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Investigation of Near Shannon Limit Coding Schemes

Turbo codes can deliver performance that is very close to the Shannon limit. This report investigates algorithms for convolutional turbo codes and block turbo codes. Both coding schemes can achieve performance near Shannon limit. The performance of the schemes is obtained using computer simulations. There are three sections in this report. First section is the introduction. The fundamental knowledge about coding, block coding and convolutional coding is discussed. In the second section, the basic concepts of convolutional turbo codes are introduced and the performance of turbo codes, especially high rate turbo codes, is provided from the simulation results. After introducing all the parameters that help turbo codes achieve such a good performance, it is concluded that output weight distribution should be the main consideration in designing turbo codes. Based on the output weight distribution, the performance bounds for turbo codes are given. Then, the relationships between the output weight distribution and the factors like generator polynomial, interleaver and puncturing pattern are examined. The criterion for the best selection of system components is provided. The puncturing pattern algorithm is discussed in detail. Different puncturing patterns are compared for each high rate. For most of the high rate codes, the puncturing pattern does not show any significant effect on the code performance if pseudo - random interleaver is used in the system. For some special rate codes with poor performance, an alternative puncturing algorithm is designed which restores their performance close to the Shannon limit. Finally, in section three, for iterative decoding of block codes, the method of building trellis for block codes, the structure of the iterative decoding system and the calculation of extrinsic values are discussed.

Kwatra, S. C.↗

Investigation of spectral analysis techniques for randomly sampled velocimetry data

It is well known that velocimetry (LV) generates individual realization velocity data that are randomly or unevenly sampled in time. Spectral analysis of such data to obtain the turbulence spectra, and hence turbulence scales information, requires special techniques. The 'slotting' technique of Mayo et al, also described by Roberts and Ajmani, and the 'Direct Transform' method of Gaster and Roberts are well known in the LV community. The slotting technique is faster than the direct transform method in computation. There are practical limitations, however, as to how a high frequency and accurate estimate can be made for a given mean sampling rate. These high frequency estimates are important in obtaining the microscale information of turbulence structure. It was found from previous studies that reliable spectral estimates can be made up to about the mean sampling frequency (mean data rate) or less. If the data were evenly samples, the frequency range would be half the sampling frequency (i.e. up to Nyquist frequency); otherwise, aliasing problem would occur. The mean data rate and the sample size (total number of points) basically limit the frequency range. Also, there are large variabilities or errors associated with the high frequency estimates from randomly sampled signals. Roberts and Ajmani proposed certain pre-filtering techniques to reduce these variabilities, but at the cost of low frequency estimates. The prefiltering acts as a high-pass filter. Further, Shapiro and Silverman showed theoretically that, for Poisson sampled signals, it is possible to obtain alias-free spectral estimates far beyond the mean sampling frequency. But the question is, how far? During his tenure under 1993 NASA-ASEE Summer Faculty Fellowship Program, the author investigated from his studies on the spectral analysis techniques for randomly sampled signals that the spectral estimates can be enhanced or improved up to about 4-5 times the mean sampling frequency by using a suitable prefiltering technique. But, this increased bandwidth comes at the cost of the lower frequency estimates. The studies further showed that large data sets of the order of 100,000 points, or more, high data rates, and Poisson sampling are very crucial for obtaining reliable spectral estimates from randomly sampled data, such as LV data. Some of the results of the current study are presented.

Sree, Dave↗

GLAD-M35: a joint P and S global tomographic model with uncertainty quantification

We present our third and final generation joint P and S global adjoint tomography (GLAD) model, GLAD-M35, and quantify its uncertainty based on a low-rank approximation of the inverse Hessian. Starting from our second-generation model, GLAD-M25, we added 680 new earthquakes to the database for a total of 2160 events. New P-wave categories are included to compensate for the imbalance between P- and S-wave measurements, and we enhanced the window selection algorithm to include more major-arc phases, providing better constraints on the structure of the deep mantle and more than doubling the number of measurement windows to 40 million. Two stages of a Broyden–Fletcher–Goldfarb–Shanno (BFGS) quasi-Newton inversion were performed, each comprising five iterations. With this BFGS update history, we determine the model’s standard deviation and resolution length through randomized singular value decomposition.

58 GEOSCIENCES↗

How thick are lunar mare basalts

It is argued that De Hon's estimates of the thickness of lunar mare basalts, made by analyzing 'ghost' craters on mare surfaces, were inflated as the result of the crater morphometric data of Pike (1977) to reconstruct rim heights of degraded craters. Crater rim heights of 82 randomly selected highland craters of various states of degradation were determined, and median rim height was compared to that of corresponding fresh impact structures. Results indicate that the thickness estimates of De Hon may be reduced by a factor of 2, and that the total volume of mare basalt produced throughout lunar history could be as little as 1-2 million cubic kilometers. A survey of geochemical and petrographic evidence indicates that lateral transport of regolith components over distances of much greater than 10 km is relatively inefficient; it is suggested that vertical mixing of a highland substrate underlying the basaltic fill may have had a primordial role in generating the observed mare width distributions and high concentrations of exotic components in intrabasin regoliths.

Hoerz, F.↗

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Networks (DGAPNs), a curiosity-driven reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. Here, the framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention Network (sGAT) that leverages self-attention over both node and edge attributes as well as encoding spatial structure -- this capability is of considerable interest in areas such as molecular and synthetic biology and drug discovery. An attentional policy network is then introduced to learn decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with enhanced stability. Exploration is efficiently encouraged by incorporating innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while increasing the diversity of proposed molecules and reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Networks (DGAPNs), a curiosity-driven reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention Network (sGAT) that leverages self-attention over both node and edge attributes as well as encoding spatial structure -- this capability is of considerable interest in areas such as molecular and synthetic biology and drug discovery. An attentional policy network is then introduced to learn decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with enhanced stability. Exploration is efficiently encouraged by incorporating innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while increasing the diversity of proposed molecules and reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗

Microscopic and Metallurgical Aspects of the Space Shuttle Columbia Accident Investigation and Reconstruction

The Space Shuttle Columbia was descending for a landing at the Kennedy Space Center (KSC) on February 1, 2003. Approximately 20 minutes prior to touchdown, the Columbia began disintegrating over the western United States; the majority of debris eventually impacted in eastern Texas and western Louisiana. A monumental effort eventually recovered approximately 84,000 pieces of debris, approximately 38% of the Orbiter's original dry weight. The debris was transported to KSC, where the items were catalogued and evaluated. Critical areas of interest, such as the left and right leading edge surfaces and the underside of the ship, were placed upon a grid to aid in the reconstruction. Items of interest included metallic structures, reinforced carbon-carbon composites, and ceramic heat insulation tiles. Many of the leading edge elements had re-solidified metallic deposits spattered on them. These deposits became known as slag and were one of the main focuses of the investigation. In order to help determine the sequence of events inside the left wing during the accident, the slag's composition, layering order, and directionality of deposition were studied. A myriad of analytical tests were performed in an attempt to ascertain the compositional and depositional characteristics of selected slag deposits, including the ordering of deposited layers within each individual slag deposit harvested. Initially, Scanning Electron Microscopy and Energy Dispersive X-Ray Spectroscopy (SEM/EDX) were performed to quickly characterize the overall composition of individual slag deposits: SEM utilizes a narrowlyfocused high-energy electron beam impinging upon a specimen. The incident beam excites and liberates lower energy secondary electrons, which are detected and analyzed, providing a visual representation of the sample's surface topography. EDX also relies on an incident electron beam, except an EDX unit measures X-ray energies generated by the impinging beam. Each element generates a unique X-ray signature; the EDX detector measures these discreet energies. EDX actually penetrates approximately 2 microns into the bulk of the sample. However, random examination of various portions of slag, coupled with the semiquantitative nature of the SEM/EDX analysis, did not yield convincingly pertinent data. Therefore, X-ray dot mapping was conducted, which provided more understandable data, both in terms of slag layering and composition. An X-ray dot map is generated by performing numerous EDX scans for individual elements, then compiling the scans in a visual representation. Eventually, specimens consisting of not only the slag, but of the adjacent RCC substrate as well were cross-sectioned. X-Ray dot mapping of the materialographicallymounted and -polished cross- sections provided a visual representation of both the layering sequence and compositional characteristics of the slag. Contemporaneously, Electron Spectroscopy for Chemical Analysis/X-Ray Photoelectron Spectroscopy (ESCA/XPS) and powdered X-Ray Diffraction (XRD) were performed to further characterize the deposits and to attempt to identify what, if any, compounds were present. The ESCA/XPS analysis allowed the analyst to "sputter" into the sample with an electron gun, aiding in the identification of the layering sequence. XPS uses photons, rather than electrons, which impinge upon the surface of the sample. XPS measures the electrons emitted from within the first 5 nm of the sample's surface. The XRD measures the scatter angles of incident X-rays; the angle and intensity of scatter depend upon the crystalline structure of the pulverized sample. XRD is considered a qualitative rather than quantitative technique. ESCA/XPS revealed that the final layer to deposit was predominantly carbonaceous. XRD was successful in identifying specific compounds, such as Al 2O3, Al and/or Al3 21SiO47, mullite (3(Al2)O3 -SiO2), and nickel-aluminides. Eventually, Electron MicroProbe Analysis (EMPA) was conducted on the marialographically-prepared cross- sections of selected slag deposits. Microprobe combines SEM and Wavelength Dispersive X-Ray Spectroscopy (WDS), and, like EDX, uses a narrowly-focused high-energy electron beam impinging upon a specimen to elicit, in the case of EPMA, characteristic X-rays with specific wavelengths. This quantitative, analytical tool proved the most useful in determining depositional layering and composition of the slag deposits. This information was utilized in verifying the location of the breach in the left leading edge of the wing of the Columbia.

McDaniels, Steven J.↗

Numerical Modeling of Turbulent Combustion

The work in numerical modeling is focused on the use of the random vortex method to treat turbulent flow fields associated with combustion while flame fronts are considered as interfaces between reactants and products, propagating with the flow and at the same time advancing in the direction normal to themselves at a prescribed burning speed. The latter is associated with the generation of specific volume (the flame front acting, in effect, as the locus of volumetric sources) to account for the expansion of the flow field due to the exothermicity of the combustion process. The model was applied to the flow in a channel equipped with a rearward facing step. The results obtained revealed the mechanism of the formation of large scale turbulent structure in the wake of the step, while it showed the flame to stabilize on the outer edges of these eddies.

Ghoneim, A. F.↗

Allowing for Horizontally Heterogeneous Clouds and Generalized Overlap in an Atmospheric GCM

While fully accounting for 3D effects in Global Climate Models (GCMs) appears not realistic at the present time for a variety of reasons such as computational cost and unavailability of 3D cloud structure in the models, incorporation in radiation schemes of subgrid cloud variability described by one-point statistics is now considered feasible and is being actively pursued. This development has gained momentum once it was demonstrated that CPU-intensive spectrally explicit Independent Column Approximation (lCA) can be substituted by stochastic Monte Carlo ICA (McICA) calculations where spectral integration is accomplished in a manner that produces relatively benign random noise. The McICA approach has been implemented in Goddard's GEOS-5 atmospheric GCM as part of the implementation of the RRTMG radiation package. GEOS-5 with McICA and RRTMG can handle horizontally variable clouds which can be set via a cloud generator to arbitrarily overlap within the full spectrum of maximum and random both in terms of cloud fraction and layer condensate distributions. In our presentation we will show radiative and other impacts of the combined horizontal and vertical cloud variability on multi-year simulations of an otherwise untuned GEOS-5 with fixed SSTs. Introducing cloud horizontal heterogeneity without changing the mean amounts of condensate reduces reflected solar and increases thermal radiation to space, but disproportionate changes may increase the radiative imbalance at TOA. The net radiation at TOA can be modulated by allowing the parameters of the generalized overlap and heterogeneity scheme to vary, a dependence whose behavior we will discuss. The sensitivity of the cloud radiative forcing to the parameters of cloud horizontal heterogeneity and comparisons of CERES-derived forcing will be shown.

Lee, D.↗

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure --- this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗

SPATIAL GRAPH ATTENTION AND CURIOSITY-DRIVEN POLICY FOR ANTIVIRAL DRUG DISCOVERY

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure - this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Y↗

NbTa_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys niobium-tantalum (Nb-Ta). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach \cite{PAW}. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements Nb. For Ta, p semi-core states as valence were chosen. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions. The calculations have been collected on NERSC-Perlmutter using the VASP 6.3.2. The VASP calculations for every atomic structure have been performed in 2 main steps: 1. Starting from an ideal body-centered-cubic (BCC) structure, geometry optimization with low precision has been executed to perform a preliminary optimization of the atomic structure. The output for this calculations is available in the files 0.CONTCAR, 0.OUTCAR, rlx1.out. 2. Using the atomic structure resulting from the preliminary geometry optimization, a second geometry optimization has been performed using normal precision. The output for this calculations is available in the files CONTCAR, OUTCAR, rlx2.out, vaspout.h5, and vasprun.xml. Cases 1-10 have been run without generating the file 'vaspout.h5'. Every chemical composition sampled across the composition range in the dataset has its own directory. The convention used to name the directories for ternary alloys is AXBYCZ, where A, B, and C refer to the constituents, and X, Y, and Z are positive integers that represent the number of atoms for each constituent and their values still sum up to 128. Each atomic structure associated with a specific chemical composition has its own sub-directory within the directory of the corresponding chemical composition. The sub-directories for each atomic structure for each chemical composition are named 'case-*', where * is a positive integer that spans all the values from 1 through 100, extremes included. The files contained in each sub-directory 'case-*' for each atomic structure are as follows: FILES contained in each subdirectory with name case-N where N ranges between 11 and 100, extremes included: 1. INCAR: input file that contains various parameters and settings for controlling the behavior of the electronic structure calculations 2. KPOINTS: input file that specifies the Bloch vectors (k points) used to sample the Brillouin zone 3. 0.POSCAR: input file that defines the atomic structure of a system 4. 0.CONTCAR: output file that provides the atomic positions and cell parameters after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 5. 0.OUTCAR: output file that contains detailed information about the progress of a calculation after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 6. rlx1.out: file with diagnostic information about the execution of the first geometry optimization with precision variable set to PREC=Low in the INCAR file 7. POSCAR: input file that defines the atomic structure of a system after the first geometry optimization has been run at low precision. This represents the input for the second geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 8. CONTCAR: output file that provides the atomic positions and cell parameters after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 9. OUTCAR: output file that contains detailed information about the progress of a calculation after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 10. rlx2.out: file with diagnostic information about the execution of the second geometry optimization with precision variable set to PREC=Normal in the INCAR file 11. vaspout.h5: hierarchical HDF5 file containing the inputs and outputs of a VASP calculation. To analyze the data in this file we recommend using py4vasp. This file is only produced if the VASP version used is compiled with HDF5 support 12. vasprun.xml: contains similar information to OUTCAR, but in an xml format. Subdirectories with name case-N, where N ranges between 1 and 10 (extremes included) contain all the files listed above except 'vaspout.h5'. Subdirectories with name case-N, where N ranges between 41 and 60 (extremes included), contain a duplicate copy of the files listed above except for KPOINTS. The names of the duplicate files end with -bis, and correspond to a second VASP calculation that has converged to a different optimized geometry. This research is sponsored by the Artificial Intelligence Initiative as part of the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725, under Directorate Discretionary awards MAT025 (Materials Science) and LRN026 (Machine Learning), and INCITE award MAT201. This work also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, under award ERCAP0025216. REFERENCES (1) Kresse, G. and Hafner, J. Ab initio molecular dynamics for liquid metals. Phys. review B 47, 558 (1993). (2) Kresse, G. and Hafner, J. Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium. Phys. Rev. B 49, 14251 (1994) (3) Kresse, G. and Furthmüller, J. Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Comput. materials science 6, 15-50 (1996) (4) Kresse, G. and Furthmüller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. review B 54, 11169 (1996) (5) Kresse, G. and Joubert, D. From ultrasoft pseudopotentials to the projector augmented-wave method. Phys. review b 59, 1758 (1999)

36 MATERIALS SCIENCE↗

Vibration Modal Characterization of a Stirling Convertor via Base-Shake Excitation

The U.S. Department of Energy (DOE), Lockheed Martin (LM), Stirling Technology Company (STC), and NASA John H. Glenn Research Center (GRC) are currently developing a high-efficiency Stirling convertor for use in a Stirling Radioisotope Generator (SRG). NASA and DOE have identified the SRG for potential use as an advanced power system for future NASA Space Science missions, providing spacecraft onboard electric power for deep space missions and power for unmanned Mars rovers. Low-level, baseshake sine vibration tests were conducted on the Stirling Technology Demonstration Convertor (TDC), at NASA GRC's Structural Dynamics Laboratory, in February 2001, as part of the development of this Stirling technology. The purpose of these tests was to provide a better understanding of the TDC's internal dynamic response to external vibratory base excitations. The knowledge obtained can therein be used to help explain the success that the TDC enjoyed in its previous random vibration qualification tests (December 1999). This explanation focuses on the TDC s internal dynamic characteristics in the 50 to 250 Hz frequency range, which corresponds to the maximum input levels of its qualification random vibration test specification. The internal dynamic structural characteristics of the TDC have now been measured in two separate tests under different motoring and dynamic loading conditions: (1) with the convertor being electrically motored, under a vibratory base-shake excitation load, and (2) with the convertor turned off, and its alternator internals undergoing dynamic excitation via hammer impact loading. This paper addresses the test setup, procedure and results of the base-shake vibration testing conducted on the motored TDC, and will compare these results with those results obtained from the dynamic impact tests (May 2001) on the nonmotored TDC.

Suarez, Vicente J.↗

Winners are not keepers: Characterizing household engagement, gains, and energy patterns in demand response using machine learning in the United States

Demand-response programs can help utilities manage rapidly evolving electric grids, but these programs are subject to the complexities of human behavior. This paper explores a novel method for uncovering heterogeneity in households. In this work, we use a machine-learning method known as a Conditional Inference Tree (c-tree) algorithm to categorize households based on their energy behavior characteristics collected via smart meters, and explore how this translates through into heterogeneity in their real-world response to a DR program. Using data from randomized controlled trial, we generate estimates of the changes in energy use caused by the program within each household group. Our results show that the c-tree approach differentiates households by their energy-use characteristics in a way that increases the spread in enrollment rates and critical peak reduction among household groups, compared with the spreads achieved via several conventional segmentation methods. Thus, the c-tree analysis enables the most tailored targeting of major potential energy savers and could provide the greatest increase in cost-effectiveness of household recruitment into DR programs. Our results also offer fresh insights into the relationships between household energy behavior characteristics – such as peak energy use and “structural winningness” (the ability to save money under a DR program without changing energy-use behaviors) – and household decisions about enrolling in DR programs and reducing energy use. Our research also demonstrates the potential of smart meter data, combined with machine learning and econometric methods, to provide significant value to utilities, program implementers, researchers, and other stakeholders.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

On the phase-locked polarization variations in Cygnus X-1

The paper presents data on the accumulated V-band orbital phase curves of polarization in Cygnus X-1 which disagree with the analysis of Simmons, Aspin, and Brown (1980). No curves which conform to the canonical model were observed, and a noncanonical structure is indicated by F tests on third, fourth, and fifth harmonics, which have a probability of 0.85 as a group. The fifth harmonic has a probability of 0.99; in contrast, the fundamental harmonic has a probability of only 0.6, which is below the detection threshold. Therefore, major conclusions of Simmons et al based on a nonsymmetrical canonical model assuming that fundamental harmonics are present, but harmonics with n greater than 2 are absent, are unacceptable. Analysis of the author's data by Simmons et al is criticized on the grounds that he did not take into account the cumulative aspects of the data and did not recognize the need to average out the random noise generated by Cygnus X-1 over many orbital cycles.

Kemp, J. C.↗

Turbulent Compressible Convection with Rotation: Mean Flows and Differential Rotation - 2

The effects of rotation on turbulent, compressible convection within stellar envelopes are studied through three-dimensional numerical simulations conducted within a local f-plane model. This work seeks to understand the types of differential rotation that can be established in convective envelopes of stars like the Sun, for which recent helioseismic observations suggest an angular velocity profile with depth and latitude at variance with many theoretical predictions. This paper analyzes the mechanisms that are responsible for the mean (horizontally averaged) zonal and meridional flows that are produced by convection influenced by Coriolis forces. The compressible convection is considered for a range of Rayleigh, Taylor, and Prandtl (and thus Rossby) numbers encompassing both laminar and turbulent flow conditions under weak and strong rotational constraints. When the nonlinearities are moderate, the effects of rotation on the resulting laminar cellular convection leads to distinctive tilts of the cell boundaries away from the vertical. These yield correlations between vertical and horizontal motions that generate Reynolds stresses that can drive mean flows, interpretable as differential rotation and meridional circulations. Under more vigorous forcing, the resulting turbulent convection involves complicated and contorted fluid particle trajectories, with few clear correlations between vertical and horizontal motions, punctuated by an evolving and intricate downflow network that can extend over much of the depth of the layer. Within such networks are some coherent structures of vortical downflow that tend to align with the rotation axis. These yield a novel turbulent alignment mechanism, distinct from the laminar tilting of cellular boundaries, that can provide the principal correlated motions and thus Reynolds stresses and subsequently mean flows. The emergence of such coherent structures that can persist amidst more random motions is a characteristic of turbulence with symmetries broken by rotation and stratification. Such structure is here found to play a crucial role in defining the mean zonal and meridional flows that coexist with the convection. Though they are subject to strong inertial oscillations, the strength and type of the mean flows are determined by a combination of the laminar tilting and the turbulent alignment mechanisms. Varying the parameters produces a wide range of mean motions. Among these, some turbulent solutions exhibit a mean zonal velocity profile that is nearly constant with depth, much as deduced by helioseismology at midlatitudes within the Sun. The solutions exhibit a definite handedness, with the direction of the persistent mean flows often prescribing a spiral with depth near the boundaries, also in accord with helioseismic deductions. The mean helicity has a profile that is positive in the upper portion of the domain and negative in the lower portion, a property bearing on magnetic dynamo processes that may be realized within such rotating layers of turbulent convection.

Brummell, Nicholas H.↗

TaV_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys tantalum-vanadium (Tanu-V). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the element V. For Ta, p semi-core states as valence were chosen. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions. The calculations have been collected on NERSC-Perlmutter and OLCF-Summit using the VASP 6.3.2. The VASP calculations for every atomic structure have been performed in 2 main steps: 1. Starting from an ideal body-centered-cubic (BCC) structure, geometry optimization with low precision has been executed to perform a preliminary optimization of the atomic structure. The output for this calculations is available in the files 0.CONTCAR, 0.OUTCAR, rlx1.out. 2. Using the atomic structure resulting from the preliminary geometry optimization, a second geometry optimization has been performed using normal precision. The output for this calculations is available in the files CONTCAR, OUTCAR, rlx2.out, vaspout.h5, and vasprun.xml. Cases 1-10 have been run without generating the file 'vaspout.h5'. Every chemical composition sampled across the composition range in the dataset has its own directory. The convention used to name the directories for binary alloys is AXBY, where A and B refer to the constituents, whereas X and Y are positive integers that represent the number of atoms for each constituent and their values still sum up to 128. Each atomic structure associated with a specific chemical composition has its own sub-directory within the directory of the corresponding chemical composition. The sub-directories for each atomic structure for each chemical composition are named 'case-*', where * is a positive integer that spans all the values from 1 through 100, extremes included. The files contained in each sub-directory 'case-*' for each atomic structure are as follows: FILES contained in each subdirectory with name case-N where N ranges between 11 and 100, extremes included: 1. INCAR: input file that contains various parameters and settings for controlling the behavior of the electronic structure calculations 2. KPOINTS: input file that specifies the Bloch vectors (k points) used to sample the Brillouin zone 3. 0.POSCAR: input file that defines the atomic structure of a system 4. 0.CONTCAR: output file that provides the atomic positions and cell parameters after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 5. 0.OUTCAR: output file that contains detailed information about the progress of a calculation after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 6. rlx1.out: file with diagnostic information about the execution of the first geometry optimization with precision variable set to PREC=Low in the INCAR file 7. POSCAR: input file that defines the atomic structure of a system after the first geometry optimization has been run at low precision. This represents the input for the second geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 8. CONTCAR: output file that provides the atomic positions and cell parameters after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 9. OUTCAR: output file that contains detailed information about the progress of a calculation after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 10. rlx2.out: file with diagnostic information about the execution of the second geometry optimization with precision variable set to PREC=Normal in the INCAR file 11. vaspout.h5: hierarchical HDF5 file containing the inputs and outputs of a VASP calculation. To analyze the data in this file we recommend using py4vasp. This file is only produced if the VASP version used is compiled with HDF5 support 12. vasprun.xml: contains similar information to OUTCAR, but in an xml format. Subdirectories with name case-N, where N ranges between 1 and 10 (extremes included) contain all the files listed above except 'vaspout.h5'. Subdirectories with name case-N, where N ranges between 41 and 60 (extremes included), contain a duplicate copy of the files listed above except for KPOINTS. The names of the duplicate files end with -bis, and correspond to a second VASP calculation that has converged to a different optimized geometry. This research is sponsored by the Artificial Intelligence Initiative as part of the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725, under Directorate Discretionary awards MAT025 (Materials Science) and LRN026 (Machine Learning), and INCITE award MAT201. This work also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, under award ERCAP0025216. REFERENCES (1) Kresse, G. and Hafner, J. Ab initio molecular dynamics for liquid metals. Phys. review B 47, 558 (1993). (2) Kresse, G. and Hafner, J. Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium. Phys. Rev. B 49, 14251 (1994) (3) Kresse, G. and Furthmuller, J. Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Comput. materials science 6, 15-50 (1996) (4) Kresse, G. and Furthmuller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. review B 54, 11169 (1996) (5) Kresse, G. and Joubert, D. From ultrasoft pseudopotentials to the projector augmented-wave method. Phys. review b 59, 1758 (1999)

36 MATERIALS SCIENCE↗

NbV_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys niobium-vanadium (Nb-V). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach \cite{PAW}. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements Nb and V. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions. The calculations have been collected on NERSC-Perlmutter and OLCF-Summit using the VASP 6.3.2. The VASP calculations for every atomic structure have been performed in 2 main steps: 1. Starting from an ideal body-centered-cubic (BCC) structure, geometry optimization with low precision has been executed to perform a preliminary optimization of the atomic structure. The output for this calculations is available in the files 0.CONTCAR, 0.OUTCAR, rlx1.out. 2. Using the atomic structure resulting from the preliminary geometry optimization, a second geometry optimization has been performed using normal precision. The output for this calculations is available in the files CONTCAR, OUTCAR, rlx2.out, vaspout.h5, and vasprun.xml. Cases 1-10 have been run without generating the file 'vaspout.h5'. Every chemical composition sampled across the composition range in the dataset has its own directory. The convention used to name the directories for binary alloys is AXBY, where A and B refer to the constituents, whereas X and Y are positive integers that represent the number of atoms for each constituent and their values still sum up to 128. Each atomic structure associated with a specific chemical composition has its own sub-directory within the directory of the corresponding chemical composition. The sub-directories for each atomic structure for each chemical composition are named 'case-*', where * is a positive integer that spans all the values from 1 through 100, extremes included. The files contained in each sub-directory 'case-*' for each atomic structure are as follows: FILES contained in each subdirectory with name case-N where N ranges between 11 and 100, extremes included: 1. INCAR: input file that contains various parameters and settings for controlling the behavior of the electronic structure calculations 2. KPOINTS: input file that specifies the Bloch vectors (k points) used to sample the Brillouin zone 3. 0.POSCAR: input file that defines the atomic structure of a system 4. 0.CONTCAR: output file that provides the atomic positions and cell parameters after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 5. 0.OUTCAR: output file that contains detailed information about the progress of a calculation after the first geometry optimization has been run with the precision variable set to PREC=Low in the INCAR file 6. rlx1.out: file with diagnostic information about the execution of the first geometry optimization with precision variable set to PREC=Low in the INCAR file 7. POSCAR: input file that defines the atomic structure of a system after the first geometry optimization has been run at low precision. This represents the input for the second geometry optimization run with the precision variable set to PREC=Normal in the INCAR file 8. CONTCAR: output file that provides the atomic positions and cell parameters after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 9. OUTCAR: output file that contains detailed information about the progress of a calculation after the second geometry optimization has been run with the precision variable set to PREC=Normal in the INCAR file 10. rlx2.out: file with diagnostic information about the execution of the second geometry optimization with precision variable set to PREC=Normal in the INCAR file 11. vaspout.h5: hierarchical HDF5 file containing the inputs and outputs of a VASP calculation. To analyze the data in this file we recommend using py4vasp. This file is only produced if the VASP version used is compiled with HDF5 support 12. vasprun.xml: contains similar information to OUTCAR, but in an xml format. Subdirectories with name case-N, where N ranges between 1 and 10 (extremes included) contain all the files listed above except 'vaspout.h5'. Subdirectories with name case-N, where N ranges between 41 and 60 (extremes included), contain a duplicate copy of the files listed above except for KPOINTS. The names of the duplicate files end with -bis, and correspond to a second VASP calculation that has converged to a different optimized geometry. This research is sponsored by the Artificial Intelligence Initiative as part of the Laboratory Directed Research and Development (LDRD) Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the US Department of Energy under contract DE-AC05-00OR22725. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725, under Directorate Discretionary awards MAT025 (Materials Science) and LRN026 (Machine Learning), and INCITE award MAT201. This work also used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, under award ERCAP0025216. REFERENCES (1) Kresse, G. and Hafner, J. Ab initio molecular dynamics for liquid metals. Phys. review B 47, 558 (1993). (2) Kresse, G. and Hafner, J. Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium. Phys. Rev. B 49, 14251 (1994) (3) Kresse, G. and Furthmüller, J. Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Comput. materials science 6, 15-50 (1996) (4) Kresse, G. and Furthmüller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. review B 54, 11169 (1996) (5) Kresse, G. and Joubert, D. From ultrasoft pseudopotentials to the projector augmented-wave method. Phys. review b 59, 1758 (1999)

36 MATERIALS SCIENCE↗