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At least 955 records · Page 53

Computing water flow through complex landscapes – Part 3: Fill–Spill–Merge: flow routing in depression hierarchies

Abstract. Depressions – inwardly draining regions – are common to many landscapes. When there is sufficient moisture, depressions take the form of lakes and wetlands; otherwise, they may be dry. Hydrological flow models used in geomorphology, hydrology, planetary science, soil and water conservation, and other fields often eliminate depressions through filling or breaching; however, this can produce unrealistic results. Models that retain depressions, on the other hand, are often undesirably expensive to run. In previous work we began to address this by developing a depression hierarchy data structure to capture the full topographic complexity of depressions in a region. Here, we extend this work by presenting the Fill–Spill–Merge algorithm that utilizes our depression hierarchy data structure to rapidly process and distribute runoff. Runoff fills depressions, which then overflow and spill into their neighbors. If both a depression and its neighbor fill, they merge. We provide a detailed explanation of the algorithm and results from two sample study areas. In these case studies, the algorithm runs 90–2600 times faster (with a reduction in compute time of 2000–63 000 times) than the commonly used Jacobi iteration and produces a more accurate output. Complete, well-commented, open-source code with 97 % test coverage is available on GitHub and Zenodo.

58 GEOSCIENCES↗

On coarse projective integration for atomic deposition in amorphous systems

Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the “equation-free” framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of this technique in realistic settings is the “lifting” operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO{sub 2} substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO{sub 2} using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Conforming Morse-Smale Complexes

Morse-Smale (MS) complexes have been gaining popularity as a tool for feature-driven data analysis and visualization. However, the quality of their geometric embedding and the sole dependence on the input scalar field data can limit their applicability when expressing application-dependent features. In this paper we introduce a new combinatorial technique to compute an MS complex that conforms to both an input scalar field and an additional, prior segmentation of the domain. The segmentation constrains the MS complex computation guaranteeing that boundaries in the segmentation are captured as separatrices of the MS complex. We demonstrate the utility and versatility of our approach with two applications. First, we use streamline integration to determine numerically computed basins/mountains and use the resulting segmentation as an input to our algorithm. This strategy enables the incorporation of prior flow path knowledge, effectively resulting in an MS complex that is as geometrically accurate as the employed numerical integration. Our second use case is motivated by the observation that often the data itself does not explicitly contain features known to be present by a domain expert. We introduce edit operations for MS complexes so that a user can directly modify their features while maintaining all the advantages of a robust topology-based representation.

97 MATHEMATICS AND COMPUTING↗

Complex functionality with minimal computation: Promise and pitfalls of reduced‐tracer ocean biogeochemistry models

Abstract Earth System Models increasingly include ocean biogeochemistry models in order to predict changes in ocean carbon storage, hypoxia, and biological productivity under climate change. However, state‐of‐the‐art ocean biogeochemical models include many advected tracers, that significantly increase the computational resources required, forcing a trade‐off with spatial resolution. Here, we compare a state‐of‐the art model with 30 prognostic tracers (TOPAZ) with two reduced‐tracer models, one with 6 tracers (BLING), and the other with 3 tracers (miniBLING). The reduced‐tracer models employ parameterized, implicit biological functions, which nonetheless capture many of the most important processes resolved by TOPAZ. All three are embedded in the same coupled climate model. Despite the large difference in tracer number, the absence of tracers for living organic matter is shown to have a minimal impact on the transport of nutrient elements, and the three models produce similar mean annual preindustrial distributions of macronutrients, oxygen, and carbon. Significant differences do exist among the models, in particular the seasonal cycle of biomass and export production, but it does not appear that these are necessary consequences of the reduced tracer number. With increasing CO 2 , changes in dissolved oxygen and anthropogenic carbon uptake are very similar across the different models. Thus, while the reduced‐tracer models do not explicitly resolve the diversity and internal dynamics of marine ecosystems, we demonstrate that such models are applicable to a broad suite of major biogeochemical concerns, including anthropogenic change. These results are very promising for the further development and application of reduced‐tracer biogeochemical models that incorporate “sub‐ecosystem‐scale” parameterizations.

58 GEOSCIENCES↗

Insights into Molecular Magnetism in Metal–Metal Bonded Systems as Revealed by a Spectroscopic and Computational Analysis of Diiron Complexes

A pair of bimetallic compounds featuring Fe–Fe bonds, [Fe( i PrNPPh 2 ) 3 FeR] (R = PMe 3 , ≡N t Bu), have been investigated using High-Frequency Electron Paramagnetic Resonance (HFEPR) as well as field- and temperature-dependent 57 Fe nuclear γ resonance (Mössbauer) spectroscopy. To gain insight into the local site electronic structure, we have concurrently studied a compound containing a single Fe(II) in a geometry analogous to that of one of the dimer sites. Our spectroscopic studies have allowed for the assessment of the electronic structure via the determination of the zero-field splitting and 57 Fe hyperfine parameters for the entire series. We also report on our efforts to correlate structure with physical properties in metal–metal bonded systems using ligand field theory guided by quantum chemical calculations. Through the insight gained in this study, we discuss strategies for the design of single-molecule magnets based on polymetallic compounds linked via direct metal–metal bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DFT and TD-DFT computation of charge transfer complex between o-phenylenediamine and 3,5-dinitrosalicylic acid

DFT and TD-DFT studies of o-phenylenediamine (PDA), 3,5-dinitrosalicylic acid (DNSA) and their charge transfer complex have been carried out at B3LYP/6-311G(d,p) level of theory. Molecular geometry and various other molecular properties like natural atomic charges, ionization potential, electron affinity, band gap, natural bond orbital (NBO) and frontier molecular analysis have been presented at same level of theory. Frontier molecular orbital and natural bond orbital analysis show the charge delocalization from PDA to DNSA.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Computing water flow through complex landscapes – Part 2: Finding hierarchies in depressions and morphological segmentations

Depressions – inwardly draining regions of digital elevation models – present difficulties for terrain analysis and hydrological modeling. Analogous “depressions” also arise in image processing and morphological segmentation, where they may represent noise, features of interest, or both. Here we provide a new data structure – the depression hierarchy – that captures the full topologic and topographic complexity of depressions in a region. We treat depressions as networks in a way that is analogous to surface-water flow paths, in which individual sub-depressions merge together to form meta-depressions in a process that continues until they begin to drain externally. This hierarchy can be used to selectively fill or breach depressions or to accelerate dynamic models of hydrological flow. Complete, well-commented, open-source code and correctness tests are available on GitHub and Zenodo.

54 ENVIRONMENTAL SCIENCES↗

Application of computational fluid dynamics to complex inlet ducts

A three-dimensional parabolic Navier-Stokes code, PEPSIG, was used to analyze the flow in the subsonic diffuser section of a typical modern inlet design. The effect of curvature of the diffuser centerline and transitioning cross sections was studied to determine the primary cause of flow distortion in the duct. Total pressure values at the engine compressor face are reported.

Towne, C. E.↗

Application of computational fluid dynamics to complex inlet ducts

A three-dimensional parabolic Navier-Stokes code, PEPSIG, was used to analyze the flow in the subsonic diffuser section of a typical modern inlet design. The effect of curvature of the diffuser centerline and transitioning cross sections was studied to determine the primary cause of flow distortion in the duct. Total pressure values at the engine compressor face are reported.

Towne, C. E.↗

Mesh generation for the computation of flowfields over complex aerodynamic shapes

Methods are presented for generating both structured and unstructured meshes about three dimensional shapes. Results for both approaches are shown and their strengths and weaknesses are compared. For relatively simple configurations, such as wing/body combinations, a structured mesh is the preferred approach. For a complete aircraft, however, structured meshes lack the necessary flexibility, but unstructured meshes do offer the opportunity to treat completely general configurations with relative ease.

Baker, Timothy↗