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925 records · Page 52

Energy-conserving contact dynamics of nonspherical rigid-body particles

Understanding the contact dynamics of nonspherical particles is crucial for accurately modeling colloidal and granular systems where shape anisotropy dictates structural organization and transport properties. We here introduce an energy-conserving contact dynamics framework for arbitrary convex rigid-body particles by implementing vertex–boundary interactions in 2D and vertex–surface and edge–edge detection in 3D. The established formulation enables continuous force evaluation and prevents particle overlap while conserving total energy during translational and rotational motion. We demonstrate the framework’s stability and its utility to capture packing behavior, anisotropic diffusion, and equations of state of polygonal and polyhedral particles as examples. The framework establishes a robust and extensible foundation for investigating nonequilibrium dynamics of complex nonspherical particulate systems, enabling enhanced understanding of phenomena across spatiotemporal scales in self- and directed-assembly, granular flows, and hydrodynamics, potentially coupled with interactions that represent underlying physical mechanisms.

Discrete element method↗

4.0 MOOSE: Enabling massively parallel Multiphysics simulation

Approaching 18 years of existence, MOOSE—the Multiphysics Object-Oriented Simulation Environment—is being developed at a higher pace than ever before. With significant support from four research institutions across the globe, and dozens of new contributors, the capabilities of the framework are being expanded to meet modeling challenges in a wide variety of fields from nuclear system design, to geomechanics, to material science. This includes new development in equation discretization techniques, solver methods, meshing capabilities, application deployment, and user interface improvements. Applications built on MOOSE benefit from all these improvements.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

The W-W02 Oxygen Fugacity Buffer at High Pressures and Temperatures: Implications for f02 Buffering and Metal-silicate Partitioning

Oxygen fugacity (fO2) controls multivalent phase equilibria and partitioning of redox-sensitive elements, and it is important to understand this thermodynamic parameter in experimental and natural systems. The coexistence of a metal and its oxide at equilibrium constitutes an oxygen buffer which can be used to control or calculate fO2 in high pressure experiments. Application of 1-bar buffers to high pressure conditions can lead to inaccuracies in fO2 calculations because of unconstrained pressure dependencies. Extending fO2 buffers to pressures and temperatures corresponding to the Earth's deep interior requires precise determinations of the difference in volume (Delta) V) between the buffer phases. Synchrotron x-ray diffraction data were obtained using diamond anvil cells (DAC) and a multi anvil press (MAP) to measure unit cell volumes of W and WO2 at pressures and temperatures up to 70 GPa and 2300 K. These data were fitted to Birch-Murnaghan 3rd-order thermal equations of state using a thermal pressure approach; parameters for W are KT = 306 GPa, KT' = 4.06, and αKT = 0.00417 GPa K-1. Two structural phase transitions were observed for WO2 at 4 and 32 GPa with structures in P21/c, Pnma and C2/c space groups. Equations of state were fitted for these phases over their respective pressure ranges yielding the parameters KT = 190, 213, 300 GPa, KT' = 4.24, 5.17, 4 (fixed), and αKT = 0.00506, 0.00419, 0.00467 GPa K-1 for the P21/c, Pnma and C2/c phases, respectively. The W-WO2 buffer (WWO) was extended to high pressure by inverting the W and WO2 equations of state to obtain phase volumes at discrete pressures (1-bar to 100 GPa, 1 GPa increments) along isotherms (300 to 3000K, 100 K increments). The slope of the absolute fO2 of the WWO buffer is positive with increasing temperature up to approximately 70 GPa and is negative above this pressure. The slope is positive along isotherms from 1000 to 3000K with increasing pressure up to at least 100 GPa. The WWO buffer is at a higher fO2 than the IW buffer at pressures lower than 40 GPa, and the magnitude of this difference decreases at higher pressures. This qualitatively indicates an increasingly lithophile character for W at higher pressures. The WWO buffer was quantitatively applied to W metal-silicate partitioning by using the WWO-IW buffer difference in combination with literature data on W metal-silicate partitioning to model the exchange coefficient (KD) for the Fe-W exchange reaction. This approach captures the pressure dependence of W metal-silicate partitioning using the WWO-IW buffer difference and models the activities of the components in the silicate and metallic phases using an expression of the Gibbs excess energy of mixing. Calculation of KD along a peridotite liquidus predicts a decrease in W siderophility at higher pressures that supports the qualitative behavior predicted by the WWO-IW buffer difference, and agrees with findings of others. Comparing the competing effects of temperature and pressure on W metal-silicate partitioning, our results indicate that pressure exerts a greater effect.

Shofner, G. A.↗

Metrics for Intercomparison of Remapping Algorithms (MIRA) protocol applied to Earth system models

Abstract. Strongly coupled nonlinear phenomena such as those described by Earth system models (ESMs) are composed of multiple component models with independent mesh topologies and scalable numerical solvers. A common operation in ESMs is to remap or interpolate component solution fields defined on their computational mesh to another mesh with a different combinatorial structure and decomposition, e.g., from the atmosphere to the ocean, during the temporal integration of the coupled system. Several remapping schemes are currently in use or available for ESMs. However, a unified approach to compare the properties of these different schemes has not been attempted previously. We present a rigorous methodology for the evaluation and intercomparison of remapping methods through an independently implemented suite of metrics that measure the ability of a method to adhere to constraints such as grid independence, monotonicity, global conservation, and local extrema or feature preservation. A comprehensive set of numerical evaluations is conducted based on a progression of scalar fields from idealized and smooth to more general climate data with strong discontinuities and strict bounds. We examine four remapping algorithms with distinct design approaches, namely ESMF Regrid (Hill et al., 2004), TempestRemap (Ullrich and Taylor, 2015), generalized moving least squares (GMLS) (Trask and Kuberry, 2020) with post-processing filters, and WLS-ENOR (Li et al., 2020). By repeated iterative application of the high-order remapping methods to the test fields, we verify the accuracy of each scheme in terms of their observed convergence order for smooth data and determine the bounded error propagation using challenging, realistic field data on both uniform and regionally refined mesh cases. In addition to retaining high-order accuracy under idealized conditions, the methods also demonstrate robust remapping performance when dealing with non-smooth data. There is a failure to maintain monotonicity in the traditional L2-minimization approaches used in ESMF and TempestRemap, in contrast to stable recovery through nonlinear filters used in both meshless GMLS and hybrid mesh-based WLS-ENOR schemes. Local feature preservation analysis indicates that high-order methods perform better than low-order dissipative schemes for all test cases. The behavior of these remappers remains consistent when applied on regionally refined meshes, indicating mesh-invariant implementations. The MIRA intercomparison protocol proposed in this paper and the detailed comparison of the four algorithms demonstrate that the new schemes, namely GMLS and WLS-ENOR, are competitive compared to standard conservative minimization methods requiring computation of mesh intersections. The work presented in this paper provides a foundation that can be extended to include complex field definitions, realistic mesh topologies, and spectral element discretizations, thereby allowing for a more complete analysis of production-ready remapping packages.

58 GEOSCIENCES↗

A microstructural approach to cytoskeletal mechanics based on tensegrity

Mechanical properties of living cells are commonly described in terms of the laws of continuum mechanics. The purpose of this report is to consider the implications of an alternative approach that emphasizes the discrete nature of stress bearing elements in the cell and is based on the known structural properties of the cytoskeleton. We have noted previously that tensegrity architecture seems to capture essential qualitative features of cytoskeletal shape distortion in adherent cells (Ingber, 1993a; Wang et al., 1993). Here we extend those qualitative notions into a formal microstructural analysis. On the basis of that analysis we attempt to identify unifying principles that might underlie the shape stability of the cytoskeleton. For simplicity, we focus on a tensegrity structure containing six rigid struts interconnected by 24 linearly elastic cables. Cables carry initial tension ("prestress") counterbalanced by compression of struts. Two cases of interconnectedness between cables and struts are considered: one where they are connected by pin-joints, and the other where the cables run through frictionless loops at the junctions. At the molecular level, the pinned structure may represent the case in which different cytoskeletal filaments are cross-linked whereas the looped structure represents the case where they are free to slip past one another. The system is then subjected to uniaxial stretching. Using the principal of virtual work, stretching force vs. extension and structural stiffness vs. stretching force relationships are calculated for different prestresses. The stiffness is found to increase with increasing prestress and, at a given prestress, to increase approximately linearly with increasing stretching force. This behavior is consistent with observations in living endothelial cells exposed to shear stresses (Wang & Ingber, 1994). At a given prestress, the pinned structure is found to be stiffer than the looped one, a result consistent with data on mechanical behavior of isolated, cross-linked and uncross-linked actin networks (Wachsstock et al., 1993). On the basis of our analysis we concluded that architecture and the prestress of the cytoskeleton might be key features that underlie a cell's ability to regulate its shape.

NASA Discipline Cell Biology↗

Developing And Scaling an OpenFOAM Model to Study Turbulent Flow in a HFIR Coolant Channel

Improving the understanding of how computational fluid dynamics (CFD) direct numerical simulations (DNS) of flows in the High Flux Isotope Reactor (HFIR) perform when run in parallel using the high performance computing (HPC) platform Summit at the Oak Ridge Leadership Computing Facility (OLCF) is of particular importance to boost the computational tools used to support HFIR conversion to low enriched fuel (LEU). Evaluation of scaling performance was driven by the increasing importance of graphics processing unit (GPU) usage in HPC, which is becoming the standard for modern supercomputers such as Summit. The desired results are to obtain a strong positive correlation between the computational resources dedicated to a problem and the relative speed-up of the simulation in comparison to a benchmark. This capability will allow substantially improvement in HFIR flow analytical capabilities, specifically when predicting turbulence properties at high Reynolds numbers. The study leverages previous simulation results performed with code PHASTA (finite element) on HPC platforms Cori (NERSC) and Theta (ALCF) [1] with computing options provided in the computing platform OpenFOAM (finite volume) at OLCF. Transitioning from PHASTA to OpenFOAM will (1) eliminate dependence on third-party software for mesh generation and manipulation, (2) reduce resource needs by employing modern architectures, and (3) build expertise for future modeling of HFIR-specific problems like heat transfer in involute geometry, entrance effects, flow structure in channel corners, and so on—all important issues when defining the available thermal margins in the transition to LEU. CPUs and GPUs differ significantly in their architecture and utilization, as discussed in the literature [2]. The most important differences are in the approach to computations and their memory. A single GPU contains a large quantity of cores, enabling it to perform with a much higher throughput than a CPU, but execution requires a different approach. GPU codes execute instructions using the Single-Instruction Multiple-Thread (SIMT) approach in which a single instruction is used for groups of threads called warps. A warp typically consists of 32 threads which must execute the same set of instructions, although on separate threads. Alternately, a CPU has far fewer cores that are much more flexible in their operation, excelling at quickly performing more complex serial computations. This is why GPUs have greater throughput when properly utilized. The second important difference is seen when comparing their memory spaces. Limited memory allocations and CPU–GPU communications cause a significant bottleneck in GPU-accelerated programs. Further study was required to properly take advantage of GPU resources. A comprehensive analysis of code performance and the model-specific features of turbulence constitutes the core of this work. In this study, a DNS simulation of HFIR channel turbulence was performed with the finite volume CFD code OpenFOAM v2112 and CUDA v11.0 on Red Hat Enterprise Linux v8.2. The OpenFOAM installation had AMGx integrated to enable GPU acceleration and utilizes the PETSc4FOAM library. The computational resources and the problem size were scaled on CPU and CPU + GPU architectures to gain a better understanding of the performance of a DNS problem on modern computing hardware. The study aimed to analyze the scaling of the code exclusively on CPUs and then to examine the scaling of the codes with GPU acceleration enabled. Scaling studies included CPU and GPU acceleration on a mesh of varying resolution to analyze the impact of problem size relative to computational resources. In the course of preparing the GPU configuration on Summit, mainly using the AMGX solvers, difficulties were encountered stemming from constant changes resulting from extensive ongoing development activities and the changing environment. This resulted in the inability to complete the GPU portion of the work. The code was compiled and tested, but production runs to assess acceleration were not performed because the used discretional compute time allocation expired as year-end approached. The Summit HPC platform is scheduled for decommissioning in 2024, making it unattractive for future use with Nvidia-based GPUs. Therefore, the work will be moved onto NERSC machines in FY24. An application was prepared and submitted, and sufficient node-hours were awarded to continue the research in the next calendar year. This report summarizes work performed thus far, which mostly focused on CPU OpenFOAM computing.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Simulating the Formation of Lunar Floor-Fracture Craters Using Elastoviscoplastic Relaxation

Lunar floor-fracture craters formed during the height of mare basalt emplacement. Due to a general temporal and spatial relation with the maria, these craters, numbering some 200, may be diagnostic of the thermal structure of the crust during this time. As the name suggests, these craters exhibit brittle failure, generally limited to the central floor region. That, and a shallower depth than fresh lunar craters, has led to two main theories as to their formation: laccolith emplacement under the crater and viscous relaxation. The implications of each model for the state of the Moon's crust during this time are quite different, so the viability of each model must be checked. Laccolith emplacement has been treated elsewhere. However, previous attempts to study the relaxation of the craters have assumed only a uniform, Newtonian viscous response of the near surface to the topographic driving forces, and simply postulated that the fractures resulted from tensile stresses associated with floor uplift. Here, we use a more sophisticated rheological model that includes not only non-Newtonian viscous behavior (i.e., the viscosity is stress-dependent), but also incorporates elastic behavior and a plastic component to the rheology to directly simulate the formation of the floor fractures. The results of our simulations show that while elastoviscoplastic relaxation is potentially viable for larger floor-fracture craters, it is not viable for craters with diameters < or = 60 km, the size of the majority of floor-fracture craters. We employ the finite element method, a numerical technique well suited for boundary-value problems, via the commercially available MARC software package. To test the viability of topographic relaxation, our goal is to prepare the simulations as to maximize the amount of relaxation. We take advantage of the natural axisymmetry of craters, simulating one radial plane. Initial shapes are based on data for fresh craters from Pike. To simplify implementation, a fourth order polynomial is used for the basin, while a third order inverse function is used for the rim. This form closely approximates the long-wavelength behavior of complex craters, while ignoring higher-frequency topography, save the rim. This approximation is appropriate because crater relaxation is strongly controlled by long-wavelength topography. Loading is accomplished assuming a uniform gravity field (1.62 m/s-square) and a uniform density of 2900 kg/cubic m. The initial stress state is set to be hydrostatic, with an additional pressure term to account for any overlying topography. This additional pressure term is tapered exponentially with depth. While the simulations quickly settle on a preferred stress state, and while the final solution is fairly insensitive to the choice of the e-folding depth of the taper, selecting an e-folding depth close to the diameter of the crater sets the initial stress state near the preferred state. We assume a diuranally averaged surface temperature of -20 C, and allow temperature to increase with depth at a rate of 50 K//km. Assuming a thermal conductivity of 2 W/in/K, this gradient translates to a heat flow of 100mW/square m, an extremely high value for the Moon. Temperature, of course, will not increase without bound. To maximize relaxation, we allow our temperature profile to increase linearly until it reaches the solidus (assumed to be 1200C) at a depth of 24.4 km, at which point it is kept constant. The presence of melt will drop the bulk viscosity; however, we have no rheological control for partial melts. Therefore, we make no attempt to simulate this situation. Elastoviscoplastic rheological model. In general, geologic materials can behave in three main ways: elastically, viscously (via solid-state creep), and brittly (plasticity is a continuum approach to simulate this phenomenon). We combine these three deformation mechanisms in an extended Maxwell solid, where the total strain can be broken down into a simple summation of the elastic, creep, and plastic strains. In relaxation phenomena in general, the system takes advantage of any means possible to eliminate deviatoric stresses by relaxing away the topography. Previous analyses have only modeled the viscous response. Comparatively, the elastic response in our model can augment the relaxation, to a point. This effect decreases as the elastic response becomes stiffer; indeed, in the limit of infinite elastic Young's modulus (and with no plasticity), the solution converges on the purely viscous solution. Igneous rocks common to the lunar near-surface have Young's modulii in the range of 10-100 GPa. To maximize relaxation, we use a Young's modulus of 10 GPa. (There is negligible sensitivity to the other elastic modulus, the Poisson's ratio; we use 0.25.) For the viscous response, we use a flow law for steady-state creep in thoroughly dried Columbia diabase, because the high plagioclase (about 70 vol%) and orthopyroxene (about 17 vol%) content is similar to the composition of the lunar highland crust as described by remote sensing and sample studies: noritic anorthosite. This flow law is highly non-Newtonian, i.e., the viscosity is highly stress dependent. That, and the variability with temperature, stands in strong contrast to previous examinations of lunar floor-fracture crater relaxation. To model discrete, brittle faulting, we assume "Byerlee's rule," a standard geodynamical technique. We implement this "rule" with an-angle of internal friction of about 40 deg, and a higher-than-normal cohesion of about 3.2 MPa (to approximate the breaking of unfractured rock). The actual behavior of geologic materials is more complex than in our rheological model, so the uncertainties in the plasticity do not represent the state-of-the-art error. Additional information is contained in the original.

Dombard, A. J.↗