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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Tolerating memory stack failures in multi-stack systems

Memory management circuitry and processes operate to improve reliability of a group of memory stacks, providing that if a memory stack or a portion thereof fails during the product's lifetime, the system may still recover with no errors or data loss. A front-end controller receives a block of data requested to be written to memory, divides the block into sub-blocks, and creates a new redundant reliability sub-block. The sub-blocks are then written to different memory stacks. When reading data from the memory stacks, the front-end controller detects errors indicating a failure within one of the memory stacks, and recovers corrected data using the reliability sub-block. The front-end controller may monitor errors for signs of a stack failure and disable the failed stack.

Mappouras, Georgios↗
DOE OSTI2012

Solution of the Skyrme-Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis. (VII) HFODD (v2.49t): A new version of the program

We describe the new version (v2.49t) of the code HFODD which solves the nuclear Skyrme Hartree-Fock (HF) or Skyrme Hartree-Fock-Bogolyubov (HFB) problem by using the Cartesian deformed harmonic-oscillator basis. In the new version, we have implemented the following physics features: (i) the isospin mixing and projection, (ii) the finite temperature formalism for the HFB and HF+BCS methods, (iii) the Lipkin translational energy correction method, (iv) the calculation of the shell correction. A number of specific numerical methods have also been implemented in order to deal with large-scale multi-constraint calculations and hardware limitations: (i) the two-basis method for the HFB method, (ii) the Augmented Lagrangian Method (ALM) for multi-constraint calculations, (iii) the linear constraint method based on the approximation of the RPA matrix for multi-constraint calculations, (iv) an interface with the axial and parity-conserving Skyrme-HFB code HFBTHO, (v) the mixing of the HF or HFB matrix elements instead of the HF fields. Special care has been paid to using the code on massively parallel leadership class computers. For this purpose, the following features are now available with this version: (i) the Message Passing Interface (MPI) framework, (ii) scalable input data routines, (iii) multi-threading via OpenMP pragmas, (iv) parallel diagonalization of the HFB matrix in the simplex breaking case using the ScaLAPACK library. Finally, several little significant errors of the previous published version were corrected.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

WE-H-207A-02: Attenuation Correction in 4D-PET Using a Single-Phase Attenuation Map

Purpose: 4D-PET imaging has been proposed as a potential solution to the respiratory motion effect in thoracic region. CT-based attenuation correction (AC) is an essential step toward quantitative imaging for PET. However, due to the temporal difference of 4D-PET and a single breath-hold CT, motion artifacts are observed in the attenuation-corrected PET images that can lead to error in tumor shape and uptake. We introduce a practical method for aligning single-phase CT to all other 4D-PET phases using a penalized non-rigid demons registration. Methods: Individual 4D-PET frames were reconstructed without AC. Non-rigid Demons registration was used to derive deformation vector fields (DVFs) between the PET matched with CT phase and other 4D-PET images. While attenuated PET images provide enough useful data for organ borders such as lung and liver, tumors are not distinguishable from background due to loss of contrast. To preserve tumor shape in different phases, from CT image an ROI covering tumor was excluded from non-rigid transformation. Mean DVF of the central region of the tumor was assigned to all voxels in the ROI. This process mimics a rigid transformation of tumor along with a non-rigid transformation of other organs. 4D XCAT phantom with spherical tumors in lung with diameters ranging from 10 to 40 mm was used to evaluate the algorithm. Results: Motion related induced artifacts in attenuation-corrected 4D-PET images were significantly reduced. For tumors smaller than 20 mm, non-rigid transformation was capable to provide quantitative results. However, for larger tumors, where tumor self-attenuation is considerable, our combined method yields superior results. Conclusion: We introduced a practical method for deforming a single CT to match all 4D-PET images for accurate AC. Although 4D-PET data include insignificant anatomical information, we showed that they are still useful to estimate DVFs for aligning attenuation map and accurate AC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Phase stability and interlayer interaction of blue phosphorene

In this work, we study the interlayer interactions between sheets of blue phosphorus with quantum Monte Carlo (QMC) methods. Here, we find that as previously observed in black phosphorus, interlayer binding of blue phosphorus cannot be described by van der Waals (vdW) interactions alone within the density functional theory framework. Specifically, while some vdW density functionals produced reasonable binding curves, none of them could provide a correct, even qualitatively, description of charge redistribution due to interlayer binding. We also show that small systematic errors in common practice QMC calculations, such as the choice of optimized geometry and finite-size corrections, are non-negligible given the energy and length scales of this problem. We mitigate some of the major sources of error and report QMC-optimized lattice constant, stacking, and interlayer binding energy for blue phosphorus. Finally, it is strongly suggested that these considerations are important and quite general in the modeling of two-dimensional phosphorus allotropes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Approximating Quasiparticle and Excitation Energies from Ground State Generalized Kohn–Sham Calculations

Quasiparticle energies and fundamental band gaps specifically are critical properties of molecules and materials. It was rigorously established that the generalized Kohn–Sham HOMO and LUMO orbital energies are the chemical potentials of electron removal and addition and thus good approximations to band edges and fundamental gaps from a density functional approximation (DFA) with minimal delocalization error. For other quasiparticle energies, their connection to the generalized Kohn–Sham orbital energies has not been established but remains highly interesting. We provide the comparison of experimental quasiparticle energies for many finite systems with calculations from the GW Green function and localized orbitals scaling correction (LOSC), a recently developed correction to semilocal DFAs, which has minimal delocalization error. Extensive results with over 40 systems clearly show that LOSC orbital energies achieve slightly better accuracy than the GW calculations with little dependence on the semilocal DFA, supporting the use of LOSC DFA orbital energies to predict quasiparticle energies. This also leads to the calculations of excitation energies of the N-electron systems from the ground state DFA calculations of the (N – 1)-electron systems. Findings show good performance with accuracy similar to TDDFT and the delta SCF approach for valence excitations with commonly used DFAs with or without LOSC. For Rydberg states, good accuracy was obtained only with the use of LOSC DFA. Our report highlights the pathway to quasiparticle and excitation energies from ground density functional calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Solar Contamination in Extreme-precision Radial-velocity Measurements: Deleterious Effects and Prospects for Mitigation

Solar contamination, due to moonlight and atmospheric scattering of sunlight, can cause systematic errors in stellar radial velocity (RV) measurements that significantly detract from the ∼10 cm s{sup −1} sensitivity required for the detection and characterization of terrestrial exoplanets in or near habitable zones of Sun-like stars. The addition of low-level spectral contamination at variable effective velocity offsets introduces systematic noise when measuring velocities using classical mask-based or template-based cross-correlation techniques. Here we present simulations estimating the range of RV measurement error induced by uncorrected scattered sunlight contamination. We explore potential correction techniques, using both simultaneous spectrometer sky fibers and broadband imaging via coherent fiber imaging bundles, that could reliably reduce this source of error to below the photon-noise limit of typical stellar observations. We discuss the limitations of these simulations, the underlying assumptions, and mitigation mechanisms. We also present and discuss the components designed and built into the NEID (NN-EXPLORE Exoplanet Investigations with Doppler spectroscopy) precision RV instrument for the WIYN 3.5 m telescope, to serve as an ongoing resource for the community to explore and evaluate correction techniques. We emphasize that while “bright time” has been traditionally adequate for RV science, the goal of 10 cm s{sup −1} precision on the most interesting exoplanetary systems may necessitate access to darker skies for these next-generation instruments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

NOVA AQUILAE 1918 (V603 Aql) FADED BY 0.44 MAG PER CENTURY FROM 1938 TO 2013

We present the light curve of the old nova V603 Aql (Nova Aql 1918) from 1898-1918 and 1934-2013 using 22,721 archival magnitudes. All of our magnitudes are either in, or accurately transformed into, the Johnson B and V magnitude systems. This is vital because offsets in old sequences and the visual-to-V transformation can cause errors of 0.1-1.0 mag if not corrected. Our V603 Aql light curve is the first time that this has been done for any nova. Our goal was to see the evolution of the mass accretion rate on a century timescale, and to test the long-standing prediction of the Hibernation model that old novae should be fading significantly in the century after their eruption is over. The 1918 nova eruption was completely finished by 1938 when the nova decline stopped, and when the star had faded to fainter than its pre-nova brightness of B = 11.43 ± 0.03 mag. We find that the nova light from 1938 to 2013 was significantly fading, with this being seen consistently in three independent data sets (the Sonneberg plates in B, the American Association of Variable Star Observers (AAVSO) V light curve, and the non-AAVSO V light curve). We find that V603 Aql has been declining in brightness at an average rate of 0.44 ± 0.04 mag per century since 1938. This work provides remarkable confirmation of an important prediction of the Hibernation model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Features of the application of the Monte Carlo method to calculations for large RBMK reactors and to model correction on the basis of data from in-core detectors

Statistical errors in sampling neutron fields in physically large systems like an RBMK are analyzed both qualitatively and quantitatively. Recommendations concerning the choice of parameters for calculations are given. A new procedure for Monte Carlo RBMK calculations with model corrections on the basis of data from in-core detectors is proposed. Dedicated software based on the CUDA software and hardware platform is developed for computational research. Results of testing the procedure and software in question via calculations for real RBMK reactors are discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

SU-E-J-258: Inter- and Intra-Fraction Setup Stability and Couch Change Tolerance for Image Guided Radiation Therapy

Purpose: Immobilization devices combine rigid patient fixation as well as comfort and play a key role providing the stability required for accurate radiation delivery. In the setup step, couch re-positioning needed to align the patient is derived via registration of acquired versus reference image. For subsequent fractions, replicating the initial setup should yield identical alignment errors when compared to the reference. This is not always the case and further couch re-positioning can be needed. An important quality assurance measure is to set couch tolerances beyond which additional investigations are needed. The purpose of this work was to study the inter-fraction couch changes needed to re-align the patient and the intra-fraction stability of the alignment as a guide to establish the couch tolerances. Methods: Data from twelve patients treated on the Accuray CyberKnife (CK) system for fractionated intracranial radiotherapy and immobilized with Aquaplast RT, U-frame, F-Head-Support (Qfix, PA, USA) was used. Each fraction involved image acquisitions and registration with the reference to re-align the patient. The absolute couch position corresponding to the approved setup alignment was recorded per fraction. Intra-fraction set-up corrections were recorded throughout the treatment. Results: The average approved setup alignment was 0.03±0.28mm, 0.15±0.22mm, 0.06±0.31mm in the L/R, A/P, S/I directions respectively and 0.00±0.35degrees, 0.03±0.32degrees, 0.08±0.45degrees for roll, pitch and yaw respectively. The inter-fraction reproducibility of the couch position was 6.65mm, 10.55mm, and 4.77mm in the L/R, A/P and S/I directions respectively and 0.82degrees, 0.71degrees for roll and pitch respectively. Intra-fraction monitoring showed small average errors of 0.21±0.21mm, 0.00±0.08mm, 0.23±0.22mm in the L/R, A/P, S/I directions respectively and 0.03±0.12degrees, 0.04±0.25degrees, and 0.13±0.15degrees in the roll, pitch and yaw respectively. Conclusion: The inter-fraction reproducibility should serve as a guide to couch tolerances, specific to a site and immobilization. More patients need to be included to make general conclusions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Couch height–based patient setup for abdominal radiation therapy

There are 2 methods commonly used for patient positioning in the anterior-posterior (A-P) direction: one is the skin mark patient setup method (SMPS) and the other is the couch height–based patient setup method (CHPS). This study compared the setup accuracy of these 2 methods for abdominal radiation therapy. The enrollment for this study comprised 23 patients with pancreatic cancer. For treatments (539 sessions), patients were set up by using isocenter skin marks and thereafter treatment couch was shifted so that the distance between the isocenter and the upper side of the treatment couch was equal to that indicated on the computed tomographic (CT) image. Setup deviation in the A-P direction for CHPS was measured by matching the spine of the digitally reconstructed radiograph (DRR) of a lateral beam at simulation with that of the corresponding time-integrated electronic portal image. For SMPS with no correction (SMPS/NC), setup deviation was calculated based on the couch-level difference between SMPS and CHPS. SMPS/NC was corrected using 2 off-line correction protocols: no action level (SMPS/NAL) and extended NAL (SMPS/eNAL) protocols. Margins to compensate for deviations were calculated using the Stroom formula. A-P deviation > 5 mm was observed in 17% of SMPS/NC, 4% of SMPS/NAL, and 4% of SMPS/eNAL sessions but only in one CHPS session. For SMPS/NC, 7 patients (30%) showed deviations at an increasing rate of > 0.1 mm/fraction, but for CHPS, no such trend was observed. The standard deviations (SDs) of systematic error (Σ) were 2.6, 1.4, 0.6, and 0.8 mm and the root mean squares of random error (σ) were 2.1, 2.6, 2.7, and 0.9 mm for SMPS/NC, SMPS/NAL, SMPS/eNAL, and CHPS, respectively. Margins to compensate for the deviations were wide for SMPS/NC (6.7 mm), smaller for SMPS/NAL (4.6 mm) and SMPS/eNAL (3.1 mm), and smallest for CHPS (2.2 mm). Achieving better setup with smaller margins, CHPS appears to be a reproducible method for abdominal patient setup.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2012

THE NINTH DATA RELEASE OF THE SLOAN DIGITAL SKY SURVEY: FIRST SPECTROSCOPIC DATA FROM THE SDSS-III BARYON OSCILLATION SPECTROSCOPIC SURVEY

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z {approx} 0.52), 102,100 new quasar spectra (median z {approx} 2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T{sub eff} < 5000 K and in metallicity estimates for stars with [Fe/H] > -0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SEGUE-2. The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the APOGEE along with another year of data from BOSS, followed by the final SDSS-III data release in 2014 December.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

SAD phasing of XFEL data depends critically on the error model

A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Performance Exploration Through Optimistic Static Program Annotations

Compilers are limited by the static information directly or indirectly encoded in the program. Low-level languages, such as C/C++, are considered problematic as their weak type system and relaxed memory semantic allows for various, sometimes non-obvious, behaviors. Since compilers have to preserve the program semantics for all program executions, the existence of exceptional behavior can prevent optimizations that the developer would consider valid and might expect. Analyses to guarantee the absence of disruptive and unlikely situations are consequently an indispensable part of an optimizing compiler. However, such analyses have to be approximative and limited in scope as global and exact solutions are infeasible for any non-trivial program. In this paper, we present an automated tool to measure the effectmissing static information has on the optimizations applied to a given program. The approach generates an optimistically optimized program version which, compared to the original, defines a performance gap that can be closed by better compiler analyses and selective static program annotations. Our evaluation on six already tuned proxy applications for high-performance codes shows speedups of up to 20.6%. This clearly indicates that static uncertainty limits performance. At the same time, we observed that compilers are often unable to utilize additional static information. Thus, manual annotation of all correct static information is therefore not only error prone but also mostly redundant.

Auto Tuning↗
DOE OSTI2024

Path-Integrated X-Ray Digital Image Correlation using Synthetic Reference Images

X-rays can provide images when an object is visibly obstructed, allowing for motion measurements via x-ray digital image correlation (DIC). However, x-ray images are path-integrated and contain data for all objects between the source and detector. If multiple objects are present in the x-ray path, conventional DIC algorithms may fail to correlate the x-ray images. A new DIC algorithm called path-integrated (PI)-DIC addresses this issue by reformulating the matching criterion for DIC to account for multiple, independently-moving objects. PI-DIC requires a set of reference x-ray images of each independent object. However, due to experimental constraints, such reference images might not be obtainable from the experiment. Here, this work focuses on the reliability of synthetically-generated reference images, in such cases. A simplified exemplar is used for demonstration purposes, consisting of two aluminum plates with tantalum x-ray DIC patterns undergoing independent rigid translations. Synthetic reference images based on the “as-designed” DIC patterns were generated. However, PI-DIC with the synthetic images suffered some biases due to manufacturing defects of the patterns. A systematic study of seven identified defect types found that an incorrect feature diameter was the most influential defect. Synthetic images were re-generated with the corrected feature diameter, and PI-DIC errors were improved by a factor of 3-4. Final biases ranged from 0.00-0.04 px, and standard uncertainties ranged from 0.06-0.11 px. In conclusion, PI-DIC accurately measured the independent displacement of two plates from a single series of path-integrated x-ray images using synthetically-generated reference images, and the methods and conclusions derived here can be extended to more generalized cases involving stereo PI-DIC for arbitrary specimen geometry and motion. This work thus extends the application space of x-ray imaging for full-field DIC measurements of multiple surfaces or objects in extreme environments where optical DIC is not possible.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Silver clusters tune up electronic properties of graphene nanoflakes: A comprehensive theoretical study

Graphene-silver composites reflect a synergic effect of both components with enhanced electronic, adsorption and catalytic properties. We introduce here the detailed theoretical study on geometric, thermodynamic and electronic properties of silver clusters Ag n (n=2–10) adsorbed on graphene nanoflakes as a model for silver-graphene composites. First, a benchmark study is performed on Ag n …coronene complexes (n=2, 4) by evaluating various functional against reported high level ab-initio method for the selection of best functional for further calculations. Then, density functional theory study at the best chosen level is performed to inquire how clustering of adsorbate attached with carbon surface can impact geometric, electronic and thermodynamic properties of silver-graphene composites. Furthermore, the interaction energies are corrected for dispersion and basis set superposition error in order to get more realistic estimate of interaction energies. In progression, we investigated the dependence of interaction energy upon cluster size and dimensionality. For Ag n …coronene, the binding energies increase monotonically as the number of atoms in the cluster increases. However, for Ag n …dodecabenzocoronene, the interaction energies show a sudden drop at Ag 7 …dodecabenzocoronene. The difference in behavior between Ag n …dodecabenzocoronene and Ag n …coronene for interaction energy is attributed to edge effect present in coronene. Furthermore, coplanar orientations of the silver clusters on polyaromatic hydrocarbons have higher interaction energies. The 2D-3D transition of the silver cluster is observed for Ag 7 …coronene. CDA analysis reveals that backdonation from dodecabenzocoronene to silver clusters is more dominant in Ag 4 –Ag 7 whereas other clusters have dominant charge transfer to dodecabenzocoronene. Charge transfer analysis via constrained density functional theory (CDFT) reveals significant energy lowering from charge donor-acceptor interactions. Further energy decomposition analysis (EDA) using absolutely-localized molecular orbitals (ALMO) suggests that, while charge-transfer is important in these systems, the sum of electrostatics, Pauli repulsion, and London dispersion are far more significant as silver cluster size increases. NCI results also support the presence of van der Waals and electrostatic interactions. The hollow top is most favorite interaction sites compared to bridge top and head top binding sites over coronene lattice. The ionization potential, electron affinity, frontier molecular orbital analysis, chemical hardness, softness, chemical potential, and Fermi levels are deliberated to verify the stability and reactivity of most stable silver-graphene composites. The remarkable outcome of the current findings makes our silver-graphene composite as a potential applicant for high performance electronic and catalytic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Energy-Screened Many-Body Expansion for Protein–Ligand Interactions: Examining Convergence for Metalloenzymes Through Seven–Body Interactions

Fragment-based quantum chemistry is a powerful strategy for calculating protein−ligand interaction energies using quantum chemistry methods. Rigorous convergence often requires hundreds of atoms in the protein binding-site model, especially if that model is constructed using distance-based criteria to select amino acid residues, while three- and four-body calculations exhibit instability related to combinatorial proliferation in the number of subsystem calculations. Here, we report an energy-based screening protocol for the many-body expansion applied to protein−ligand interactions, implemented in the open-source FRAGME∩T code. Using a combination of aggressive screening based on semiempirical quantum chemistry, with an improved graph-theoretical algorithm to eliminate unimportant subsystems, we are able to perform n-body calculations up to n = 7 using density functional theory in triple-ζ basis sets. Distance cutoffs further reduce the cost without compromising accuracy. Rapid and stable convergence of the many-body expansion is obtained by n = 4, for a pair of metalloenzymes in which a divalent ion coordinates directly to the ligand. As compared to previous results that relied solely on distance cutoffs, oscillations in the n-body corrections are reduced or eliminated, although residual errors remain in one case. This work demonstrates that benchmark-quality protein−ligand interaction energies can be systematically converged using a method with excellent parallel efficiency and scalability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗