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148 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

FROSch Preconditioners for Land Ice Simulations of Greenland and Antarctica

Numerical simulations of Greenland and Antarctic ice sheets involve the solution of large-scale highly nonlinear systems of equations on complex shallow geometries. This work is concerned with the construction of Schwarz preconditioners for the solution of the associated tangent problems, which are challenging for solvers mainly because of the strong anisotropy of the meshes and wildly changing boundary conditions that can lead to poorly constrained problems on large portions of the domain. Here, two-level GDSW (Generalized Dryja–Smith–Widlund) type Schwarz preconditioners are applied to different land ice problems, i.e., a velocity problem, a temperature problem, as well as the coupling of the former two problems. We employ the MPI-parallel implementation of multi-level Schwarz preconditioners provided by the package FROSch (Fast and Robust Schwarz)from the Trilinos library. The strength of the proposed preconditioner is that it yields out-of-the-box scalable and robust preconditioners for the single physics problems. To our knowledge, this is the first time two-level Schwarz preconditioners are applied to the ice sheet problem and a scalable preconditioner has been used for the coupled problem. The pre-conditioner for the coupled problem differs from previous monolithic GDSW preconditioners in the sense that decoupled extension operators are used to compute the values in the interior of the sub-domains. Several approaches for improving the performance, such as reuse strategies and shared memory OpenMP parallelization, are explored as well. In our numerical study we target both uniform meshes of varying resolution for the Antarctic ice sheet as well as non uniform meshes for the Greenland ice sheet are considered. We present several weak and strong scaling studies confirming the robustness of the approach and the parallel scalability of the FROSch implementation. Among the highlights of the numerical results are a weak scaling study for up to 32 K processor cores (8 K MPI-ranks and 4 OpenMP threads) and 566 M degrees of freedom for the velocity problem as well as a strong scaling study for up to 4 K processor cores (and MPI-ranks) and 68 M degrees of freedom for the coupled problem.

58 GEOSCIENCES↗
DOE OSTI2024

Multilevel well modeling in aggregation-based nonlinear multigrid for multiphase flow in porous media

A full approximation scheme (FAS) nonlinear multigrid solver for two-phase flow and transport problems driven by wells with multiple perforations is developed here. It is an extension to our previous work on FAS solvers for diffusion and transport problems. The solver is applicable to discrete problems defined on unstructured grids as the coarsening algorithm is aggregation-based and algebraic. To construct coarse basis that can better capture the radial flow near wells, coarse grids in which perforated well cells are not near the coarse-element interface are desired. This is achieved by an aggregation algorithm proposed in this paper that makes use of the location of well cells in the cell-connectivity graph. Numerical examples in which the FAS solver is compared against Newton's method on benchmark problems are given. In particular, for a refined version of the SAIGUP model, the FAS solver is at least 35% faster than Newton's method for time steps with a CFL number greater than 10.

58 GEOSCIENCES↗
DOE OSTI2021

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Considering computational speed vs. accuracy: Choosing appropriate mesoscale RVE boundary conditions

Modeling a material’s microstructure using continuum theories allows for inspection of the relationship between coarse scale and fine scale behaviors. Computational limits generally require selection of a sub-volume from a bulk sample in order to directly model the microstructure. Boundary conditions are applied to the sub-volume to mimic the excluded bulk material. Appropriate selection of boundary conditions helps effectively determine the appropriate spatial scale required of the sub-volume. Applicable boundary conditions include direct displacement, periodic, and uniform traction. While direct displacement and periodic boundary conditions are commonly used, uniform traction boundary conditions have seen limited use due to rigid body stability issues in simulations of compression or shear deformation. A new application of uniform traction boundary conditions was developed through linear constraint equations, similar to approaches employed by direct displacement and periodic boundary conditions, to quench rigid body motions with minimal interference of the relative deformation of the model. These boundary conditions were tested by compressing several synthetically generated periodic microstructures using the finite element method. Evaluating the effective stiffness along the compression axis, the direct displacement boundary condition produced the stiffest response, whereas the uniform traction boundary condition produced the most compliant. Periodic boundary conditions produced the same response for all volumes analyzed and both the direct displacement and uniform traction boundary conditions trended toward the periodic response as the domain volume increased. Computational performance was also evaluated for each boundary condition using implicit and explicit solvers. Direct displacement boundary conditions presented the lowest computational cost of all of the boundary conditions followed by periodic then uniform traction. The computational expense of periodic and uniform traction boundary conditions limited the viable spatial scale and mesh resolutions able to be simulated. Selection of appropriate boundary conditions for specific uses need to be a balance between allowable computational expense and accuracy of the method. Techniques for evaluating which boundary conditions to use are discussed.

42 ENGINEERING↗