Harnessing modern parallel computing resources to achieve complex multiphysics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such ...development by providing simplified interfaces for specification of partial differential equations, boundary conditions, material properties, and all aspects of a simulation without the need to consider the parallel, adaptive, nonlinear, finite element solve that is handled internally. Through the use of interfaces and inheritance, each portion of a simulation becomes reusable and composable in a manner that allows disparate research groups to share code and create an ecosystem of growing capability that lowers the barrier for the creation of multiphysics simulation codes. Included within the framework is a unique capability for building multiscale, multiphysics simulations through simultaneous execution of multiple sub-applications with data transfers between the scales. Other capabilities include automatic differentiation, scaling to a large number of processors, hybrid parallelism, and mesh adaptivity. To date, MOOSE-based applications have been created in areas of science and engineering such as nuclear physics, geothermal science, magneto-hydrodynamics, seismic events, compressible and incompressible fluid flow, microstructure evolution, and advanced manufacturing processes.
Fluid-structure interaction (FSI) problems are computationally very challenging. In this paper we consider the monolithic approach for solving the fully coupled FSI problem. Most existing techniques, ...such as multigrid methods, do not work well for the coupled system since the system consists of elliptic, parabolic and hyperbolic components all together. Other approaches based on direct solvers do not scale to large numbers of processors. In this paper, we introduce a multilevel unstructured mesh Schwarz preconditioned Newton–Krylov method for the implicitly discretized, fully coupled system of partial differential equations consisting of incompressible Navier–Stokes equations for the fluid flows and the linear elasticity equation for the structure. Several meshes are required to make the solution algorithm scalable. This includes a fine mesh to guarantee the solution accuracy, and a few isogeometric coarse meshes to speed up the convergence. Special attention is paid when constructing and partitioning the preconditioning meshes so that the communication cost is minimized when the number of processor cores is large. We show numerically that the proposed algorithm is highly scalable in terms of the number of iterations and the total compute time on a supercomputer with more than 10,000 processor cores for monolithically coupled three-dimensional FSI problems with hundreds of millions of unknowns.
This study analyzed the difference between biofilm and planktonic
Brucella abortus
using metabolomics and proteomics.
Brucella abortus
was cultured in different media to induce
Brucella abortus
...biofilm formation and planktonic cells, followed by metabolomics and proteomics analyses for these two samples. Significant differential metabolites were identified, followed by KEGG pathway analysis. Differentially expressed proteins were identified, followed by subcellular localization, GO annotation, and KEGG pathway enrichment. Additionally, a correlation analysis of metabolomics and proteomics was performed. Metabolomics analysis showed 7682 positive and 4433 negative metabolites, including 188 positive and 117 negative significant differential metabolites. These differential metabolites were enriched in fatty acid/unsaturated fatty acid biosynthesis and linoleic acid metabolism. Proteomics analysis revealed 1759 proteins, including 486 differentially expressed proteins, which were enriched in various metabolic and degradation-related pathways. Subcellular localization showed that 74.3% of the differential proteins were cytoplasmic proteins. Correlation analysis showed that 1-palmitoyl-2-oleoyl-phosphatidylglycerol had the most significant correlations with proteins, followed by cytosine. Both metabolites correlated with the protein Q57EI7 (RbsB-1, ribose ABC transporter). One common pathway, fatty acid biosynthesis, was identified by both proteomics and metabolomics analyses that involved the metabolites, oleic acid, and protein Q57DK3 (biotin carboxylase). There were metabolomic and proteomic differences between
Brucella abortus
biofilm and planktonic cells, and these results provide novel insights into the biofilm-forming process of
Brucella abortus
.
The last 2 years have been a period of unprecedented growth for the MOOSE community and the software itself. The number of monthly visitors to the website has grown from just over 3,000 to now ...averaging 5,000. In addition, over 1,800 pull requests have been merged since the beginning of 2020, and the new discussions forum has averaged 600 unique visitors per month. The previous publication has been cited over 200 times since it was published 2 years ago. This paper serves as an update on some of the key additions and changes to the code and ecosystem over the last 2 years, as well as recognizing contributions from the community.
•A multilevel preconditioner is studied for both NDA and transport equations.•The overall algorithm is shown to be scalable using thousands of processor cores.
The multigroup neutron transport ...criticality calculations using modern supercomputers have been widely employed in a nuclear reactor analysis for studying whether or not a system is self-sustaining. However, the design and development of efficient parallel algorithms for the transport criticality calculations is challenging especially when the number of processor cores is large and an unstructured mesh is adopted. In particular, both the compute time and the memory usage have to be carefully taken into consideration due to the dimensionality of the neutron transport equations. In this paper, we study a monolithic multilevel Schwarz preconditioner for the transport criticality calculations based on a nonlinear diffusion acceleration (NDA) method. In NDA, the multigroup nonlinear diffusion equations are computed using an inexact Jacobian-free Newton method with an initial guess generated from a few inverse power iterations. The computed scalar fluxes and eigenvalue are used to evaluate the fission and scattering terms of the transport equations, and then the nonlinear system of transport equations is simplified to a linear system of equations. The linear systems of equations arising from the discretizations of the nonlinear diffusion equations and the transport equations need to be efficiently solved. We propose a monolithic multilevel Schwarz method that is capable of efficiently handling the systems of linear equations for both the transport system and the diffusion system. However, in the multilevel method, algebraically constructing coarse spaces is expensive and often unscalable. We study a subspace-based coarsening algorithm to address such a challenge by exploring the matrix structures of the transport equations and the nonlinear diffusion equations. We numerically demonstrate that the monolithic multilevel preconditioner with the subspace-based coarsening algorithm is twice as fast as that equipped with an unmodified coarsening approach on thousands of processor cores for an unstructured mesh neutron transport problem with billions of unknowns.
Fission gas release within uranium dioxide nuclear fuel occurs as gas atoms diffuse through grains and arrive at grain boundary (GB) bubbles; these GB bubbles grow and interconnect with grain edge ...bubbles; and grain edge tunnels grow and connect to free surfaces. In this study, a hybrid multi-scale/multi-physics simulation approach is presented to investigate these mechanisms of fission gas release at the mesoscale. In this approach, fission gas production, diffusion, clustering to form intragranular bubbles, and re-solution within grains are included using spatially resolved cluster dynamics in the Xolotl code. GB migration and intergranular bubble growth and coalescence are included using the phase field method in the MARMOT code. This hybrid model couples Xolotl to MARMOT using the MultiApp and Transfer systems in the MOOSE framework, with Xolotl passing the arrival rate of gas atoms at GBs and intergranular bubble surfaces to MARMOT and MARMOT passing evolved GBs and bubble surface positions to Xolotl. The coupled approach performs well on the two-dimensional simulations performed in this work, producing similar results to the standard phase field model when Xolotl does not include fission gas clustering or re-solution. The hybrid model performs well computationally, with a negligible cost of coupling Xolotl and MARMOT and good parallel scalability. The hybrid model predicts that intragranular fission gas clustering and bubble formation results in up to 70% of the fission gas being trapped within grains, causing the increase in the intergranular bubble fraction to slow by a factor of six. Re-solution has a small impact on the fission gas behavior at 1800 K but it has a much larger impact at 1000 K, resulting in a twenty-times increase in the concentration of single gas atoms within grains. Due to the low diffusion rate, this increase in mobile gas atoms only results in a small acceleration in the growth of the intergranular bubble fraction. Finally, the hybrid model accounts for migrating GBs sweeping up gas atoms. This results in faster intergranular bubble growth with smaller initial grain sizes, since the additional GB migration results in more immobile gas clusters reaching GBs.
Fusion is an attractive clean-energy solution, thanks to its various advantages, such as reduced radioactivity, little high-level nuclear waste, ample fuel supplies, and increased safety. However, ...the harsh operating environment introduced by a complex fusion plasma system makes design and integration of fusion blankets incredibly challenging and time-consuming. This work focuses on developing a fully integrated multiphysics simulation framework based on an advanced open-source platform-the Multiphysics Object-Oriented Simulation Environment (MOOSE)-to alleviate the difficulties in fusion blanket design and integration. MOOSE is a massively parallel finite element/volume multiphysics simulation platform that has been widely adopted within the nuclear fission community. Even though fission and fusion are fundamentally different, they involve similar multiphysics phenomena. A fully integrated open-source multiphysics simulation framework tailored for the fusion blanket design will be implemented by leveraging the well-established multiphysics capabilities in MOOSE. Once successfully developed, this fully integrated framework will rapidly evaluate a blanket design concept and offer insights for subsequent iterations. As the first step, we will mainly aim to integrate neutronics analysis, system thermal hydraulics simulation, and full 3-D heat transfer calculations. The efficacy of the integrated framework will be verified using an innovative solid ceramic blanket design. While the project's final goal is to enable a fully integrated multiphysics simulation platform for various fusion blanket concepts, this work, as a preliminary step, will mainly focus on a solid ceramic breeder helium-cooled blanket.
Increasingly globalized and complex food supply chains contribute to a growing problem of meat fraud. Meat adulteration with pork is especially exceptionable to the global population for health ...concern and religious faith reasons. To prevent unfair competition and protect consumer rights, an efficient and rapid assay to identify the species of meat products is crucial. In this study, a real-time loop-mediated isothermal amplification (real-time LAMP) assay was developed for the detection of a porcine gene in meat products. The designed primers were highly selective for the porcine gene. The amplification showed no cross-reactivity with 11 other meats. The established method required 20 min with an initial amplification curve of approximately 10 min and demonstrated a detection limit of 1.76 pg/μL porcine DNA, which is 1000 times more sensitive than PCR. This study is the first attempt at detecting porcine-derived ingredients using a real-time LAMP assay in commercial products. This method meets specificity, rapidness, robustness, and sensitivity criteria; its practical application will greatly aid in battling adulteration in the food industry.
•The real-time LAMP was developed and compared to PCR, qPCR.•The method had good specificity, which is 1000 times more sensitive than PCR.•The minimum detect ability could reach 1.76 pg/μL.•First attempt at detecting porcine-derived ingredients using real-time LAMP.•Provided a new way to detect pork-derived ingredients in meat adulteration.
Nonlinear fluid–structure interaction (FSI) problems on unstructured meshes in 3D appear in many applications in science and engineering, such as vibration analysis of aircrafts and patient-specific ...diagnosis of cardiovascular diseases. In this work, we develop a highly scalable, parallel algorithmic and software framework for FSI problems consisting of a nonlinear fluid system and a nonlinear solid system, that are coupled monolithically. The FSI system is discretized by a stabilized finite element method in space and a fully implicit backward difference scheme in time. To solve the large, sparse system of nonlinear algebraic equations at each time step, we propose an inexact Newton–Krylov method together with a multilevel, smoothed Schwarz preconditioner with isogeometric coarse meshes generated by a geometry preserving coarsening algorithm. Here “geometry” includes the boundary of the computational domain and the wet interface between the fluid and the solid. We show numerically that the proposed algorithm and implementation are highly scalable in terms of the number of linear and nonlinear iterations and the total compute time on a supercomputer with more than 10,000 processor cores for several problems with hundreds of millions of unknowns.
•We present an open source FEM for the incompressible Navier-Stokes equations based on the MOOSE framework.•Coordinate system agnostic weak formulation.•SUPG/PSPG stabilized finite element ...formulation.•Discussion of object-oriented software design.•Sample code and input file snippets.•Lid-driven cavity, axisymmetric diffuser, 3D sphere flow calculations.
The Multiphysics Object Oriented Simulation Environment (MOOSE) framework is a high-performance, open source, C++ finite element toolkit developed at Idaho National Laboratory. MOOSE was created with the aim of assisting domain scientists and engineers in creating customizable, high-quality tools for multiphysics simulations. While the core MOOSE framework itself does not contain code for simulating any particular physical application, it is distributed with a number of physics “modules” which are tailored to solving e.g. heat conduction, phase field, and solid/fluid mechanics problems. In this report, we describe the basic equations, finite element formulations, software implementation, and regression/verification tests currently available in MOOSE’s navier_stokes module for solving the Incompressible Navier-Stokes (INS) equations.
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