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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,783 records · Page 99
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Vectorization, threading, and cache-blocking considerations for hydrocodes on emerging architectures

This work reports on considerations for improving computational performance in preparation for current and expected changes to computer architecture. The algorithms studied will include increasingly complex prototypes for radiation hydrodynamics codes, such as gradient routines and diffusion matrix assembly (e.g., in [1-6]). The meshes considered for the algorithms are structured or unstructured meshes. The considerations applied for performance improvements are meant to be general in terms of architecture (not specifically graphical processing unit (GPUs) or multi-core machines, for example) and include techniques for vectorization, threading, tiling, and cache blocking. Out of a survey of optimization techniques on applications such as diffusion and hydrodynamics, we make general recommendations with a view toward making these techniques conceptually accessible to the applications code developer. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Are we all in concordance with the meaning of the word conformance , and is our definition in conformity with standard definitions?

Here, we report that the term conformance is used widely in the geologic carbon sequestration (GCS) community to convey something about the sound understanding and performance of a GCS system. Some of the various definitions of conformance are considered along with a recommendation on a GCS-specific meaning of the word including illustrative graphics to help communicate the proposed definition.

58 GEOSCIENCES↗
DOE OSTI2015

STOCK: Structure mapper and online coarse-graining kit for molecular simulations

We present a web toolkit STructure mapper and Online Coarse-graining Kit for setting up coarse-grained molecular simulations. The kit consists of two tools: structure mapping and Boltzmann inversion tools. The aim of the first tool is to define a molecular mapping from high, e.g. all-atom, to low, i.e. coarse-grained, resolution. Using a graphical user interface it generates input files, which are compatible with standard coarse-graining packages, e.g. VOTCA and DL_CGMAP. Our second tool generates effective potentials for coarse-grained simulations preserving the structural properties, e.g. radial distribution functions, of the underlying higher resolution model. The required distribution functions can be provided by any simulation package. Simulations are performed on a local machine and only the distributions are uploaded to the server. The applicability of the toolkit is validated by mapping atomistic pentane and polyalanine molecules to a coarse-grained representation. Effective potentials are derived for systems of TIP3P (transferable intermolecular potential 3 point) water molecules and salt solution. The presented coarse-graining web toolkit is available at http://stock.cmm.ki.si.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

The GPU-enabled divide-expand-consolidate RI-MP2 method (DEC-RI-MP2)

We report porting of the Divide-Expand-Consolidate Resolution of the Identity second-order Møller–Plesset perturbation (DEC-RI-MP2) method to the graphic processing units (GPUs) using OpenACC compiler directives. It is shown that the OpenACC compiler directives implementation efficiently accelerates the rate-determining step of the DEC-RI-MP2 method with minor implementation effort. Moreover, the GPU acceleration results in a better load balance and thus in an overall scaling improvement of the DEC algorithm. The resulting cross-platform hybrid MPI/OpenMP/OpenACC implementation has scalable and portable performance on heterogeneous HPC architectures. The GPU-enabled code was benchmarked using a reduced version of the S12L test set of Stefan Grimme (Grimme, Chem. Eur. J. 2012, 18, 9955) consisting of supramolecular complexes up to 158 atoms and 4292 contracted basis functions (cc-pVTZ). The test set results demonstrate the general applicability of the DEC-RI-MP2 method showing results consistent with the DEC-RI-MP2 introductory paper (Baudin et al., J. Chem. Phys. 2016, 144, 054102) on molecules of complicated electronic structures. © 2016 Wiley Periodicals, Inc.

Chemistry↗
DOE OSTI2018

TopoMS: Comprehensive topological exploration for molecular and condensed-matter systems

We introduce TopoMS, a computational tool enabling detailed topological analysis of molecular and condensed-matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared-memory parallel approach, TopoMS provides scalable, numerically robust, and topologically consistent analysis. TopoMS can be used as a command-line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph. This paper presents algorithmic details of TopoMS and compares it with state-of-the-art tools: Bader charge analysis v1.0 (Arnaldsson et al., 01/11/17) and molecular graph extraction using Critic2 (Otero-de-la-Roza et al., Comput. Phys. Commun. 2014, 185, 1007). TopoMS not only combines the functionality of these individual codes but also demonstrates up to 4× performance gain on a standard laptop, faster convergence to fine-grid solution, robustness against lattice bias, and topological consistency. TopoMS is released publicly under BSD License.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Double-buffered, heterogeneous CPU + GPU integral digestion algorithm for single-excitation calculations involving a large number of excited states

The most widely used quantum-chemical models for excited states are single-excitation theories, a category that includes configuration interaction with single substitutions, time-dependent density functional theory, and also a recently developed ab initio exciton model. When a large number of excited states are desired, these calculations incur a significant bottleneck in the “digestion” step in which two-electron integrals are contracted with density or density-like matrices. We present an implementation that moves this step onto graphical processing units (GPUs), and introduce a double-buffer scheme that minimizes latency by computing integrals on the central processing units (CPUs) concurrently with their digestion on the GPUs. An automatic code generation scheme simplifies the implementation of high-performance GPU kernels. For the exciton model, which requires separate excited-state calculations on each electronically coupled chromophore, the heterogeneous implementation described here results in speedups of 2–6× versus a CPU-only implementation. For traditional time-dependent density functional theory calculations, we obtain speedups of up to 5× when a large number of excited states is computed.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

BrazilClim : The overcoming of limitations of pre‐existing bioclimate data

Abstract Species distribution modelling has become instrumental in assessing the influence of environmental conditions on the occurrence or abundance of taxa. The set of environmental layers used for this purpose is a crucial aspect, for which different climate‐based (bioclimatic) datasets have been recently developed. These bioclimatic variables result from combinations of precipitation and temperatures surfaces. Here, we explored both the performance and possibility of improving some of the currently available bioclimatic databases, through an evaluation of the precipitation and temperatures surfaces used to generate them. For this purpose, we used a combination of statistic and graphic approaches. We focused on Brazil, not only due to its natural megadiversity, but also due to its continental size and orographic heterogeneity: an excellent ground for refining methods replicable elsewhere. We found a better match between the climatic data measured on‐field and Tropical Rainfall Measuring Mission (TRMM 3B43 v7) in the case of precipitation, and the surfaces provided by the National Oceanic and Atmospheric Administration (NOAA) in the case of temperatures, sources uncommonly used for species niche modelling. We gauge‐calibrated the best performing surfaces using machine‐learning algorithms and generated corrected surfaces that allowed us to create BrazilClim: a database of bioclimatic variables, based on improved primary surfaces, which will result in more assertive predicted distributions and more actual pictures of the species' ecological requirements for megadiverse Brazil, an approach replicable elsewhere. All primary and bioclimatic surfaces generated for this study may be freely downloaded.

Ramoni‐Perazzi, Paolo↗
DOE OSTI2019

Parallel beamlet dose calculation via beamlet contexts in a distributed multi‐GPU framework

Purpose Dose calculation is one of the most computationally intensive, yet essential tasks in the treatment planning process. With the recent interest in automatic beam orientation and arc trajectory optimization techniques, there is a great need for more efficient model‐based dose calculation algorithms that can accommodate hundreds to thousands of beam candidates at once. Foundational work has shown the translation of dose calculation algorithms to graphical processing units ( GPU s), lending to remarkable gains in processing efficiency. But these methods provide parallelization of dose for only a single beamlet, serializing the calculation of multiple beamlets and under‐utilizing the potential of modern GPU s. In this paper, the authors propose a framework enabling parallel computation of many beamlet doses using a novel beamlet context transformation and further embed this approach in a scalable network of multi‐ GPU computational nodes. Methods The proposed context‐based transformation separates beamlet‐local density and TERMA into distinct beamlet contexts that independently provide sufficient data for beamlet dose calculation. Beamlet contexts are arranged in a composite context array with dosimetric isolation, and the context array is subjected to a GPU collapsed‐cone convolution superposition procedure, producing the set of beamlet‐specific dose distributions in a single pass. Dose from each context is converted to a sparse representation for efficient storage and retrieval during treatment plan optimization. The context radius is a new parameter permitting flexibility between the speed and fidelity of the dose calculation process. A distributed manager‐worker architecture is constructed around the context‐based GPU dose calculation approach supporting an arbitrary number of worker nodes and resident GPU s. Phantom experiments were executed to verify the accuracy of the context‐based approach compared to Monte Carlo and a reference CPU ‐ CCCS implementation for single beamlets and broad beams composed by addition of beamlets. Dose for representative 4 π beam sets was calculated in lung and prostate cases to compare its efficiency with that of an existing beamlet‐sequential GPU ‐ CCCS implementation. Code profiling was also performed to evaluate the scalability of the framework across many networked GPU s. Results The dosimetric accuracy of the context‐based method displays <1.35% and 2.35% average error from the existing serialized CPU ‐ CCCS algorithm and Monte Carlo simulation for beamlet‐specific PDD s in water and slab phantoms, respectively. The context‐based method demonstrates substantial speedup of up to two orders of magnitude over the beamlet‐sequential GPU ‐ CCCS method in the tested configurations. The context‐based framework demonstrates near linear scaling in the number of distributed compute nodes and GPU s employed, indicating that it is flexible enough to meet the performance requirements of most users by simply increasing the hardware utilization. Conclusions The context‐based approach demonstrates a new expectation of performance for beamlet‐based dose calculation methods. This approach has been successful in accelerating the dose calculation process for very large‐scale treatment planning problems ‐ such as automatic 4 π IMRT beam orientation and VMAT arc trajectory selection, with hundreds of thousands of beamlets ‐ in clinically feasible timeframes. The flexibility of this framework makes it as a strong candidate for use in a variety of other very large‐scale treatment planning tasks and clinical workflows.

Neph, Ryan↗
DOE OSTI2019

A second‐generation virtual‐pinhole PET device for enhancing contrast recovery and improving lesion detectability of a whole‐body PET/CT scanner

Purpose We have developed a second‐generation virtual‐pinhole (VP) positron emission tomography (PET) device that can position a flat‐panel PET detector around a patient's body using a robotic arm to enhance the contrast recovery coefficient (CRC) and detectability of lesions in any region‐of‐interest using a whole‐body PET/computed tomography (CT) scanner. Methods We constructed a flat‐panel VP‐PET device using 32 high‐resolution detectors, each containing a 4 4 MPPC array and 16 16 LYSO crystals of 1.0 1.0 3.0 mm 3 each. The flat‐panel detectors can be positioned around a patient's body anywhere in the imaging field‐of‐view (FOV) of a Siemens Biograph 40 PET/CT scanner by a robotic arm. New hardware, firmware and software have been developed to support the additional detector signals without compromising a scanner's native functions. We stepped a 22 Na point source across the axial FOV of the scanner to measure the sensitivity profile of the VP‐PET device. We also recorded the coincidence events measured by the scanner detectors and by the VP‐PET detectors when imaging phantoms of different sizes. To assess the improvement in the CRC of small lesions, we imaged an elliptical torso phantom measuring 316 228 162 mm 3 that contains spherical tumors with diameters ranging from 3.3 to 11.4 mm with and without the VP‐PET device. Images were reconstructed using a list mode Maximum‐Likelihood Estimation‐Maximization algorithm implemented on multiple graphics processing units (GPUs) to support the unconventional geometries enabled by a VP‐PET system. The mean and standard deviation of the CRC were calculated for tumors of different sizes. Monte Carlo simulation was also conducted to image clusters of lesions in a torso phantom using a PET/CT scanner alone or the same scanner equipped with VP‐PET devices. Receiver operating characteristic (ROC) curves were analyzed for three system configurations to evaluate the improvement in lesion detectability by the VP‐PET device over the native PET/CT scanner. Results The repeatability in positioning the flat‐panel detectors using a robotic arm is better than 0.15 mm in all three directions. Experimental results show that the average CRC of 3.3, 4.3, and 6.0 mm diameter tumors was 0.82%, 2.90%, and 5.25%, respectively, when measured by the native scanner. The corresponding CRC was 2.73%, 6.21% and 10.13% when imaged by the VP‐PET insert device with the flat‐panel detector under the torso phantom. These values may be further improved to 4.31%, 9.65% and 18.01% by a future dual‐panel VP‐PET insert device if DOI detectors are employed to triple its detector efficiency. Monte Carlo simulation results show that the tumor detectability can be improved by a VP‐PET device that has a single flat‐panel detector. The improvement is greater if the VP‐PET device employs a dual‐panel design. Conclusions We have developed a prototype flat‐panel VP‐PET device and integrated it with a clinical PET/CT scanner. It significantly enhances the contrast of lesions, especially for those that are borderline detectable by the native scanner, within regions‐of‐interest specified by users. Simulation demonstrated the enhancement in lesion detectability with the VP‐PET device. This technology may become a cost‐effective solution for organ‐specific imaging tasks.

Jiang, Jianyong↗
DOE OSTI2017

Pseudo-Spectral Methods for the Laplace-Beltrami Equation and the Hodge Decomposition on Surfaces of Genus One

The inversion of the Laplace-Beltrami operator and the computation of the Hodge decomposition of a tangential vector field on smooth surfaces arise as computational tasks in many areas of science, from computer graphics to machine learning to computational physics. In this work, we present a high-order accurate pseudo-spectral approach, applicable to closed surfaces of genus one in three-dimensional space, with a view toward applications in plasma physics and fluid dynamics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Morpheus Spectral Counter: A computational tool for label-free quantitative mass spectrometry using the Morpheus search engine

Label-free quantitative MS based on the Normalized Spectral Abundance Factor (NSAF) has emerged as a straightforward and robust method to determine the relative abundance of individual proteins within complex mixtures. Here, we present Morpheus Spectral Counter (MSpC) as the first computational tool that directly calculates NSAF values from output obtained from Morpheus, a fast, open-source, peptide-MS/MS matching engine compatible with high-resolution accurate-mass instruments. NSAF has distinct advantages over other MS-based quantification methods, including a higher dynamic range as compared to isobaric tags, no requirement to align and re-extract MS1 peaks, and increased speed. MSpC features an easy to use graphic user interface that additionally calculates both distributed and unique NSAF values to permit analyses of both protein families and isoforms/proteoforms. MSpC determinations of protein concentration were linear over several orders of magnitude based on the analysis of several high-mass accuracy datasets either obtained from PRIDE or generated with total cell extracts spiked with purified Arabidopsis 20S proteasomes. Lastly, the MSpC software was developed in C# and is open sourced under a permissive license with the code made available at http://dcgemperline.github.io/Morpheus_SpC/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Fundamental investigations into the free‐radical copolymerization of N ‐phenylmaleimide and norbornene

ABSTRACT A fundamental investigation into the copolymerization of N ‐phenylmaleimide and norbornene via conventional free‐radical polymerization techniques was conducted. Reaction conditions were optimized for molecular weight and percent yield by tuning overall concentration and initiator loading. The copolymerization kinetics were monitored using in‐situ , variable temperature nuclear magnetic resonance and first‐order behavior was observed with respect to each monomer. Although the related copolymerization of norbornene and maleic anhydride was well‐known to proceed in a perfectly alternating manner, the copolymerization of norbornene and N ‐phenylmaleimide was found to deviate from strictly alternating copolymerization behavior, producing significant amounts of sequentially enchained N ‐phenylmaleimide units within the polymeric backbone. This deviation from perfectly alternating behavior was confirmed by analysis of individual monomer conversion rates and by measurement of monomer reactivity ratios using the Mayo–Lewis graphical analysis method. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54 , 985–991

Gmernicki, Kevin R.↗
DOE OSTI2013

Composition-Mediated Order-Disorder Transformation in FePt Nanoparticles

Thumbnail image of graphical abstract Heat-treated alloy FePt nanoparticles transform into L10 FePt and mixed L10/L12 FePt3 intermetallic phases. Enrichment in Pt in some nanoparticles, rather than intrinsic thermodynamic effects, drives phase segregation. FePt nanoparticles of uniform, equimolar composition are expected to transform into phase-pure, highly ordered L10 FePt nanoparticles.

Johnston-Peck, Aaron C.↗
DOE OSTI2017

Selecting the Best Wild Card Entries in a Covering Array

For some covering arrays, there are some wild card positions in the array where there is flexibility about what factor levels can be chosen with no impact on the basic properties of covering array, because all of the required pairs have been covered. The choice of how to fill these wild card positions can influence other properties, such as the degrees of orthogonality or three-way coverage of the array. Here in this article, some criteria are proposed for identifying the best choices for the wild card positions to create covering arrays with highly desirable properties. Accompanying graphical summaries are also described to highlight differing performance for several examples.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Examining robustness of model selection with half-normal and LASSO plots for unreplicated factorial designs

When there are constraints on resources, an unreplicated factorial or fractional factorial design can allow efficient exploration of numerous factor and interaction effects. A half-normal plot is a common graphical tool used to compare the relative magnitude of effects and to identify important effects from these experiments when no estimate of error from the experiment is available. An alternative is to use a least absolute shrinkage and selection operation plot to examine the pattern of model selection terms from an experiment. We examine how both the half-normal and least absolute shrinkage and selection operation plots are impacted by the absence of individual observations or an outlier, and the robustness of conclusions obtained from these 2 techniques for identifying important effects from factorial experiments. As a result, the methods are illustrated with 2 examples from the literature.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Assessing robustness of factor ranking for supersaturated designs

Supersaturated designs can potentially be a beneficial tool for efficiently exploring a large number of factors with a moderately sized design. However, because more factors are being considered than there are runs, the stability of the identified factors depends heavily on effect sparsity and the lack of highly influential observations. A helpful tool for the analysis of supersaturated designs is least absolute shrinkage and selection operation (LASSO), which is useful when the effects of many explanatory variables are sparse in a high-dimensional dataset. To understand the impact of individual observations on the selected factors, the LASSO influence plot was created. This work describes an application of this plot and its variants that can be used to identify influential points, increase understanding of the impact of individual observations on model parameters, and the robustness of results in analyses with supersaturated designs. These graphical methods can serve as a complement to other regression diagnostics techniques in the LASSO regression setting.

3-D LASSO influence plots↗