processors. Integration of these technologies to achieve the SVS concept provides pilots with high-integrity information that improves situational awareness with respect to terrain, obstacles, traffic, and flight path. This paper attempts to emphasize the system aspects of SVS - true systems, rather than just terrain on a flight display - and to document from an historical viewpoint many of the best practices that evolved during the SVS Project from the perspective of some of the NASA researchers most heavily involved in its execution. The Integrated SVS Concepts are envisagements of what production-grade Synthetic Vision systems might, or perhaps should, be in order to provide the desired functional capabilities that eliminate low visibility as a causal factor to accidents and enable clear-day operational benefits regardless of visibility conditions.

Bailey, Randall E.↗

NASA NTRS2018

The InSAR Scientific Computing Environment 3.0: A Flexible Framework for NISAR Operational and User-Led Science Processing

The InSAR Scientific Computing Environment (ISCE) was first developed under the NASA Advanced Information Systems Technology as a flexible, extensible object-oriented framework for Interferometric Synthetic Aperture Radar (InSAR) processing. The ISCE framework uses Python 3 at the workflow level, controlling modules of compiled code for functional processing, and managing inputs, outputs, and other flow control services. The currently released version, called ISCE 2.1, is distributed to the research community through the Western North America InSAR Consortium under a research license. The ISCE team is working on the next generation of the code in order to prepare for the NASAISRO SAR (NISAR) mission operational processing. Innovations in this code include augmentation or conversion of the custom Python framework elements in ISCE with the Pyre framework, new workflows for interferometric and polarimetric stack processing, a more intuitive and graphically based user interface, and flow control for hybrid computing environments including CPU/GPU clusters, logging and error tracking facilities, and new more efficient computational modules that exploit graphical processor units (GPUs) when available. The ISCE 3.0 framework is designed to work in an operational environment as well as on a single user’s laptop or compute cluster, with services to discover capabilities and scale computations accordingly.

Buckley, Sean M.↗