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This is a set of utilities for reading and manipulating PIO files written in python and C++. These files are intended to be building blocks for other scripts / programs that will use them to do great things. The PIO format itself is described in LA-UR-05-7425 at page 102 and embodied in code LA-CC-05-052. In addition to reading the raw PIO files, the bundled utilities will expand variable that use a compressed sparse row notation
This manuscript introduces CMinx, a program for generating application programming interface (API) documentation written in the CMake language, and CMake modules in particular. Since most of CMinx’s intended audience is comprised of C/C++ developers, CMinx is designed to operate similar to Doxygen, the de facto C/C++ API documentation tool. Specifically, developers annotate their CMake source with “documentation” comments, which are traditional CMake block comments starting with an extra “[” character. The documentation comments, written in reST, describe to the reader how the functions, parameters, and variables should be used. Running CMinx on the annotated source code generates reST files containing the API documentation. The reST files can then be converted into static websites with tools such as Sphinx or easily converted to another format via Pandoc.
Scientific Computational Imaging Code (SCICO) is a Python package for solving the inverse problems that arise in scientific imaging applications. Its primary focus is providing methods for solving ill-posed inverse problems by using an appropriate prior model of the reconstruction space. SCICO includes a growing suite of operators, cost functionals, regularizers, and optimization routines that may be combined to solve a wide range of problems, and is designed so that it is easy to add new building blocks. SCICO is built on top of JAX rather than NumPy, enabling GPU/TPU acceleration, just-in-time compilation, and automatic gradient functionality, which is used to automatically compute the adjoints of linear operators. An example of how to solve a multi-channel tomography problem with SCICO is shown in Figure 1. The SCICO source code is available from GitHub, and pre-built packages are available from PyPI. It has extensive online documentation, including API documentation and usage examples, which can be run online at Google Colab and binder.
We present simulations of an oxygen gas puff Z-pinch on a University scale generator at the Weizmann Institute of Science. The work accounts for the detailed geometry of the nozzle, the initial neutral gas density distribution, and the subsequent implosion. The modeling results show significant improvement with data for the current at the time of stagnation in comparison with a previous effort [Rosenzweig et al., Phys. Plasmas 27, 022705 (2020)]. As a first step, we performed simulations of the flow of neutral diatomic oxygen from a plenum through a nozzle within a recessed cathode, across a gap, and into the anode with a recessed grounded honeycomb. These simulations show an agreement with the measured initial gas density profiles within the region not blocked by the recesses and accessible to visible measurements. The computed neutral gas flow profile serves as the initial condition for a radiation magnetohydrodynamic simulation of the implosion using the MACH2-TCRE code. By considering the specific details of the nozzle and chamber geometry, we find agreement with the measured current profile, including the inductive notch. The simulations predict that the plasma undergoes a strong pinch within the hidden anode recess. The simulations also predict the strongest radiation pulse occurs within the anode recess and at the time of the observed inductive notch.
We present efforts at improving the performance of FLASH, a multi-scale, multi-physics simulation code principally for astrophysical applications, by using huge pages on Ookami, an HPE Apollo 80 A64FX platform. FLASH is written principally in modern Fortran and makes use of the PARAMESH library to manage a block-structured adaptive mesh. We explored options for enabling the use of huge pages with several compilers, but we were only able to successfully use huge pages when compiling with the Fujitsu compiler. As a result, the use of huge pages substantially reduced the number of translation lookaside buffer misses, but overall performance gains were marginal.
Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.
This dataset contains daily netcdf files with horizontal wind profiles retrieved with the WINDoe retrieval (Gebauer and Bell 2024) at Block Island (BLOC). WINDoe retrievals datasets are also available at Nantucket Island (NANT, nant.windoe.z01.c1) and Rhode Island (RHOD, rhod.windoe.z01.c1). WINDoe is an optimal estimation algorithm to retrieve wind profiles combining multiple instruments. The code is available in this github repository (https://github.com/OAR-atmospheric-observations/WINDoe/tree/main), and the retrieval is described by Gebauer and Bell (2024). WINDoe allows combining the individual datasets and outputs into one profile taking into account the information and uncertainties of each dataset. The use of WINDoe minimizes data gaps and maximizes data availability, compared to using wind profiles from only one of the instruments. The regular height grid eases comparisons to numerical weather prediction models. Code modifications have been made that include reading in WFIP3 specific instruments, averaging Doppler lidar radial velocities at various azimuth angles to avoid overfitting, and allowing the user to define a height grid by the user in the vipfile. The instruments used as input to the retrieval are a radar wind profiler (low- and high resolution mode) providing data in and above the boundary layer, a scanning Doppler lidar usually providing data throughout the boundary layer, a profiling lidar providing data from 50 to 200 m at BLOC and NANT, and from 10 to 280 m at Rhode Island, and a surface tower (4 m at NANT and RHOD and 10 m at BLOC). From the scanning lidars, we used radial velocity measurements at 60 deg elevation angle at six different azimuth angles with a resolution of approximately 30 m along the line of sight and the lowest range gate at approximately 70 m. The wind profiles are retrieved with WINDoe up to 3.74 km with 10 m vertical resolution. The profiles are retrieved every 15 min at BLOC and NANT and every 60 min at RHOD.
The High Temperature Test Facility (HTTF) at Oregon State University (OSU) is a scaled integral effects experiment designed to investigate transient behavior in high-temperature gas-cooled nuclear reactors (HTGR) with prismatic fuel and reflector blocks [1]. Several tests have been completed at the HTTF including depressurized conduction cooldown (DCC) and pressurized conduction cooldown (PCC) transients. This summary reports on the analysis of test PG-26 using the INL system code REALP5-3D [2] as well as the ANL system code SAM [3]. Test PG-26 is a progression of the Double Ended Inlet-Outlet Crossover Duct Break transient that is referred to as a DCC [4]. Core initial conditions (i.e., before the DCC started) have been met using low power (<100 kW) and two of ten available electric heater banks. The DCC transient was initiated during the 50th hour of the test. The break valves were opened, and hot helium from the core and cold helium from the reactor cavity simulation tank (RCST) started mixing. The gases flowed in a countercurrent fashion, where the top half of the hot duct contained hot helium that flowed in one direction and cold helium that flowed in the other direction in the bottom half of the duct. After the pressure and density reached equilibrium, the event entered a diffusion mode. The onset of a reverse natural circulation was not observed during the DCC period of the test.
In order to provide the means to predict from molecular dynamics (MD) simulations the structures of copolymer-based micelles in solution, we developed coarse grain force field (CGq FF) parameters for poly(ethylene glycol) (PEG) and for poly(ε-caprolactone) (PCL). A key advance here is the use of quantum mechanics to train the parameters describing the non-bonded (NB) interactions between the CG beads. The functional forms are the same as the MARTINI CG FF so standard MD codes can be used. Our CGq FF describes well the experimentally observed properties for the polymer–air and polymer–water interfaces, indicating the accuracy of the NB interactions. Additionally, the structural properties (density, radius of gyration ( R g ), and end-to-end distance ( h )) match both experiment and all atom (AA) simulations. We illustrate the application of this CGq FF by following the formation of a spherical micelle from 250 chains of PEG 23 - b -PCL 9 diblock copolymer, each block with molecular weight of 1000 Daltons (10 500 beads, corresponding to 123 250 atoms), in a water box with 119 139 water beads (426 553 water molecules).
This work provides a summary of selected experimental capabilities being developed to support nonnuclear testing and demonstration of technology in support of microreactors under the U.S. Department of Energy’s (DOE’s) Microreactor Program. Major capabilities include the Single Primary Heat Extraction and Removal Emulator (SPHERE) and the Microreactor Agile Non-nuclear Experimental Test Bed (MAGNET). The SPHERE facility allows for controlled testing of the steady-state and transient heat rejection capabilities of a single heat pipe using electrical heaters that simulate nuclear heating. The facility is capable of monitoring axial temperature profiles along the heat pipe and surrounding test articles during startup, steady-state operation, and transients. Instrumentation includes noncontact infrared thermal imaging, surface thermocouples, spatially distributed fiber optic temperature and strain sensors, electrical power meters, and a water-cooled, gas-gap calorimeter for quantifying heat rejection from the heat pipe. The facility can be operated under both vacuum and inert-gas conditions. The MAGNET facility is a large-scale, 250-kW electrically heated microreactor test bed to enable nonnuclear experimental evaluation of a variety of microreactor concepts. It can be supplied to electrically heat a scaled section of a microreactor and further test the capabilities of heat rejection systems. The initial MAGNET experiments will support technology maturation and reduce uncertainty and risk associated with the design, operation, and deployment of monolithic heat pipe–based reactors. However, this test bed can broadly be applied to multiple microreactor concepts to evaluate a wide range of thermal-hydraulic and structural phenomena such as interface coupling with power conversion units and other collocated systems. MAGNET can evaluate integral thermomechanical effects during electrical heating of an array of heat pipes in a larger test article. Examples of initial testing will include thermal stresses in the monolith and the impact of debonding of a heat pipe from the core block and how that failure could impact surrounding heat pipes, i.e., understanding the potential for cascading failure. This work also discusses some modeling capabilities that can support experiment design, analysis, and interpretation, including the heat pipe code Sockeye and a comparison of thermal-structural simulations performed using ABAQUS and STAR-CCM+.
A method for automatically generating the “mesh namelist block” portion of a PAGOSA input file, which specifies the boundaries and zone sizes of the computational mesh, has been developed. This application standardizes the mesh block for 2-, and 3-dimensional problems and is computed after the user specifies the extent and resolution of the mesh and the number of processors which will be used to run the problem. The inputs may be provided directly through a series of command-line guided questions, or a separate input file. The mesh block is written to both standard output and to disk.
The spectral element code Nek5000 is an open-source, higher-order computational fluid dynamics code developed at Argonne National Laboratory. It is designed to solve incompressible Navier-Stokes equations, but it also has a low-Mach-number approximation feature available. Large eddy simulation is approached by explicit filtering of the velocity field (and other fields) to mimic the effect of dissipation due to the unresolved scale. The computational domain is decomposed into second-order hexahedral elements that conform to the boundaries. However, generating a high-quality pure-hexahedral mesh can be challenging for some problems. For simple geometries, traditional blocking methods can be used to decompose the domain into smaller blocks to generate a so-called structural mesh. A structural mesh can maintain good orthogonality but can have a highly skewed mesh to conform to the geometry, as well as unnecessary refinement in the far field. Moreover, for geometries with relative complexity, blocking the geometry becomes impossible. To address these issues, we adopted a let-to-hex strategy to generate a pure hexahedral mesh for Nek5000. First, we generate a pure tetrahedral mesh for the geometry; then we divide one tetrahedral element into four hexahedral elements. A pure tetrahedral mesh could be easily generated for complex geometries by using many current meshing codes. In this paper, we use the commercial codes ANSYS meshing and ANSYSICEM to generate the pure tetrahedral mesh and then convert it to a pure hexahedral mesh. Boundary layers are extruded in ANSYSICEM to maintain near-wall resolution.
This paper presents results from modeling of a depressurized conduction cooldown (DCC) transient at the High Temperature Test Facility (HTTF) as part of the OECD-NEA Thermal Hydraulics Code Validation Benchmark for High-Temperature Gas-Cooled Reactors using HTTF Data . This paper briefly describes the benchmark and the models being used. It then presents a comparison of steady state and transient results based on the Problem 2 Exercise 1A and 1B definitions. We compare block and helium temperature distributions, mass flow distribution, and energy balance in steady state. All models show comparable mass flow distributions and energy balances. The temperatures within the core and outer regions are comparable in all models too, but inner reflector temperatures can vary significantly. Despite that, we find that the models are in good agreement for the full-power steady state. In the DCC, we look at block temperature at the core midplane and RCCS water exit temperature. The INL and ANL models are found to be in excellent agreement with one another on block temperature over time, while the agreement when the KAERI and NRG models are added into consideration is good. Differences in the transient heat removal from the RCCS cause the differences in block temperature over time in these models. The CNL models show similar trends to the INL, ANL, KAERI, and NRG models, but the temperatures are high because the volumes used in calculating the average temperature include the heater rods in the CNL models only. The HUN-REN model shows results that suggest significantly lower heat removal in the RCCS which merit further investigation.
Pronghorn-SC is a subchannel code within the Multiphysics Object-Oriented Simulation Environment (MOOSE). Initially designed to simulate flows in water-cooled, square lattice, subchannel assemblies, Pronghorn-SC has been expanded to simulate liquid-metal-cooled flows in triangular lattices, hexagonal subchannel assemblies. For this purpose, the algorithm of Pronghorn-SC was adapted to solve the subchannel equations as they are applicable to a hexagonal wire-wrapped sodium-cooled fast reactor. Cheng–Todreas models for pressure drop and cross-flow models were adopted and a coolant heat conduction term was added. To solve these equations, an improved implicit algorithm was developed robust enough to deal with the numerical issues, associated with low flow and recirculation phenomena. To confirm the prediction capability of Pronghorn-SC, calculations and comparisons with available experimental data of 19- and 37-pin assemblies were performed, as well as other subchannel codes. Finally, a flow blockage modeling feature was added. This capability was validated for both water-cooled square sub-assemblies and sodium-cooled hexagonal sub-assemblies, using experimental data of partially and fully blocked cases.
Figure 1 shows a high-level call chart for MPACT. The call chart uses the actual procedure names, starting with the main program name, MPACT. The only exception is the italicized names where the upstream procedure contains a number of subroutines calls. These calls are logically separated into blocks, such as setup basic info/inputs. Brief descriptions of what the procedure accomplishes are provided where needed. More detailed procedure information, including procedure arguments and definitions, can be found directly in the procedure header in the MPACT source code or Doxygen documentation (http://www.doxygen.nl/).
This report works through two sample design analyses of representative Grade 91 components using the ASME Boiler & Pressure Vessel Code Section III, Division 5, Appendix HBB-T rules for the strain and deformation and creep-fatigue design criteria using a design by inelastic analysis approach. The component geometries and loadings were selected to span a wide variety of potential applications. The sample components are an endplate geometry, which is fairly representative of typical pressure vessel construction, and a core block, representing a critical component in a heat pipe microreactor, which has a complicated geometry and complex thermal stress history. These sample problems serve several functions. First, they are complete worked examples of how to apply the current design by inelastic analysis rules. Second, they serve as test cases to evaluate the current rules and provide feedback on how they could be optimized to deal with complicated component geometries or to be better automated in modern finite element analysis software. Finally, the analysis here uses an inelastic constitutive model for Grade 91 developed by Argonne National Laboratory and proposed for inclusion in the ASME Boiler & Pressure Vessel Code Section III, Division 5 rules as a reference constitutive model. Using this constitutive model in the sample problem analyses tests the model in the context of the ASME Code rules. The final conclusions of this report are that the material model and the current Code rules are satisfactory, but that the Code rules could be optimized to simplify automation and reduce over conservatism. Future work should address the specific optimization topics discussed in this report.
A classical reduced order model (ROM) for dynamical problems typically involves only the spatial reduction of a given problem. Recently, a novel space–time ROM for linear dynamical problems has been developed [Choi et al., Space–tume reduced order model for large-scale linear dynamical systems with application to Boltzmann transport problems, Journal of Computational Physics, 2020], which further reduces the problem size by introducing a temporal reduction in addition to a spatial reduction without much loss in accuracy. The authors show an order of a thousand speed-up with a relative error of less than 10−5 for a large-scale Boltzmann transport problem. In this work, we present for the first time the derivation of the space–time least-squares Petrov–Galerkin (LSPG) projection for linear dynamical systems and its corresponding block structures. Utilizing these block structures, we demonstrate the ease of construction of the space–time ROM method with two model problems: 2D diffusion and 2D convection diffusion, with and without a linear source term. For each problem, we demonstrate the entire process of generating the full order model (FOM) data, constructing the space–time ROM, and predicting the reduced-order solutions, all in less than 120 lines of Python code. We compare our LSPG method with the traditional Galerkin method and show that the space–time ROMs can achieve O(10−3) to O(10−4) relative errors for these problems. Depending on parameter–separability, online speed-ups may or may not be achieved. For the FOMs with parameter–separability, the space–time ROMs can achieve O(10) online speed-ups. Finally, we present an error analysis for the space–time LSPG projection and derive an error bound, which shows an improvement compared to traditional spatial Galerkin ROM methods.
Two modeling tools, a thermohydraulics code and a computational model in COMSOL Multiphysics, have been developed, tested and then applied to the analysis of fluid flow and heat transfer in a thermal convection loop (TCL). Such a device has recently been used to experimentally evaluate corrosion compatibility of APMT (Fe–21Cr–5Al–3Mo) steel with high-temperature molten eutectic lead-lithium (PbLi) alloy at Oak Ridge National Lab, TN, USA. Here, the 1-D thermohydraulics code allows for rapid calculations of the loop parameters as a function of the applied heat flux. The supplemental COMSOL finite-element computations provide detailed 3-D velocity and temperature field data but are much more time consuming. Both modelling tools demonstrate an excellent agreement in the computed circulation velocity as well as maximum and minimum temperatures. The performed TCL analysis focuses on flow development in the “hot” and “cold” legs, formation of Dean vortices in corner regions, blocking effect of the immersed samples, and radiative and convective cooling effects under the experiment-relevant conditions for Prandtl number Pr = 0.015, Grashof numbers Gr ~10 7 , and Reynolds numbers Re ~10 4 .