PNNL-13501 - Pacific Northwest National Laboratory

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tetra-scale computing, envisioned as being in the near future for parallel computing. Multi-block grids comprising orthogonal sub-grids will allow incorporation of subsurface complexities into the computational domain without significantly increasing the total number of required grid cells. Approach This project has focused on implementing capabilities for orthogonal curvilinear coordinate grids and multi-block grids into a series of sequential and parallel multifluid subsurface flow and transport simulators. Curvilinear coordinate grid capabilities were implemented into the software using the conventional approach of transforming the governing differential equations that describe subsurface flow and transport, using grid metrics (i.e., geometric transformations between the physical domain and computational domain). For static grids the grid metrics are computed once, resulting in minimal additional computational effort. For dynamic grids, such as adaptive grids used to simulate the migration of dense brines from leaking storage tanks into the vadose zone, grid metrics are computed for each grid level. The parallel implementation of the subsurface flow and transport simulator uses a FORTRAN preprocessor, which interprets directives imbedded in the source coding, to convert the source coding from sequential Fortran to parallel FORTRAN with message passing protocols. Multi-block grids require different data structures and distributions than the conventional single-block structured grid. The principal focus for implementing multi-block capabilities in parallel has been in the development of directives and preprocessor translators to handle multiblock data forms. Results and Accomplishments The principal outcomes of the project have been the development of capabilities for solving multifluid subsurface flow and transport problems on curvilinear coordinates and the development of a FORTRAN preprocessor directive, data structure, and interpreter for multi-block grids. To demonstrate these computational capabilities, an experiment involving multifluid flow in a bedded porous media with a sloped interface is being simulated using a structured Cartesian grid, tilted Cartesian grid, and boundary-fitted orthogonal grid. Simulation results for the different grids will be compared against laboratory data, where the key issues are the behavior of a light-nonaqueous-phase-liquid near a sloped textural interface. The ability of the simulator to predict 260 FY 2000 <strong>Laboratory</strong> Directed Research and Development Annual Report the observed behavior of the light-nonaqueous-phaseliquid migration strongly depends on the soil-moisture characteristic function and the geometric representation of the computational grid. For this study, a boundary-fitted curvilinear grid has a significant advantage over Cartesian and tilted Cartesian grids in that it accurately honors both the geometry of the sloped interface and the container boundaries. Curvilinear coordinate system capabilities have been incorporated into eleven operational modes of the multifluid subsurface flow and transport simulators (sequential and parallel implementations): 1) water (aqueous system with passive gas), 2) water-air (aqueousgas system), 3) water-salt (aqueous-brine system with passive gas), 4) water-salt-air (aqueous-brine-gas system), 5) water-air-energy (nonisothermal aqueous-gas system), 6) water-salt-air-energy (nonisothermal aqueous-brine-gas system), 7) water-oil (aqueous-nonaqueous liquid system with passive gas), 8) water-oil-air (aqueous-nonaqueous liquid-gas system), 9) water-oil-dissolved oil (aqueousnonaqueous liquid system with passive gas and kinetic dissolution), 10) water-oil-surfactant (aqueousnonaqueous liquid-surfactant system with passive gas), and 11) water-oil-alcohol (aqueous-nonaqueous liquidternary mixture with passive gas). Writing long-lasting computer codes that distribute data and computations across an array of parallel processors is difficult in the advancing technology of computer hardware and system software. The concept chosen to develop enduring scientific software for this project was that of using a programmable parallel FORTRAN preprocessor, which translates sequential FORTRAN coding with embedded directives into parallel coding. The embedded parallel coding distributes arrays, supports task and data parallelism, implements parallel input/output and other processes required to use distributed memory, shared memory symmetric multiprocessor, and clustered parallel computer systems. This approach allows the code developer to focus on the science and applied mathematics of multifluid subsurface flow and transport without having to deal with the details and protocols of parallel processing. Implementing this approach for multi-block grids required the development of preprocessor directives and programming the preprocessor to interpret these directives. The preprocessor has been programmed to handle block structures using the derived types and structures capabilities of FORTRAN 90. Preprocessor routines were written to handle defining blocks, allocating variables, creating variables, and distributing blocks across the processors.
Summary and Conclusions Boundary-fitted curvilinear grid capabilities were incorporated into a suite of multifluid subsurface flow and transport simulators (sequential and parallel implementations), being used to provide scientific rationale to the restoration and management of the vadose zone and groundwater at contaminated government sites (e.g., Hanford Site). Directives and coding were developed for a FORTRAN 90 programmable preprocessor for multi-block applications. We concluded that multi-block grids comprising structured curvilinear sub-grids are an effective approach for simulating complex geometries in the subsurface (such as geologic features and engineered structures), yielding accurate representations while maintaining the efficiencies of parallel computing. Reference Rosing M. 1999. A Programmable Preprocessor for Parallelizing Fortran-90. Peak Five, Fort Collins, Colorado. Earth System Science 261
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Laboratory Directed Research and De
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Laboratory Directed Research and De
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Computational Science and Engineeri
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Policy and Management Sciences Asse
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Introduction Department of Energy O
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5. After reviews by the Technical a
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• The Technical Council peer revi
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methods applicable to combustion, s
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Summary Each national laboratory mu
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Study Control Number: PN0004/1411 A
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Table 1. Positive and negative ions
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m/z Arbitrary Units Figure 1. Mass
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introduce low-volatility compounds
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arrangement, but the charge is reta
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two liquid chromatographic gradient
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Integrated Microfabricated Devices
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Matrix Assisted Laser Desorption/Io
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Molecular Beam Synthesis and Charac
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temperature distribution of the des
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expected to result in significant a
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Study Control Number: PN99069/1397
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Seuss DT and KA Prather. 1999. “M
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Analysis of Receptor-Modulated Ion
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laboratory (Lu and Xie 1997; Lu et
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Automated DNA Fingerprinting Microa
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Comparison of 4 Xanthomonas Isolate
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Approach Hematopoietic (bone marrow
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Anti-Human lgG Human lgG Protein G
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Characterization of Global Gene Reg
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PCR products for immobilization on
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identify novel proteins of importan
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Immunoprecipitaton of tyrosinephosp
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Coupled NMR and Confocal Microscopy
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In the optical microscopy image, th
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Development and Applications of a M
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Figure 3. Hepa-1 cells undergoing a
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cellular processing (such as post-t
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8. Initial demonstration of an off-
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expression systems for several year
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accumulation of protein products, i
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Fungal Conversion of Agricultural W
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Fungal Conversion of Waste Glucose/
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Summary and Conclusions We demonstr
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are shown in Figure 1(a) and 1(b),
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Anchorage-Independent Growth (% con
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selection of seedlings demonstratin
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NMR-Based Structural Genomics Micha
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Solution-State Structure and Fold-C
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Plant Root Exudates and Microbial G
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Summary and Conclusions • The gre
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Jones-Oliveira JB, JS Oliveira, HE
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• securely moves files to a targe
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Plenary invited lecture, “The Ele
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Figure 1. X3DGEN tetrahedral mesh o
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Figure 5a. OSO volume rendering of
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Development of Models of Cell-Signa
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SOS p 23 EGFR Professor Rodland at
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Oliveira JS, JB Jones-Oliveira, and
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Figure 2. Associating a dataset mar
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to 1) incorporate three-dimensional
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shown in Figure 1. Simulated result
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HostBuilder: A Tool for the Combina
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Invariant Discretization Methods fo
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Graphics, Inc., workstation. The co
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Mixed Hamiltonian Methods for Geoch
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guyanaite, and grimaldiite (see Fig
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in the Environmental Molecular Scie
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Simulation and Modeling of Electroc
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Summary and Conclusions We implemen
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Since the implementation of the gen
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asis of previous performance, perce
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Bioinformatics for High-Throughput
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Summary and Conclusions In previous
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User Cat - Supervisor (client) Anal
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The second goal was to research way
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Figure 1. A visualization technique
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and interactions. The flexibility o
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Figure 4. A filtered version of Fig
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Development of Modeling Tools for J
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Figure 2. Schematic of experimental
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Integrated Modeling and Simulation
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(a) (b) (c) (d) Figure 1. Results o
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Thurman DA. August 2000. Collaborat
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MARC Input initial m esh and result
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(Johnson 1999; Colligan 1999; Gould
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Modeling of High-Velocity Forming f
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Global divergence error 1 10 -14 0
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that users were unlikely to appreci
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Earth System Science
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the lateral extent of the plume so
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Biogeochemical Processes and Microb
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Analyses of populations of viable a
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The first task was to establish fiv
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purged for 2 minutes. The gas sampl
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developing code architecture to min
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Study Control Number : PN98028/1274
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High Power Density Solid Oxide Fuel
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Hybrid Plasma Process for Vacuum De
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Matson DW, PM Martin, WD Bennett, J
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We showed the proof-of-principle ap
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Bandgap Energy (eV) 2.9 2.85 2.8 2.
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Ultrathin Electrolyte Test Results
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Detailed Investigations on Hydrogen
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identified low energy step structur
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Development of Novel Photo-Catalyst
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-2 -1 Energy (eV) 0 1 2 Cu2O SrTiO3
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Here, we perform adsorption and des
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exceed those in the all-metal devic
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Intensity (a.u.) 0 100 200 300 400
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integrated voltage (V) 0.10 0.08 0.
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The first step was to implement thi
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Spontaneous Formation of Cu2O Nano-
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Actinide Chemistry at the Aqueous-M
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Figure 5. Close-up atomic force mic
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to 300°C and 400°C. Unfortunately
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Summary and Conclusions Transmutati
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Advanced Calibration/Registration T
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Figure 1a. Violet filter Figure 1b.
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Autonomous Ultrasonic Probe for Pro
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containing nitrous oxide, an optica
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Chemical Detection Using Cavity Enh
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Figure 3 is a color rendered simula
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appropriate study has been performe
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Exploitation of Conventional Chemic
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Figures 3 and 4 illustrate the impa
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enefits of using a modified spread-
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Single Channel Signal 0.0025 0.0020
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Therefore, in order to extract the
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A next-generation technology is nee
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Wind Dir. Figure 2. Negative ion co
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Volumetric Imaging of Materials by
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amplitude and peak frequency change
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Figure 3. 13 C NMR spectrum of corn
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Approach Two flow loops, one that o
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Modification of Ion Exchange Resins
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Permanganate Treatment for the Deco
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minimized by medium exchange. After
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Figure 1. Thermogravimetric analysi
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Validation and Scale-Up of Monosacc
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Concentration (g/100g solution) Con
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Analysis of High-Volume, Hyper-Dime
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ecent figure of merit values. Shoul
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Probabilistic Methods Development f
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a) Traditional PCA-based process co
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Acronyms and Abbreviations 2-D two-
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PNNL-13501 - Pacific Northwest National Laboratory

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