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The OMICS group at PNNL has developed a wide range of software utilities over the last 15+ years. These tools are used to manage data files, transform data, visualize data, and automate data processing. The software is distributed on GitHub as open source, typically under the Apache 2.0 license agreement. See https://github.com/PNNL-Comp-Mass-Spec Lipid analysis tool developed by PNNL
Time-to-solution for structure-based screening of massive chemical databases for COVID-19 drug discovery has been decreased by an order of magnitude, and a virtual laboratory has been deployed at scale on up to 27,612 GPUs on the Summit supercomputer, allowing an average molecular docking of 19,028 compounds per second. Over one billion compounds were docked to two SARS-CoV-2 protein structures with full optimization of ligand position and 20 poses per docking, each in under 24 hours. GPU acceleration and high-throughput optimizations of the docking program produced 350× mean speedup over the CPU version (50× speedup per node). GPU acceleration of both feature calculation for machine-learning based scoring and distributed database queries reduced processing of the 2.4 TB output by orders of magnitude. The resulting 50× speedup for the full pipeline reduces an initial 43 day runtime to 21 hours per protein for providing high-scoring compounds to experimental collaborators for validation assays.
Burden distribution in a blast furnace is vital to its smooth running. We have applied mathematical models to guide the charging process to achieve desired burden distribution. Furthermore, the accuracies of such models depend on the prediction of falling curve, stock profile and burden descent mode. Among them, the stock profile model greatly influences the final burden distribution. In this study, a special evaluation index for the accuracy of the modelled burden profile based on charging volume is established. Six existing stock profile models were evaluated and compared with the published experiment data of a scaled blast furnace. It is found that all the models predicted the stock profile well. But, certain models showed increased accuracy for the particular case.
Standard closed-orbit techniques for Twiss parameter measurement are not applicable to the open-ended Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab. The evolution of selected sets of real orbits in the accelerator models the behavior of a "synthetic" beam. This process should provide the distributed optical information needed to optimize beamline tuning for an open-ended system. This work will discuss the development and current state of this technique, as well as examples of its use in the CEBAF machine.
This Lab-Directed Research and Development (LDRD) sought to develop technology that enhances scenario construction speed, entity behavior robustness, and scalability in Live-Virtual-Constructive (LVC) simulation. We investigated issues in both simulation architecture and behavior modeling. We developed path-planning technology that improves the ability to express intent in the planning task while still permitting an efficient search algorithm. An LVC simulation demonstrated how this enables 'one-click' layout of squad tactical paths, as well as dynamic re-planning for simulated squads and for real and simulated mobile robots. We identified human response latencies that can be exploited in parallel/distributed architectures. We did an experimental study to determine where parallelization would be productive in Umbra-based force-on-force (FOF) simulations. We developed and implemented a data-driven simulation composition approach that solves entity class hierarchy issues and supports assurance of simulation fairness. Finally, we proposed a flexible framework to enable integration of multiple behavior modeling components that model working memory phenomena with different degrees of sophistication.
Hydraulic fracturing technology (fracking), coupled with horizontal drilling, has facilitated exploitation of huge natural gas (gas) reserves in the Devonian-age Marcellus Shale Formation (Marcellus) of the Appalachian Basin. The most-efficient technique for stimulating Marcellus gas production involves hydraulic fracturing (injection of a water-based fluid and sand mixture) along a horizontal well bore to create a series of hydraulic fractures in the Marcellus. The hydraulic fractures free the shale-trapped gas, allowing it to flow to the well bore where it is conveyed to pipelines for transport and distribution. The hydraulic fracturing process has two significant effects on the local environment. First, water withdrawals from local sources compete with the water requirements of ecosystems, domestic and recreational users, and/or agricultural and industrial uses. Second, when the injection phase is over, 10 to 30% of the injected water returns to the surface. This water consists of flowback, which occurs between the completion of fracturing and gas production, and produced water, which occurs during gas production. Collectively referred to as returned frac water (RFW), it is highly saline with varying amounts of organic contamination. It can be disposed of, either by injection into an approved underground injection well, or treated to remove contaminants so that the water meets the requirements of either surface release or recycle use. Depending on the characteristics of the RFW and the availability of satisfactory disposal alternatives, disposal can impose serious costs to the operator. In any case, large quantities of water must be transported to and from well locations, contributing to wear and tear on local roadways that were not designed to handle the heavy loads and increased traffic. The search for a way to mitigate the situation and improve the overall efficiency of shale gas production suggested a treatment method that would allow RFW to be used as make-up water for successive fracs. RFW, however, contains dissolved salts, suspended sediment and oils that may interfere with fracking fluids and/or clog fractures. This would lead to impaired well productivity. The major technical constraints to recycling RFW involves: identification of its composition, determination of industry standards for make-up water, and development of techniques to treat RFW to acceptable levels. If large scale RFW recycling becomes feasible, the industry will realize lower transportation and disposal costs, environmental conflicts, and risks of interruption in well development schedules.
The natural subsurface is highly heterogeneous with minerals distributed in different spatial patterns. Fundamental understanding of how mineral spatial distribution patterns regulate sorption process is important for predicting the transport and fate of chemicals. Existing studies about the sorption was carried out in well-mixed batch reactors or uniformly packed columns, with few data available on the effects of spatial heterogeneities. As a result, there is a lack of data and understanding on how spatial heterogeneities control sorption processes. In this project, we aim to understand and develop modeling capabilities to predict the sorption of Cr(VI), an omnipresent contaminant in natural systems due to its natural occurrence and industrial utilization. We systematically examine the role of spatial patterns of illite, a common clay, in determining the extent of transport limitation and scaling effects associated with Cr(VI) sorption capacity and kinetics using column experiments and reactive transport modeling. Our results showed that the sorbed mass and rates can differ by an order of magnitude due to of the illite spatial heterogeneities and transport limitation. With constraints from data, we also developed the capabilities of modeling Cr(VI) in heterogeneous media. The developed model is then utilized to understand the general principles that govern the relationship between sorption and connectivity, a key measure of the spatial pattern characteristics. This correlation can be used to estimate Cr(VI) sorption characteristics in heterogeneous porous media. Insights gained here bridge gaps between laboratory and field application in hydrogeology and geochemical field, and advance predictive understanding of reactive transport processes in the natural heterogeneous subsurface. We believe that these findings will be of interest to a large number of environmental geochemists and engineers, hydrogeologists, and those interested in contaminant fate and transport, water quality and water composition, and natural attenuation processes in natural systems.
This document will describe the process for building the Distributed Infrastructure Offering Real- Time Access to Modeling and Analysis (DIORAMA) software from source. There are many packages included in DIORAMA depending on phenomenology and sensor suite. Each developed package depends on several other packages. The dependency graph in figure 1 shows the complicated dependencies of each package. Because of these dependencies the packages must be built in the order outlined in this guide.
We designed and implemented an in situ version of particle source convergence for the OpenMC particle transport simulator. OpenMC is a Monte Carlo based-particle simulator for neutron criticality calculations. For the transport simulation to be accurate, source particles must converge on a spatial distribution. Typically, convergence is obtained by iterating the simulation by a user-settable, fixed number of steps, and it is assumed that convergence is achieved. We instead implement a method to detect convergence, using the stochastic oscillator for identifying convergence of source particles based on their accumulated Shannon Entropy. Using our in situ convergence detection, we are able to detect and begin tallying results for the full simulation once the proper source distribution has been confirmed. Our method ensures that the simulation is not started too early, by a user setting too optimistic parameters, or too late, by setting too conservative a parameter.
Independent of the methods of nuclear waste disposal, the degradation of packaging materials could lead to mobilization and transport of radionuclides into the geosphere. This process can be significantly accelerated due to the association of radionuclides with the backfill materials or mobile colloids in groundwater. The transport of these colloids is complicated by the inherent coupling of physical and chemical heterogeneities (e.g., pore space geometry, grain size, charge heterogeneity, and surface hydrophobicity) in natural porous media that can exist on the length scale of a few grains. In addition, natural colloids themselves are often heterogeneous in their surface properties (e.g., clay platelets possess opposite charges on the surface and along the rim). Both physical and chemical heterogeneities influence the transport and retention of radionuclides under various groundwater conditions. However, the precise mechanisms how these coupled heterogeneities influence colloidal transport are largely elusive. This knowledge gap is a major source of uncertainty in developing accurate models to represent the transport process and to predict distribution of radionuclides in the geosphere.
General circulation models and downscaled regional models exhibit persistent biases in deep convective initiation location and timing, cloud top height, stratiform area and precipitation fraction, and anvil coverage (e.g., Del Genio 2012, Del Genio et al. 2012, Hohenegger and Stevens 2013, Song et al. 2013). Despite important impacts on the distribution of atmospheric heating, moistening, momentum, and precipitation (e.g., Hartmann et al. 1984, Fritsch et al. 1986, Houze 1989, 2004, Donner et al. 2001, Del Genio and Kovari 2002, Schumacher et al. 2004, Nesbitt et al. 2006, Storelvmo 2012), nearly all climate models fail to represent mesoscale convective organization (Del Genio 2012), while system evolution is not represented at all (Ovchinnikov et al. 2006). Recent advances in cumulus parameterization coupled with increasing model resolution have improved predictions, but even relatively higher-resolution models without parameterized deep convection have some persistent kinematic and microphysical biases (e.g., Blossey et al. 2007, Matsui et al. 2009, Luo et al. 2010, Lang et al. 2011, Varble et al. 2011, Fridlind et al. 2012, Hagos et al. 2014, Varble et al. 2014a-b, Fan et al. 2017, Stanford et al. 2017, Han et al. 2019). To improve representation of convective systems in models requires adequate characterization of their predictability as a function of environmental conditions. Because of the significant sensitivities of deep convective initiation, intensity, lifetime, propagation, and mesoscale convective organization to many factors including multi-scale atmospheric circulations, ambient environmental stability, humidity, wind distributions, and cloud microphysical processes, this characterization relies on comprehensively observing many cases of convective initiation, non-initiation, organization, and non-organization.
The recent boom in the oil and natural gas industry of hydraulic fracture of source rocks has caused a new era in oil and gas production worldwide. However, there are many parts of this process that are poorly understood and thus hard to control. One of the few things that can be controlled is the process of injection to create the fractures in the subsurface and the subsequent injection of proppants to maintain the permeability of the fractured formation, allowing hydrocarbons to be extracted. The goal of this work was to better understand the injection process and resulting proppant distribution in the fracture through a combination of lab-scale experiments and computational models.
The Whole Powder Pattern Modelling (WPPM) approach of diffraction line profile analysis (LPA) was applied for the first time on PuO 2 in order to understand the evolution of the microstructural properties as a function of process conditions. Crystallite size distributions and defect concentrations were determined by WPPM on three different PuO 2 samples - including one with a bimodal distribution and compared to the result of more common LPA analyses used in PuO 2 literature studies (e.g. Scherrer equation, double Voigt method). The conclusion was that a lognormal distribution of spherical crystallites with dislocations most closely represent the microstructure of PuO 2 produced by heating Pu 2 (C 2 O 4 ) 3 (H 2 O) 6 •3H 2 O between 650°C and 850°C. The volume-weighted mean column length (Lvol) parameter obtained from the double Voigt method for the monomodal samples were the same as the Lvol obtained from the WPPM within uncertainty. The two LPA methods did not agree on the Lvol parameters of the bimodal distribution sample with only the WPPM getting values that were consistent with the individual components. The WPPM can potentially provide more insight into future studies of the influences on the microstructure properties of PuO 2 .
This document provides recommended strategies for increasing implementation of grid-interactive efficient building (GEB) measures in federal performance contracts. This document outlines distributed energy resource screening processes, contractual considerations for GEB technologies within performance contracts, and guidance for integration of GEB analysis procedures and technologies into each phase of a performance contract.
A solid oxide fuel cell (SOFC) is a clean and efficient energy conversion device. The development of intermediate-temperature SOFCs has made it preferable to use metallic interconnects (MICs) to greatly reduce the cost and significantly increase the efficiency compared to ceramic interconnect materials. However, gaseous chromium species will evaporate from the chromium-containing layer formed on the surface of commonly used MICs and balance of plant (BoP) components. Volatile chromium species have been shown to form solid deposits which poison the cathodes of SOFCs, causing drastic cell performance degradation and thereby limiting commercialization. In order to alleviate the Cr poisoning and achieve long-term high performance of SOFC stacks, various Al 2 O 3 -forming austenitic (AFA) stainless steels applied at different temperatures are evaluated in this project. Based on our Phase I results (500 h operation), it is shown that on the AFAs, an alumina-based protective layer forms under high temperature that is invulnerable to water vapor effects and suppresses the diffusion of chromium and manganese which can prevent the generation of spinels on the alloy surface. Therefore, 310S, OC4 and OC5 at 800 °C and 625, OC11 and OC11LZ at 900 °C are selected to be tested in the Phase II long-term operation. From the results, we find that besides the lower Cr evaporation rates and better oxidation resistance of AFAs than benchmark alloys after short-term (500 h) operation, AFAs also possess the sturdy and compact alumina layer after a long-term operation (5000 h). A protective oxide layer is of great importance for the long-term high-temperature operation of structural materials. The high-temperature oxidation behavior of AFAs and commercial 310S and 625 alloys in Air + 10% H 2 O at 800 °C and 900 °C is systematically investigated. Severe breakaway oxidation and minor spallation are observed for the 310S and 625 after the long-term operation, while the AFAs show high oxidation resistance. It is found that the formation of a continuous alumina layer could greatly prevent the volatilization of chromium vapors. In addition, the corresponding evolving models are discussed. Chromium evaporation from BoP components in high-temperature environment could severely deteriorate the electrochemical performance of SOFC. Several methods were applied to evaluate the Cr evaporation rates of BoP after 500 h exposure at 800 °C to 900 °C in air with 10% H 2 O. An optimal method was designed to exclude the effect of silicon (Si) deposits from quartz tube and sodium (Na) deposits from the sodium carbonate on the oxidation process and the chemical interaction between Cr gaseous species and alumina tube which could provide further quantitative correlation of the evaporated Cr species quantities and degradation rates of SOFC. Based on the great performance of AFAs after long-term operation, AFAs are assembled with Anode-supported cells (ASC) to investigate the the Cr deposition of anode-supported cell under a constant current density of 0.5 A cm -2 at 800 °C with AFA alloys compared with commercial alloys. In addition, the anodic and cathodic processes are deconvoluted by distribution of relaxation times (DRT) method which are comprehensively discussed. It is found out that the voltage exhibited a slight decrease of 5.09 % and 1.54 % in the presence of OC11 and OC11LZA alloy, respectively. However, a considerable decrease of 22.14 % and 12.06 % was determined in the presence of 310S and 625 alloy, respectively. AFAs possessing the low-cost, low Cr evaporation rates and the high oxidation resistance will make it of great potential to replace the existing BoP components.
Here, we demonstrated the Clean Sustainable Electrochemical Treatment (CleanSET) process that enables the distributed clean-up of biomass-derived wastewater while simultaneously generating hydrogen (H 2 ). The specific goal of this project is to 1) demonstrate the selective removal of chemical oxygen demand (COD), total carbon (TC), and total nitrogen (TN) of different wastewaters, 2) optimize the electrode composition to improve electrochemical performance, and 3) perform a high-level techno-economic analysis to obtain levelized costs of disposal (LCOD) .
In this work, the location-specific microstructures in terms of grain morphology, texture, γ′ precipitates, carbides, and residual strains were investigated in a series of laser-wire direct energy deposition (LW-DED) Haynes 282 alloys with varied processing parameters. A bimodal grain distribution was found in these as-printed and heat-treated alloys with columnar grains within the layers and fine equiaxed grains at the interlayer regions. Dominant <001> texture along the build direction with more obvious <111> orientation preference exists at the bottom layers, compared to the top layers. The gradient γ′-precipitates size distribution contributes predominantly to the observed gradient hardness distribution in the as-printed samples. The heat-treated 282 exhibit comparable yield strengths to those conventionally-processed counterparts, while the observed small deviation in their yield strengths is attributed to the Hall-Petch effect. This work establishes the correlation between location-specific microstructures and mechanical properties, providing valuable insights into future printing parameters and heat-treatment optimization.
Scientific workflows are increasingly relying on machine learning (ML), simulation, and hybrid techniques to predict, understand, and optimize the behavior of complex experiments. High-performance computing has greatly improved researchers’ ability to acquire diverse data modalities in these workflows. Recent studies suggest that the performance of machine learning models can be improved by integrating data from various sources. Unfortunately, these workloads pose unprecedent pressure on the network storage to meet the demands associated with accessing these multimodal data. To mitigate the impact of intensive IO, we propose a solution that utilizes a multi-tier High-Performance Computing (HPC) distributed storage and data processing framework, placing computation where the data resides for better performance. By adopting this project, the scientific community will gain new opportunities to explore multimodal storage-driven possibilities, integrating multiple scientific data sources with advanced streaming frameworks. Additionally, our framework effectively utilizes computing resources and bridges the gaps identified by HPC experts. Our proposed approach tackles scalability and persistence challenges by leveraging native persistency, which has posed difficulties in traditional approaches. Furthermore, we seek to enhance fault-tolerance and load-balance of computations by leveraging real-time streaming in diverse scientific computing environments, thereby propelling advanced scientific computing research into the next generation.