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At least 631 records · Page 35

TDEP: Temperature Dependent Effective Potentials

The Temperature Dependent Effective Potential (TDEP) method is a versatile and efficient approach to include temperature in ab initio materials simulations based on phonon theory. TDEP can be used to describe thermodynamic properties in classical and quantum ensembles, and several response properties ranging from thermal transport to Neutron and Raman spectroscopy. A stable and fast reference implementation is given in the software package of the same name described here. The underlying theoretical framework and foundation is briefly sketched with an emphasis on discerning the conceptual difference between bare and effective phonon theory, in both self-consistent and non-self-consistent formulations. References to numerous applications and more in-depth discussions of the theory are given.

36 MATERIALS SCIENCE↗

Image processing analysis of nuclear track parameters for CR-39 detector irradiated by thermal neutron

CR-39 detector which covered with boric acid (H{sub 3}Bo{sub 3}) pellet was irradiated by thermal neutrons from ({sup 241}Am - {sup 9}Be) source with activity 12Ci and neutron flux 10{sup 5} n. cm{sup −2}. s{sup −1}. The irradiation times -T{sub D} for detector were 4h, 8h, 16h and 24h. Chemical etching solution for detector was sodium hydroxide NaOH, 6.25N with 45 min etching time and 60 C° temperature. Images of CR-39 detector after chemical etching were taken from digital camera which connected from optical microscope. MATLAB software version 7.0 was used to image processing. The outputs of image processing of MATLAB software were analyzed and found the following relationships: (a) The irradiation time -T{sub D} has behavior linear relationships with following nuclear track parameters: i) total track number - N{sub T} ii) maximum track number - MRD (relative to track diameter - D{sub T}) at response region range 2.5 µm to 4 µm iii) maximum track number - M{sub D} (without depending on track diameter - D{sub T}). (b) The irradiation time -T{sub D} has behavior logarithmic relationship with maximum track number - M{sub A} (without depending on track area - A{sub T}). The image processing technique principally track diameter - D{sub T} can be take into account to classification of α-particle emitters, In addition to the contribution of these technique in preparation of nano- filters and nano-membrane in nanotechnology fields.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Algorithm and program for precise determination of unit-cell parameters of single crystal taking into account the sample eccentricity

A technique has been developed to refine the unit-cell parameters of single crystals with minimization of the influence of instrumental errors on the result. The corresponding computational procedure HuberUB is added to the software package of Huber-5042 diffractometer with a point detector and closedcycle helium cryostat Displex DE-202. The parameters of unit cell, its orientation, the goniometer zero angles, the sample eccentricity, the distances in the goniometer, and the radiation wavelength were refined by the nonlinear least-squares method, which allows imposition of constraints on the unit-cell parameters, depending on the crystal symmetry. The technique is approved on a LuB{sub 12} single crystal. The unit-cell parameters are determined in a temperature range of 20–295 K, with an absolute error not larger than 0.0004 Å (the relative error is of ~5 × 10{sup –5}). The estimates of the unit-cell parameters obtained by the proposed method are evidenced to be unbiased. Some specific features of the behavior of parameters in the ranges of 120–140 and 20–50 K are revealed, which correlate with the anomalies of the physical properties of the crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Viscoelastic Material Characterization and Modeling of Photovoltaic Module Packaging Materials for Direct Finite-Element Method Input

Numerical tools, such as the finite-element method, are increasingly used to design and evaluate the photovoltaic (PV) modules, providing for the reduction of development time and improved performance and reliability. However, high-fidelity material models are necessary to accurately model the complex structural behavior of the involved packaging materials. A common simplification used in recent years is to model the polymer materials (i.e., encapsulant and backsheet) as linear elastic, which will lead to inaccurate results. Therefore, in this work, we present a thorough characterization of the time- and temperature-dependent mechanical response of predominant PV module encapsulant and backsheet materials. Based on this material characterization, we developed and experimentally validated generalized Maxwell models to describe each material's viscoelastic response. In addition, we included measurements of the coefficient of thermal expansion and presented all material models in such a fashion for direct input into commercial finite-element method modeling software.

FEM↗

SU-F-I-14: 3D Breast Digital Phantom for XACT Imaging

Purpose: The X-ray induced acoustic computed tomography (XACT) is a new imaging modality which combines X-ray contrast and high ultrasonic resolution in a single modality. Using XACT in breast imaging, a 3D breast volume can be imaged by only one pulsed X-ray radiation, which could dramatically reduce the imaging dose for patients undergoing breast cancer screening and diagnosis. A 3D digital phantom that contains both X-ray properties and acoustic properties of different tissue types is indeed needed for developing and optimizing the XACT system. The purpose of this study is to offer a realistic breast digital phantom as a valuable tool for improving breast XACT imaging techniques and potentially leading to better diagnostic outcomes. Methods: A series of breast CT images along the coronal plane from a patient who has breast calcifications are used as the source images. A HU value based segmentation algorithm is employed to identify breast tissues in five categories, namely the skin tissue, fat tissue, glandular tissue, chest bone and calcifications. For each pixel, the dose related parameters, such as material components and density, and acoustic related parameters, such as frequency-dependent acoustic attenuation coefficient and bandwidth, are assigned based on tissue types. Meanwhile, other parameters which are used in sound propagation, including the sound speed, thermal expansion coefficient, and heat capacity are also assigned to each tissue. Results: A series of 2D tissue type image is acquired first and the 3D digital breast phantom is obtained by using commercial 3D reconstruction software. When giving specific settings including dose depositions and ultrasound center frequency, the X-ray induced initial pressure rise can be calculated accordingly. Conclusion: The proposed 3D breast digital phantom represents a realistic breast anatomic structure and provides a valuable tool for developing and evaluating the system performance for XACT.

60 APPLIED LIFE SCIENCES↗

Verification of statistical method CORN for modeling of microfuel in the case of high grain concentration

Two methods of modeling a double-heterogeneity fuel are studied: the deterministic positioning and the statistical method CORN of the MCU software package. The effect of distribution of microfuel in a pebble bed on the calculation results is studied. The results of verification of the statistical method CORN for the cases of the microfuel concentration up to 170 cm{sup –3} in a pebble bed are presented. The admissibility of homogenization of the microfuel coating with the graphite matrix is studied. The dependence of the reactivity on the relative location of fuel and graphite spheres in a pebble bed is found.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

flowVS: channel-specific variance stabilization in flow cytometry

Abstract Background Comparing phenotypes of heterogeneous cell populations from multiple biological conditions is at the heart of scientific discovery based on flow cytometry (FC). When the biological signal is measured by the average expression of a biomarker, standard statistical methods require that variance be approximately stabilized in populations to be compared. Since the mean and variance of a cell population are often correlated in fluorescence-based FC measurements, a preprocessing step is needed to stabilize the within-population variances. Results We present a variance-stabilization algorithm, called flowVS, that removes the mean-variance correlations from cell populations identified in each fluorescence channel. flowVS transforms each channel from all samples of a data set by the inverse hyperbolic sine (asinh) transformation. For each channel, the parameters of the transformation are optimally selected by Bartlett’s likelihood-ratio test so that the populations attain homogeneous variances. The optimum parameters are then used to transform the corresponding channels in every sample. flowVS is therefore an explicit variance-stabilization method that stabilizes within-population variances in each channel by evaluating the homoskedasticity of clusters with a likelihood-ratio test. With two publicly available datasets, we show that flowVS removes the mean-variance dependence from raw FC data and makes the within-population variance relatively homogeneous. We demonstrate that alternative transformation techniques such as flowTrans, flowScape, logicle, and FCSTrans might not stabilize variance. Besides flow cytometry, flowVS can also be applied to stabilize variance in microarray data. With a publicly available data set we demonstrate that flowVS performs as well as the VSN software, a state-of-the-art approach developed for microarrays. Conclusions The homogeneity of variance in cell populations across FC samples is desirable when extracting features uniformly and comparing cell populations with different levels of marker expressions. The newly developed flowVS algorithm solves the variance-stabilization problem in FC and microarrays by optimally transforming data with the help of Bartlett’s likelihood-ratio test. On two publicly available FC datasets, flowVS stabilizes within-population variances more evenly than the available transformation and normalization techniques. flowVS-based variance stabilization can help in performing comparison and alignment of phenotypically identical cell populations across different samples. flowVS and the datasets used in this paper are publicly available in Bioconductor.

60 APPLIED LIFE SCIENCES↗

Temperature Dependent Raman Spectroscopic Study of the Fe Doped La{sub 0.67}Sr{sub 0.33}MnO{sub 3} Prepared Using Ball Milling Method

Polycrystalline samples of La{sub 0.67}Sr{sub 0.33}Mn{sub 0.65}Fe{sub 0.35}O{sub 3} (LSMFO) were synthesized using the standard ball mill method with different calcination temperatures ranging from 800 to 1100°C for 7 h. The phase purity of these samples was confirmed using X-ray diffraction (XRD) patterns. All samples were found to have rhombohedral crystal structure with R 3-bar c space group. The lattice parameters, cell volume, bond angle and bond length have been obtained using the Rietveld refinement by FullProf software. The average crystallite size calculated using the Debye-Scherrer formula was found between 27 and 60 nm. Surface morphology of the prepared samples has been examined using a scanning electron microscope (SEM). SEM images show the formation of well-arranged grain sizes distributed from 240 to 400 nm, much larger than one estimated using the Scherrer formula. All tiny particles are highly agglomerated with the increasing temperature and porosity decreases with increasing temperature. An analysis of the frequency and peak broadening of Raman modes as a function of temperature clearly shows the significant temperature effect on the A{sub 1g} and E{sub g} modes of LSMFO. The shifts and broadening of the A{sub 1g} and E{sub g} modes are discussed in light of the oxygen sublattice distortion. Our study shows the reduction in distortion with increasing calcination temperature, which suggests a decrease in the JT effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Understanding I/O workload characteristics of a Peta-scale storage system

Understanding workload characteristics is critical for optimizing and improving the performance of current systems and software, and architecting new storage systems based on observed workload patterns. In this paper, we characterize the I/O workloads of scientific applications of one of the world's fastest high performance computing (HPC) storage cluster, Spider, at the Oak Ridge Leadership Computing Facility (OLCF). OLCF flagship petascale simulation platform, Titan, and other large HPC clusters, in total over 250 thousands compute cores, depend on Spider for their I/O needs. We characterize the system utilization, the demands of reads and writes, idle time, storage space utilization, and the distribution of read requests to write requests for the Peta-scale Storage Systems. From this study, we develop synthesized workloads, and we show that the read and write I/O bandwidth usage as well as the inter-arrival time of requests can be modeled as a Pareto distribution. We also study the I/O load imbalance problems using I/O performance data collected from the Spider storage system.

I/O↗

RAJA Performance Suite

The RAJA Performance Suite is designed to evaluate performance of the RAJA performance portability library on a wide variety of important high performance computing (HPC) algorithmic lulmels. These kernels assess compiler optimizations and various parallel programming model backends accessible through RAJA, such as OpenMP, CUDA, etc. The Initial version of the suite contains 25 computational kernels, each of which appears in 6 variants: Baseline SequcntiaJ, RAJA SequentiaJ, Baseline OpenMP, RAJA OpenMP, Baseline CUDA, RAJA CUDA. All variants of each kernel perform essentially the same mathematical operations and the loop body code for each kernel is identical across all variants. There are a few kernels, such as those that contain reduction operations, that require CUDA-specific coding for their CUDA variants. ActuaJ computer instructions executed and how they run in parallel differs depending on the parallel programming model backend used and which optimizations are perfonned by the compiler used to build the Perfonnance Suite executable. The Suite will be used primarily by RAJA developers to perform regular assessments of RAJA performance across a range of hardware platforms and compilers as RAJA features are being developed. It will also be used by LLNL hardware and software vendor panners for new defining requirements for future computing platform procurements and acceptance testing. In particular, the RAJA Performance Suite will be used for compiler acceptance testing of the upcoming CORAUSierra machine {initial LLNL delivery expected in late-2017/early 2018) and the CORAL-2 procurement. The Suite will aJso be used to generate concise source code reproducers of compiler and runtime issues we uncover so that we may provide them to relevant vendors to be fixed.

Hornung, RichardD.↗

Preparation, Applications, and Digital Simulation of Carbon Interdigitated Array Electrodes

Carbon interdigitated array (IDA) electrodes with features sizes down to 1.2 μm were fabricated by controlled pyrolysis of patterned photoresist. Cyclic voltam-metry of reversible redox species produced the expected steady-state currents. The collection efficiency depends on the IDA electrode spacing, which ranged from around 2.7 to 16.5 μm, with the smaller dimensions achieving higher collection efficiencies of up to 98%. The signal amplification because of redox cycling makes it possible to detect species at relatively low concentrations (10–5 molar) and the small spacing allows detection of transient electrogenerated species with much shorter lifetimes (submillisecond). Digital simulation software that accounts for both the width and height of electrode elements as well as the electrode spacing was developed to model the IDA electrode response. The simulations are in quantitative agreement with experimental data for both a simple fast one electron redox reaction and an electron transfer with a following chemical reaction at the IDAs with larger gaps whereas currents measured for the smallest IDA electrodes, that were larger than the simulated currents, are attributed to convection from induced charge electrokinetic flow. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the Department of Energy, Office of Science Office of Basic Energy Sciences.

Liu, Fei↗

IRIS-GNN: Leveraging Graph Neural Networks for Scheduling on Truly Heterogeneous Runtime Systems

The diversity of accelerators in computer systems poses significant challenges for software developers, such as managing vendor-specific compiler toolchains, code fragmentation requiring different kernel implementations, and performance portability issues. To address these, the Intelligent Runtime System (IRIS) was developed. IRIS works across various systems, from smartphones to supercomputers, enabling automatic performance scaling based on available accelerators. It introduces abstract tasks for seamless execution transitions between accelerators while ensuring memory consistency and task dependencies. Although IRIS simplifies system details, optimal dynamic scheduling still requires user input to understand workload structures. To address this, we introduce a new scheduling policy for IRIS, termed IRIS-GNN, which is the first IRIS hybrid policy that operates in conjunction with the dynamic policies. This policy employs a Graph-Neural Network (GNN) to conduct Graph Classification of any task graphs submitted to IRIS. This GNN analyzes the structure and attributes of the task graph, categorizing it as either locality, concurrency, or mixed. This classification subsequently guides the selection of the dynamic policy used by IRIS. We provide a comparison of the performance of IRIS-GNN against the complete spectrum of IRIS’s dynamic policies, assess the overhead introduced by the GNN within this scheduling framework, and ultimately explore its practical application in real-world scenarios.

Johnston, Beau↗

RAJA - LLNL HPC Architecture Portability Encapsulation Layer Version 1.0

RAJA is a collection of C++ software abstractions designed to make HPC applications portable across a range of hardware architectures and programming models. The main conceptual abstraction in FAJA is a loop. RAJA provides abstractions for types, loop execution and scheduling, and loop iteration space portioning and ordering cooperate to insulate algorithms in application code that domain experts write from implementations details of those algorithms that may need to depend on the underlying computer hardware for high performance.

ECP↗

Modeling and Simulation of Compression Molding Process for Sheet Molding Compound (SMC) of Chopped Carbon Fiber Composites

Compression molded SMC composed of chopped carbon fiber and resin polymer which balances the mechanical performance and manufacturing cost presents a promising solution for vehicle lightweight strategy. However, the performance of the SMC molded parts highly depends on the compression molding process and local microstructure, which greatly increases the cost for the part level performance testing and elongates the design cycle. ICME (Integrated Computational Material Engineering) approaches are thus necessary tools to reduce the number of experiments required during part design and speed up the deployment of the SMC materials. As the fundamental stage of the ICME workflow, commercial software packages for SMC compression molding exist yet remain not fully validated especially for chopped fiber systems. In this study, SMC plaques are prepared through compression molding process. The corresponding simulation models are built in Autodesk Moldflow with the same part geometry and processing conditions as in the molding tests. The output variables of the compression molding simulations, including press force history and fiber orientation of the part, are compared with experimental data. Influence of the processing conditions to the fiber orientation of the SMC plaque is also discussed. It is found that generally Autodesk Moldflow can achieve a good simulation of the compression molding process for chopped carbon fiber SMC, yet quantitative discrepancies still remain between predicted variables and experimental results.

36 MATERIALS SCIENCE↗

RAJA - LLNL HPC Architecture Portability Encapsulation Layer Version 1.0

RAJA is a collection of C++ software abstractions designed to make HPC applications portable across a range of hardware architectures and programming models. The main conceptual abstraction in FAJA is a loop. RAJA provides abstractions for types, loop execution and scheduling, and loop iteration space portioning and ordering cooperate to insulate algorithms in application code that domain experts write from implementations details of those algorithms that may need to depend on the underlying computer hardware for high performance.

Hornung, Richard↗

Transitioning NWChem to the Next Generation of Manycore Machines

The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM, AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.

Environmental Molecular Sciences Laboratory↗

The experiment filtering tool in the MACSENS workbench - 14341

The MACSENS (outils Moret d'Aide a la Caracterisation et aux etudes de SENSibilite) workbench is dedicated to the advanced validation work for criticality studies. The aim of this kind of tool is to determine the experiments from a validation database being the 'closest' to an application case and, from there, to evaluate a calculation bias with a related uncertainty. To achieve this goal, the MACSENS workbench relies on different kind of information stored in various databases depending on the origin of the data. Two main kinds of data can be identified. The first one concerns the data used to describe the experiments of the validation database (e.g. the inputs needed to perform a calculation). These values characterize the chemical and geometrical models. They can be considered as constant, as they do not vary once evaluated, and some of them can be from a non-numerical nature (reflector material for example...). The second kind of data gathers the results obtained with the use of a simulation code, such as reaction rates, fluxes and leakages, sensitivities, k{sub eff}, etc. These values depend on the version of the code and are purely numerical. In the early 2000's, regarding the increasing number of experiments evaluated in the ICSBEP handbook, the OECD/NEA (Organization for Economic Co-operation and Development/Nuclear Energy Agency), under the ICSBEP (International Criticality Safety Benchmark Evaluation Project) working group direction, decided to store such information in a database and to provide a software, called DICE (Database for the International Criticality safety benchmark Evaluation project), allowing users to search easily criticality experiments of interest. Up to now, more than 4400 critical or subcritical configurations have been compiled by ICSBEP, described and stored in the DICE database. Over time, a validation work has been done on the data, with the participation of IRSN, and a quality assurance policy has been defined. For these reasons, the DICE database is highly reliable. These features were fundamental for the MACSENS developers, who were looking for a database containing descriptive data of the experiments included in the MORET code validation database. The paper describes the solution chosen by IRSN to take advantage of the DICE database content and to overcome the DICE limits. It also explains the quality assurance policy applied to guaranty the reliability of the stored data. It will also discuss the use of the experiment-filtering module of the MACSENS workbench to select a set of experiments and to examine numerical parameter trends for an application case. (authors)

42 ENGINEERING↗

An affordable platform for automated synthesis and electrochemical characterization

In recent years, self-driving laboratories (SDLs) have emerged as a powerful tool to expedite various areas of chemical research. For optimal functionality, these laboratories must be adaptable, readily modifying configurations to meet researchers' specific needs. Despite these advances, much of chemistry still depends on proprietary equipment from specialized vendors, which can be restrictive and difficult to customize for diverse lab setups. Moreover, ensuring reproducibility requires full disclosure of equipment details. In this work, we introduce an automated system featuring a cost-effective, self-designed potentiostat and a straightforward synthesis platform. We provide complete transparency by disclosing the electronic schematics of the potentiostat and the software used in the system. Our aim is to reduce the barriers to entry for SDLs and promote the principles of open science.

Pablo-García, Sergio↗