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A simple json format for storing and exchanging code calculation and experimental results

Calculation codes and code systems give their results in a plethora of different formats and/or files. For instance, MCNP gives a user the MCNP specific output file, the mctal file, the ptrac file, etc. while PARTISN has a PARTISN specific output file and a number of binary files with various kinds of information about the calculation. However, the results we are interested in are always the same. These can be single values such as the effective multiplication factor k eff or the effective delayed neutron fraction β eff . It can be histogram data (such as particle spectra, reaction rates, sensitivity profiles, etc.) or even pointwise data (for example the nuclide composition as a function of time, etc.). It is also worthwhile to note that this would also apply to experimental data that we may wish to compare with as well. Calculation and experimental results can basically be split into two components: attributes (or metadata) and the actual result itself. Attributes represent information about the result that are not necessarily required for its’ interpretation but that are still good to have. Often, these attributes are what we will want to filter results on. This means that these attributes are often the answer to specific questions we may have about the result. The following is a non exhaustive list of such basic questions: what type of result is it: e.g. the effective multiplication factor k eff , the effective delayed neutron fraction β eff , etc.; which case does it relate to: e.g. a specific ICSBEP case such as PU-MET-FAST-001-001; which code and version produced this result: e.g. MCNP 6.2, etc.; which nuclear data library was used to obtain the result: e.g. ENDF/B-VIII.0 or JEFF 3.3; which nuclide and reaction does it apply to (for reaction rates and sensitivity profiles); which volume in the geometry was it calculated in? The second component of the calculation or experimental result is the actual numerical data of the result. It is this data that we want to compare, exchange, plot, interpret, etc. It consists of values with optional uncertainties and units. It also includes the underlying structure (if any structure is required to interpret the result). Depending on the type of result, it may be a single value (e.g. the effective multiplication factor), an array of values (e.g. a reaction rate or particle spectrum) or even a multidimensional array. In order to exchange results between different organisations, for instance for benchmarking, people often resort to spreadsheets or custom text files that need to be filled out. While this approach works well if little information is to be exchanged, it can become cumbersome when dealing with large amounts of data (like for instance particle spectra for thousands of cases). In addition, such an approach does not always capture the metadata we may be interested in to allow for automated processing of these files. The purpose of this report is to propose a standardised json structure to store any type of result and present an associated python interface to interact with these results directly. For such a structure to be useful, it must fulfill a specific set of functional requirements that we try to meet with this proposal. The format must allow for the calculation result to stand by itself. This means that we should not have to look in multiple places to be able to understand it. For example, if the result relates to a particle spectrum, the group structure in which the result is given should be stored with it. The format should be code agnostic. This means that we do not need to know where it came from to understand it. The format should be result type agnostic. This means that the format must be generic enough so that we can even use it for results we have not thought of yet. The format should be relatively easy to interact with through different scripting or programming languages (i.e. the machine interface) while still providing a clean structure that can be used directly by any human.

97 MATHEMATICS AND COMPUTING↗

Technical Gaps in Hanford High-Level Waste Solids Settling Behavior and Settling Time Evaluation for Direct Feed High-Level Waste (DFHLW) Operations

Settling of high-level waste (HLW) solids in process vessels is a key conceptual process step in providing HLW feed directly to the Hanford Waste Treatment and Immobilization Plant (WTP) HLW Vitrification Facility. Direct Feed High-Level Waste (DFHLW) is a potential approach to initiating HLW vitrification prior to completing of the WTP Pretreatment Facility. Settling would be used with subsequent supernatant decant to concentrate HLW feed. To support planning for DFHLW, Washington River Protection Solutions (WRPS) requested support from the Pacific Northwest National Laboratory to evaluate the current data set available to predict the time needed for HLW solids to settle, to identify gaps in the understanding and predictive capability of HLW solids waste settling times, and to provide scoping estimates of the potential settling time. Eight technical gaps were identified for predicting settling times and characteristics of the formed sediment layers including: Gap 1: In-Tank Settling Rates Faster than Settling of Laboratory Samples, Gap 2: Effect of Sludge Leaching/Washing on Predicted Settling Times, Gap 3: Predicting Waste Settling from Waste Chemistry (Waste Type), Gap 4: Predicting Waste Settling from Particle Size and Density Distributions (PSDDs), Gap 5: Insufficient Laboratory and In-Tank Settling Data to Represent Hanford Waste, Gap 6: Methods for Real-Time, In-Tank Tracking of Settling, Gap 7: Prediction of Sediment Erosion Resistance as a Function of Settling Time, and Gap 8: Prediction of Sediment Solids Content as a Function of Settling Time. In addition to the data gaps, an overarching observation of the settling rate and settled layer data is the significant variation in behavior. At similar solids concentrations, settling rates can vary by as much as 3 orders of magnitude depending on the source waste tank, and significantly different settling rates are noted between laboratory and in situ tests for the same waste tank. The range of average solids concentration in existing HLW sediment, which may have been quiescent for decades, can vary from less than 7 wt% to greater than 74 wt% solids. The shear strengths (or yield stresses) measured on laboratory samples range from less than 27 Pa to greater than 6400 Pa. These variations can challenge process planning for the application of a settle/decant process for DFHLW. This report describes the significance of the gaps to the settle/decant process and presents uncertainties by way of examples. Potential technical approaches for resolving these gaps are described and the estimated difficulty in resolving these gaps is evaluated. Based on the significance of the gap and the difficulty of resolution, recommendations are made to address specific gaps. Scoping estimates of the potential settling times for DFHLW solids have been made based on the existing data set with its associated gaps. Depending on the process vessel depth and final sediment concentration, substantial fractions of the scoping estimate results for settling times for characterized HLW exceed the 2-week period that has been previously assumed for process planning. There is also significant disparity, potentially greater than a factor of 5000 difference, in the estimated settling times depending on process vessel depth and final sediment solid concentration. This variation in results underscores the significance of the identified gaps and uncertainties with respect to process planning for utilizing settle/decant operations for DFHLW.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

WFOT: A Wave Function Overlap Tool between Single- and Multi-Reference Electronic Structure Methods for Spectroscopy Simulation

We report the development of a novel diagnostic tool, named wave function overlap tool (WFOT), designed to evaluate the overlap between wave functions computed at single-reference [i.e., time-dependent density functional theory or configuration interaction singles (CIS)] and multireference (i.e., CASSCF/CASPT2) electronic structure levels of theory. It relies on truncating the single- and multireference WFs to CIS-like expansions spanning the same configurational space and maximizing the molecular orbital overlap by means of a unitary transformation. To demonstrate the functionality of the tool, we calculate the transient spectrum of acetylacetone by evaluating excited state absorption signals with multireference quality on top of single-reference on-the-fly dynamics simulations. Semiautomatic spectra generation is facilitated by interfacing the tool with the COBRAMM package, which also allows one to use WFOT with several quantum chemistry codes such as Gaussian, NWChem, and OpenMolcas. Finally, other exciting possibilities for the utilization of the code beyond the simulation of transient absorption spectroscopy are eventually discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Excitation energies with linear response density matrix functional theory along the dissociation coordinate of an electron-pair bond in N-electron systems

Time dependent density matrix functional theory in its adiabatic linear response formulation delivers exact excitation energies ω{sub α} and oscillator strengths f{sub α} for two-electron systems if extended to the so-called phase including natural orbital (PINO) theory. The Löwdin-Shull expression for the energy of two-electron systems in terms of the natural orbitals and their phases affords in this case an exact phase-including natural orbital functional (PILS), which is non-primitive (contains other than just J and K integrals). In this paper, the extension of the PILS functional to N-electron systems is investigated. With the example of an elementary primitive NO functional (BBC1) it is shown that current density matrix functional theory ground state functionals, which were designed to produce decent approximations to the total energy, fail to deliver a qualitatively correct structure of the (inverse) response function, due to essential deficiencies in the reconstruction of the two-body reduced density matrix (2RDM). We now deduce essential features of an N-electron functional from a wavefunction Ansatz: The extension of the two-electron Löwdin-Shull wavefunction to the N-electron case informs about the phase information. In this paper, applications of this extended Löwdin-Shull (ELS) functional are considered for the simplest case, ELS(1): one (dissociating) two-electron bond in the field of occupied (including core) orbitals. ELS(1) produces high quality ω{sub α}(R) curves along the bond dissociation coordinate R for the molecules LiH, Li{sub 2}, and BH with the two outer valence electrons correlated. All of these results indicate that response properties are much more sensitive to deficiencies in the reconstruction of the 2RDM than the ground state energy, since derivatives of the functional with respect to both the NOs and the occupation numbers need to be accurate.

74 ATOMIC AND MOLECULAR PHYSICS↗

Wave function for harmonically confined electrons in time-dependent electric and magnetostatic fields

We derive via the interaction “representation” the many-body wave function for harmonically confined electrons in the presence of a magnetostatic field and perturbed by a spatially homogeneous time-dependent electric field—the Generalized Kohn Theorem (GKT) wave function. In the absence of the harmonic confinement – the uniform electron gas – the GKT wave function reduces to the Kohn Theorem wave function. Without the magnetostatic field, the GKT wave function is the Harmonic Potential Theorem wave function. We further prove the validity of the connection between the GKT wave function derived and the system in an accelerated frame of reference. Finally, we provide examples of the application of the GKT wave function.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Flow-driven spectral chaos (FSC) method for simulating long-time dynamics of arbitrary-order non-linear stochastic dynamical systems

Uncertainty quantification techniques such as the time-dependent generalized polynomial chaos (TD-gPC) use an adaptive orthogonal basis to better represent the stochastic part of the solution space (aka random function space) in time. However, because the random function space is constructed using tensor products, TD-gPC-based methods are known to suffer from the curse of dimensionality. Here, we introduce a new numerical method called the flow-driven spectral chaos (FSC) which overcomes this curse of dimensionality at the random-function-space level. The proposed method is not only computationally more efficient than existing TD-gPC-based methods but is also far more accurate. The FSC method uses the concept of enriched stochastic flow maps to track the evolution of a finite-dimensional random function space efficiently in time. To transfer the probability information from one random function space to another, two approaches are developed and studied herein. In the first approach, the probability information is transferred in the mean-square sense, whereas in the second approach the transfer is done exactly using a new theorem that was developed for this purpose. The FSC method can quantify uncertainties with high fidelity, especially for the long-time response of stochastic dynamical systems governed by ODEs of arbitrary order. Six representative numerical examples, including a nonlinear problem (the Van-der-Pol oscillator), are presented to demonstrate the performance of the FSC method and corroborate the claims of its superior numerical properties. Finally, a parametric, high-dimensional stochastic problem is used to demonstrate that when the FSC method is used in conjunction with Monte Carlo integration, the curse of dimensionality can be overcome altogether.

(nonlinear) stochastic dynamical systems↗

Pressure solution creep of random packs of spheres

Abstract We performed numerical calculations of compaction in aggregates of spherical grains, using Lehner and Leroy's (2004, hereinafter LL) constitutive model of pressure solution at grain contacts. That model is founded on a local definition of the thermodynamic driving force and leads to a fully coupled formulation of elastic deformation, dissolution, and diffusive transport along the grain boundaries. The initial geometry of the aggregate was generated by random packing of spheres with a small standard deviation of the diameters. During the simulations, isostatic loading was applied. The elastic displacements at the contacts were calculated according to Digby's (1981) nonlinear contact force model, and deformation by dissolution was evaluated using the LL formulation. The aggregate strain and porosity were tracked as a function of time for fixed temperature, applied effective pressure, and grain size. We also monitored values of the average and standard deviation of total load at each contact, the coordination number for packing, and the statistics of the contact dimensions. Because the simulations explicitly exclude processes such as fracturing, plastic flow, and transport owing to surface curvature, they can be used to test the influence of relative changes in the kinetics of dissolution and diffusion processes caused by contact growth and packing rearrangements. We found that the simulated strain data could be empirically fitted by two successive power laws of the form, ε x ∝ t ξ , where ξ was equal to 1 at very early times, but dropped to as low as 0.3 at longer times. The apparent sensitivity of strain rate to stress found in the simulations was much lower than predicted from constitutive laws that assume a single dominant process driven by average macroscopic loads. Likewise, the apparent activation enthalpy obtained from the simulated data was intermediate between that assumed for dissolution and diffusion, and, further, tended to decrease with time. These results are similar to the experimental observations of Visser et al.'s (2012), who used an aggregate geometry and physical conditions closely resembling the present numerical simulations.

Bernabé, Y.↗

3D-Printable Silicone Materials with Hydrogen Getter Capability

Organic getters are used to reduce the amount of reactive hydrogen in applications such as nuclear plants and transuranic waste. Here, the present study examines the performance of getter loaded silicone elastomers in reducing reactive hydrogen gas from the gas phase and their capability of being 3D printed using direct ink writing techniques. The samples are placed in closed vessels and exposed to hydrogen atmosphere at pressures of 580 torr and 750 mtorr and at a temperature of 25 °C. The hydrogen consumption is measured as a function of time and normalized to getter concentration in the polymer. The performance of the getter-loaded silicone elastomer containing 1,4-bis[phenylethynyl]benzene (DEB) as the organic getter and Pd/C catalyst (ratio of 3:1 DEB to catalyst) decreases with increasing the resin's curing temperature. Chemical analysis suggests that DEB reacts with the silicone resin at high temperatures. In addition, it is demonstrated that the increased surface area of 3D printed composites results in improved getter performance.

36 MATERIALS SCIENCE↗

Targeting Gut Bacteria Using Inulin‐Conjugated Mesoporous Silica Nanoparticles

Abstract To facilitate the creation of novel nanocarrier systems targeting the intestinal microbiome, inulin‐conjugated mesoporous silica nanoparticles (MSNs) are described herein for the first time. Surface functionalization is achieved on either hydrophilic or hydrophobic mesoporous nanoparticles using different conjugation methods. The targeting performance of the resulting materials is assessed and compared upon incubation with human stool. It appears that amide formation is the most favorable coupling method on hydrophilic MSNs to achieve the desired bioconjugate. Remarkably, high affinity of gut bacteria to the conjugated particles can be obtained, paving the way to novel targeted drug delivery systems.

36 MATERIALS SCIENCE↗

Rapid Synthesis of Rhodium-Palladium Alloy Nanocatalysts

The chemistry of metastable RhPd alloys is not well understood, and well-characterized nanoparticle (NP) examples remain rare. Well-defined and near-monodisperse RhPd NPs were prepared in a simple one-pot approach by using microwave-assisted or conventional heating in reaction times as short as 30 s. The catalytic hydrogenation activity of supported RhPd NP catalysts revealed that short synthesis times resulted in the most-active and most-stable hydrogenation catalysts, whereas longer synthesis times promoted partial Rh-Pd core–shell segregation. Relative to Rh NPs, RhPd NPs resisted deactivation over longer reaction times. Density functional theory (DFT) was employed to estimate the binding energies of H and alkenes on (1 1 1) Rh, Pd, and Rh 0.5 Pd 0.5 surfaces. The DFT results concurred with experiment and concluded that the alkene hydrogenation activity trend was of the order Pd<RhPd<Rh. Rh-to-Pd charge-transfer in the RhPd alloys was found to play an important role in modulating the H binding energy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

On the memory attribution problem: A solution and case study using MPI

As parallel applications running on large–scale computing systems become increasingly memory constrained, the ability to attribute memory usage to the various components of the application is becoming increasingly important. We present the design and implementation of memnesia, a novel memory usage profiler for parallel and distributed message–passing applications. Our approach captures both application– and message–passing library–specific memory usage statistics from unmodified binaries dynamically linked to a message–passing communication library. Using microbenchmarks and proxy applications, we evaluated our profiler across three Message Passing Interface (MPI) implementations and two hardware platforms. Furthermore, the results show that our approach and the corresponding implementation can accurately quantify memory resource usage as a function of time, scale, communication workload, and software or hardware system architecture, clearly distinguishing between application and MPI library memory usage at a per–process level. With this new capability, we show that job size, communication workload, and hardware/software architecture influence peak runtime memory usage. In practice, this tool provides a potentially valuable source of information for application developers seeking to measure and optimize memory usage.

97 MATHEMATICS AND COMPUTING↗

In situ non-destructive measurement of biofilm thickness and topology in an interferometric optical microscope

Biofilms are ubiquitous and deleteriously impact a wide range of industrial processes, medical and dental health issues, and environmental problems such as transport of invasive species and the fuel efficiency of ocean going vessels. Biofilms are difficult to characterize when fully hydrated, especially in a non-destructive manner, because of their soft structure and water-like bulk properties. Herein we describe a non-destructive high resolution method of measuring and monitoring the thickness and topology of live biofilms of using white light interferometric optical microscopy. Using this technique, surface morphology, surface roughness, and biofilm thickness can be measured non-destructively and with high resolution as a function of time without disruption of the biofilm activity and processes. The thickness and surface topology of a P. putida biofilm were monitored growing from initial colonization to a mature biofilm. Typical bacterial growth curves were observed. Increase in surface roughness was a leading indicator of biofilm growth.

biofilm↗

Anomalous structural recovery in the near glass transition range in a polymer glass: Data revisited in light of temperature variability in vacuum oven‐based experiments*

Abstract There is considerable interest in data reported by Cangialosi et al. [Cangialosi, D., Boucher, V. M., Alegría, A., & Colmenero, J. (2013). Physical Review Letters , 111 (9), 095701] that purportedly showed unusual irregular responses in the isothermal structural recovery behavior of glasses because the observation challenges the general view of the dynamics being smooth functions of time as observed in extensive dilatometric experiments by Kovacs [Kovacs, A. J. (1964). In Fortschritte der Hochpolymeren‐Forschung , 3 , 394–507. Springer, Berlin, Heidelberg.] in the 1960s. The reported data show an apparent two mechanism structural (enthalpy) recovery at aging temperatures ranging from 6 to 17 K below which is also controversial as it could not be reproduced in work from Koh and Simon [Koh, Y. P., & Simon, S. L. (2013). Macromolecules , 46(14), 5815–5821.] where a second plateau observed in the enthalpy loss curve was not reproduced in nearly 1‐year‐long experiments at 15 K below . Therefore, it is important to determine what might be possible reasons for the apparent non‐smooth relaxations. Here, we examine the possibility that the poor temperature control of a typical vacuum oven could explain the anomalous results. We used the Tool–Narayanaswamy–Moynihan (TNM) model of structural recovery to calculate the effect of typical vacuum oven temperature variation on the structural recovery of polystyrene and find that we can reproduce the reported experimental results. The issue of temperature control using a vacuum oven is discussed, and data from thermocouple measurements of temperature at various locations inside a vacuum oven are shown.

36 MATERIALS SCIENCE↗

Moisture ingress prediction in polyisobutylene-based edge seal with molecular sieve desiccant

Often photovoltaic modules are constructed with materials that are sensitive to water. This is most often the case with thin film technologies, including perovskite cells, where the active layers are a few microns thick and can be sensitive to moisture, liquid water or both. When moisture or liquid water can ingress, a small amount of water can lead to corrosion and depending on the resulting reactions, a larger local detrimental effect is possible. To prevent moisture from contacting photovoltaic components, impermeable frontsheets and backsheets are used with a polyisobutylene (PIB)-based edge seal material around the perimeter. Here, we evaluate the ability of a PIB-based edge seal using a molecular sieve desiccant to keep moisture out for the expected module lifetime. Moisture ingress is evaluated using test coupons where the edge seal is placed between 2 pieces of glass, one of which has a metallic calcium film on it, and monitoring the moisture ingress distance as a function of time. We expose samples to different temperature and humidity conditions to create permeation models useful for extrapolation to field use. This extrapolation indicates that this PIB material is capable of keeping moisture out of a module for the desired lifetime.

14 SOLAR ENERGY↗

On the sizes and lifetimes of cold pools

Cold pools of air, which are formed by evaporating precipitation, play a critical role in the triggering of new precipitation. Despite their recognized importance, little effort has been devoted to building simple models of their dynamics. Here, analytical equations are derived for the radius, height, and buoyancy of a cylindrical cold pool as a function of time, and a scale analysis reveals that entrainment is a dominant influence. These governing equations yield simple expressions for the maximum sizes and lifetimes of cold pools. The terminal radius of a cold pool is relatively insensitive to its initial conditions, with a typical maximum radius of about 14 times the initial radius, give or take a factor of 2. The terminal time of a cold pool, on the other hand, can vary over orders of magnitude depending on its initial potential and kinetic energies. Lastly, these predictions are validated against large-eddy simulations.

54 ENVIRONMENTAL SCIENCES↗

On entanglement spreading from holography

A global quench is an interesting setting where we can study thermalization of subsystems in a pure state. We investigate entanglement entropy (EE) growth in global quenches in holographic field theories and relate some of its aspects to quantities characterizing chaos. More specifically we obtain four key results: 1. We prove holographic bounds on the entanglement velocity vE and the butterfly effect speed vB that arises in the study of chaos. 2. We obtain the EE as a function of time for large spherical entangling surfaces analytically. We show that the EE is insensitive to the details of the initial state or quench protocol. 3. In a thermofield double state we determine analytically the two-sided mutual information between two large concentric spheres separated in time. 4. We derive a bound on the rate of growth of EE for arbitrary shapes, and develop an expansion for EE at early times. In a companion paper, these results are put in the broader context of EE growth in chaotic systems: we relate EE growth to the chaotic spreading of operators, derive bounds on EE at a given time, and compare the holographic results to spin chain numerics and toy models. In this paper, we perform holographic calculations that provide the basis of arguments presented in that paper.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Two splits, three ways: advances in double splitting quenches

In this work we introduce a method for calculating holographic duals of BCFTs with more than two boundaries. We apply it to calculating the dynamics of entanglement entropy in a 1+1d CFT that is instantaneously split into multiple segments and calculate the entanglement entropy as a function of time for the case of two splits, showing that our approach reproduces earlier results for the double split case. Our manuscript lays the groundwork for future calculations of the entanglement entropy for more than two splits and systems at nonzero temperature.

AdS-CFT correspondence↗