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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Speedup of UEDGE Parameter Scans Using Machine-Learning Optimized OpenMP Parallelization and a Continuation Solver

This article presents the OpenMP parallelization of the preconditioning Jacobian assembly and right‐hand side residual evaluation in UEDGE. A continuation algorithm, utilizing the internal NKSOL implicit Jacobian‐Free Newton‐Krylov solver to efficiently scan physical parameters, is also presented. The implemented parallelization reduces the computational time for a benchmark scan run on 32 threads by compared to the serial version when using trained random forest regression models to identify the optimal decomposition of the system of equations. Random forest regression models applied to the UEDGE time‐dependent and continuation solver algorithms did not yield meaningful improvement in computational performance. A benchmark DIII‐D gas injection rate scan in the 0.35–0.75 kA interval, performed on a test cluster using the parallelized code and continuation solver, produced 1066 steady‐state solutions with a 22 s average wall‐clock computational time per steady‐state solution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

An interoperable implementation of collective‐variable based enhanced sampling methods in extended phase space within the OpenMM package

Collective variable (CV)-based enhanced sampling techniques are widely used today for accelerating barrier-crossing events in molecular simulations. A class of these methods, which includes temperature accelerated molecular dynamics (TAMD)/driven-adiabatic free energy dynamics (d-AFED), unified free energy dynamics (UFED), and temperature accelerated sliced sampling (TASS), uses an extended variable formalism to achieve quick exploration of conformational space. These techniques are powerful, as they enhance the sampling of a large number of CVs simultaneously compared to other techniques. Extended variables are kept at a much higher temperature than the physical temperature by ensuring adiabatic separation between the extended and physical subsystems and employing rigorous thermostatting. Here, in this work, we present a computational platform to perform extended phase space enhanced sampling simulations using the open-source molecular dynamics engine OpenMM. The implementation allows users to have interoperability of sampling techniques, as well as employ state-of-the-art thermostats and multiple time-stepping. This work also presents protocols for determining the critical parameters and procedures for reconstructing high-dimensional free energy surfaces. As a demonstration, we present simulation results on the high dimensional conformational landscapes of the alanine tripeptide in vacuo, tetra-N-methylglycine (tetra-sarcosine) peptoid in implicit solvent, and the Trp-cage mini protein in explicit water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Depth‐dependent concentrations of hematopoietic stem cells in the adult skeleton: Implications for active marrow dosimetry

Purpose The hematopoietically active (or red) bone marrow is the target tissue assigned in skeletal dosimetry models for assessment of stochastic effects (leukemia induction) as well as tissue reactions (marrow toxicity). Active marrow, however, is in reality a surrogate tissue region for specific cell populations, namely the hematopoietic stem and progenitor cells. Present models of active marrow dosimetry implicitly assume that these cells are uniformly localized throughout the marrow spaces of trabecular spongiosa. Data from Watchman et al. and Bourke et al., however, clearly indicate that there is a substantial spatial concentration gradient of these cells with the highest concentrations localized near the bone trabeculae surfaces. The purpose of the present study was thus to explore the dosimetric implications of these spatial gradients on active marrow dosimetry. Methods Images of several bone sites from a 45‐yr female were retagged to group active marrow voxels into 50 μm increments of marrow depth, after which electron and alpha‐particle depth‐dependent specific absorbed fractions were computed for four source tissues — active marrow, inactive marrow, bone trabeculae volumes, and bone trabeculae surfaces. Corresponding depth‐dependent S values (dose to a target tissue per decay in a source tissue) were computed and further weighted by the relative target cell concentration. These depth‐weighted radionuclide S values were systematically compared to the more traditional volume‐averaged radionuclide S values of the MIRD schema for both individual bones of the skeleton and their skeletal‐averaged quantities. Results For both beta‐emitters and alpha‐emitters localized in the active and inactive marrow, depth‐weighted S values were shown to differ from volume‐averaged S values by only a few percent, as dose gradients across the marrow tissues are nonexistent. For bone volume and bone surface sources of alpha‐emitters and lower energy beta‐emitters, when marrow dose gradients are expected, explicit consideration of target cell spatial concentration gradients are shown to significantly impact marrow dosimetry. Conclusions For medical isotopes currently utilized for treatment of skeletal metastases, namely 153 Sm and 223 Ra, accounting for hematopoietic stem and progenitor cell concentration gradients resulted in maximum percent differences to reference skeletal‐averaged S values of ~21% and 55%, respectively.

Geyer, Amy M.↗
DOE OSTI2018

A Generalized Backward Euler algorithm for the numerical integration of a viscous breakage model

This paper discusses the formulation and the numerical performance of a fully implicit algorithm used to integrate a rate-dependent model defined within a breakage mechanics framework. For this purpose, a Generalized Backward Euler (GBE) algorithm has been implemented according to two different linearization strategies: The former is derived by a direct linearization of the constitutive equations, while the latter introduces rate effects through a consistency parameter. Additionally, the accuracy and efficiency of the GBE algorithm have been investigated by (1) performing material point analyses and (2) solving initial boundary value problems. In both cases, the overall performance of the underlying algorithm is inspected for a range of loading rates, thus simulating comminution from slow to fast dynamic problems. As the viscous response of the breakage model can be recast through a viscous nucleus function, the presented algorithm can be considered as a general framework to integrate constitutive equations relying on the overstress approach typical of Perzyna-like viscoplastic models.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A hybrid calibration approach to Hertz-type contact parameters for discrete element models

This study aims at providing a hybrid calibration framework to estimate Hertz-type contact parameters (particle-scale shear modulus and Poisson ratio) for both two-dimensional and three-dimensional discrete element modelling (DEM). On the basis of statistically isotropic granular packings, a set of analytical formulae between macroscopic material parameters (Young modulus and Poisson ratio) and particle-scale Hertz-type contact parameters for granular systems are derived under small-strain isotropic stress conditions. However, the derived analytical solutions are only estimated values for general models. By viewing each DEM modelling as an implicit mathematical function taking the particle-level parameters as independent variables and employing the derived analytical solutions as the initial input parameters, an automatic iterative scheme is proposed to obtain the calibrated parameters with higher accuracies. Considering highly nonlinear features and discontinuities of the macro-micro relationship in Hertz-based discrete element models, the adaptive moment estimation algorithm is adopted in this study because of its capacity of dealing with noise gradients of cost functions. Here, the proposed method is validated with several numerical cases including randomly distributed monodisperse and polydisperse packings. Noticeable improvements in terms of calibration efficiency and accuracy have been made.

Constitutive law↗
DOE OSTI2016

A rank-exploiting infinite Arnoldi algorithm for nonlinear eigenvalue problems

We consider the nonlinear eigenvalue problem M ( λ ) x = 0, where M ( λ ) is a large parameter-dependent matrix. In several applications, M ( λ ) has a structure where the higher-order terms of its Taylor expansion have a particular low-rank structure. We propose a new Arnoldi-based algorithm that can exploit this structure. More precisely, the proposed algorithm is equivalent to Arnoldi's method applied to an operator whose reciprocal eigenvalues are solutions to the nonlinear eigenvalue problem. The iterates in the algorithm are functions represented in a particular structured vector-valued polynomial basis similar to the construction in the infinite Arnoldi method [Jarlebring, Michiels, and Meerbergen, Numer. Math., 122 (2012), pp. 169–195]. In this paper, the low-rank structure is exploited by applying an additional operator and by using a more compact representation of the functions. This reduces the computational cost associated with orthogonalization, as well as the required memory resources. The structure exploitation also provides a natural way in carrying out implicit restarting and locking without the need to impose structure in every restart. In conclusion, the efficiency and properties of the algorithm are illustrated with two large-scale problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

A fully coupled two-level Schwarz preconditioner based on smoothed aggregation for the transient multigroup neutron diffusion equations

The neutron multigroup diffusion equations is an important approximation of the neutron transport equation, and has been widely used for studying the motion of neutrons and their interactions with the stationary background materials. Solving the multigroup diffusion equations faces challenging because many variables are coupled together and a lot of computing resources are required. In this paper, we focus on the development of a scalable parallel algorithm framework for the system of equations arising from the discretization of the multigroup diffusion equations using a finite element method in space and using an implicit scheme in time. The parallel agorithm framweork consists of an inexact Jacobian-free Newton for the nonlinear equations, a Krylov subspace method for the Jacobian system and a parallel Schwarz preconditioner for the acceleration of the algorithm convergence. A coarse space based on smoothed aggregation is introduced to construct a two-level method to improve the parallel performance of the Schwarz preconditioner. We numerically shown that compared with the one-level method, the proposed two-level method works significantly better in terms of the number of linear iterations and the compute time for a system of equations with millions of unknowns and a supercomputer with thousands of processors.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Recursive integral method with Cayley transformation

Summary The recently developed RIM (recursive integral method) finds eigenvalues in a region of the complex plane. It computes an indicator to test if the region contains eigenvalues using an approximate spectral projection. If the indicator shows that the region contains eigenvalues, it is subdivided into smaller regions, which are then recursively tested and subdivided until any eigenvalues are isolated to a specified precision. We propose an enhancement to RIM that uses Cayley transformations and Arnoldi's method to greatly decrease the number of factorizations required to solve the linear systems that arise from a discretized contour integral to compute the indicator, which substantially reduces the computational cost. We demonstrate the efficacy of our method with numerical examples and compare with the implicitly restarted Arnoldi method, as implemented in eigs in MATLAB.

Huang, R.↗
DOE OSTI2021

Optimizing multigrid reduction-in-time and Parareal coarse-grid operators for linear advection

Parallel-in-time methods, such as multigrid reduction-in-time (MGRIT) and Parareal, provide an attractive option for increasing concurrency when simulating time-dependent partial differential equations (PDEs) in modern high-performance computing environments. While these techniques have been very successful for parabolic equations, it has often been observed that their performance suffers dramatically when applied to advection-dominated problems or purely hyperbolic PDEs using standard rediscretization approaches on coarse grids. In this paper, we apply MGRIT or Parareal to the constant-coefficient linear advection equation, appealing to existing convergence theory to provide insight into the typically nonscalable or even divergent behavior of these solvers for this problem. To overcome these failings, we replace rediscretization on coarse grids with improved coarse-grid operators that are computed by applying optimization techniques to approximately minimize error estimates from the convergence theory. Therefore, one of our main findings is that, in order to obtain fast convergence as for parabolic problems, coarse-grid operators should take into account the behavior of the hyperbolic problem by tracking the characteristic curves. Our approach is tested for schemes of various orders using explicit or implicit Runge–Kutta methods combined with upwind-finite-difference spatial discretizations. In all cases, we obtain scalable convergence in just a handful of iterations, with parallel tests also showing significant speed-ups over sequential time-stepping.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

High‐order methods for low Reynolds number flows around moving obstacles based on universal meshes

Summary We propose a family of methods for simulating two‐dimensional incompressible, low Reynolds number flow around a moving obstacle whose motion is prescribed. The methods make use of a universal mesh: a fixed background mesh that adapts to the geometry of the immersed obstacle at all times by adjusting a few elements in the neighborhood of the obstacle's boundary. The resulting mesh provides a conforming triangulation of the fluid domain over which discretizations of any desired order of accuracy in space and time can be constructed using standard finite element spaces together with off‐the‐shelf time integrators. We demonstrate the approach by using Taylor‐Hood elements to approximate the fluid velocity and pressure. To integrate in time, we consider implicit Runge‐Kutta schemes as well as a fractional step scheme. We illustrate the methods and study their convergence numerically via examples that involve flow around obstacles that undergo prescribed deformations. Copyright © 2015 John Wiley & Sons, Ltd.

Gawlik, Evan S.↗
DOE OSTI2016

Microscale modeling of effective mechanical and electrical properties of textiles

Here, a computational framework for assisting in the development of novel textiles is presented. Electronic textiles are key in the rapidly growing field of wearable electronics for both consumer and military uses. There are two main challenges to the modeling of electronic textiles: the discretization of the textile microstructure and the interaction between electromagnetic and mechanical fields. A director-based beam formulation with an assumed electrical current is used to discretize the fabric at the level of individual fibrils. The open-source package FEniCS was used to implement the finite element model. Contact integrals were added into the FEniCS framework so that multiphysics contact laws can be incorporated in the same framework, leveraging the code generation and automated differentiation capabilities of FEniCS to produce the tangents needed by the implicit solution method. The computational model is used to construct and determine the mechanical, thermal, and electrical properties of a representative volume elements of a plain woven textile. Dynamic relaxation to solve the mechanical fields and the electrical and thermal fields is solved statically for a given mechanical state. The simulated electrical responses are fit to a simplified Kirchhoff network model to determine effective resistances of the textile.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Variational projection methods for gradient crystal plasticity using Lie algebras

Summary A computational method is developed for evaluating the plastic strain gradient hardening term within a crystal plasticity formulation. While such gradient terms reproduce the size effects exhibited in experiments, incorporating derivatives of the plastic strain yields a nonlocal constitutive model. Rather than applying mixed methods, we propose an alternative method whereby the plastic deformation gradient is variationally projected from the elemental integration points onto a smoothed nodal field. Crucially, the projection utilizes the mapping between Lie groups and algebras in order to preserve essential physical properties, such as orthogonality of the plastic rotation tensor. Following the projection, the plastic strain field is directly differentiated to yield the Nye tensor. Additionally, an augmentation scheme is introduced within the global Newton iteration loop such that the computed Nye tensor field is fed back into the stress update procedure. Effectively, this method results in a fully implicit evolution of the constitutive model within a traditional displacement‐based formulation. An elemental projection method with explicit time integration of the plastic rotation tensor is compared as a reference. A series of numerical tests are performed for several element types in order to assess the robustness of the method, with emphasis placed upon polycrystalline domains and multi‐axis loading. Copyright © 2016 John Wiley & Sons, Ltd.

Truster, Timothy J.↗
DOE OSTI2018

Topology optimization of finite strain viscoplastic systems under transient loads [Dynamic topology optimization based on finite strain visco-plasticity]

In this paper, a transient finite strain viscoplastic model is implemented in a gradient-based topology optimization framework to design impact mitigating structures. The model's kinematics relies on the multiplicative split of the deformation gradient, and the constitutive response is based on isotropic hardening viscoplasticity. To solve the mechanical balance laws, the implicit Newmark-beta method is used together with a total Lagrangian finite element formulation. The optimization problem is regularized using a partial differential equation filter and solved using the method of moving asymptotes. Sensitivities required to solve the optimization problem are derived using the adjoint method. To demonstrate the capability of the algorithm, several protective systems are designed, in which the absorbed viscoplastic energy is maximized. Finally, the numerical examples demonstrate that transient finite strain viscoplastic effects can successfully be combined with topology optimization.

42 ENGINEERING↗
DOE OSTI2022

The Schwarz alternating method for transient solid dynamics

Abstract In our earlier work, we formulated the Schwarz alternating method as a means for concurrent multiscale coupling in finite deformation solid mechanics for quasi‐static problems. Herein, we advance this method for the study of transient dynamic multiscale solid mechanics problems where information is exchanged back and forth between small and large scales. The extension to dynamics relies on the notion of a global time stepper. Within each global time step, the subdomains are coupled by the standard Schwarz iterative process. Remarkably, each subdomain can use its own time step or even its own time integrator to advance its solution in time, provided that they synchronize at each global time step. We study the performance of the Schwarz method on several examples designed for this purpose. Our numerical experiments demonstrate that the method is capable of coupling regions with different mesh resolutions, different element types, and different time integration schemes (e.g., implicit and explicit), all without introducing any artifacts that afflict other coupling methods for transient dynamics. Finally, we apply the dynamic Schwarz alternating method to the simulation of a bolted joint subjected to dynamic loading, as a demonstration of the performance of the method in a realistic scenario.

Mota, Alejandro↗
DOE OSTI2024

A large deformation multiphase continuum mechanics model for shock loading of soft porous materials

A large deformation, coupled finite-element (FE) model is developed to simulate the multiphase response of soft porous materials subjected to high strain-rate loading. The approach is based on the theory of porous media (TPM) at large deformations. Simplifications to the one-dimensional regime studied in the numerical simulations follow. An overview of several different time integration schemes is presented for the purpose of solving the nonlinear dynamic coupled balance of momenta (mixture and fluid) and balance of mass of the mixture equations. Numerical examples are presented for (i) verification against closed-form analytical solutions assuming small loads, (ii) demonstrating large deformation effects at high strain-rate, and (iii) showing differences in deformations between a single-phase elastodynamics model with occluded compressible pore fluid and a multiphase poroelastodynamics model at high strain-rate. The multiphase model shows that the relative motion of the pore fluid significantly dampens the deformation response of the solid skeleton as compared to the single-phase model, and makes it possible to extract quantitative values for the stresses of the different constituents, thereby allowing one to form preliminary conclusions about the onset of damage in the solid skeleton. The novelty of the current work is developing a multiphase, large deformation, mixture theory numerical model for high strain-rate loading of soft porous materials. It was discovered that explicit, adaptive time-stepping Runge–Kutta schemes offer high accuracy at relatively low cost when compared to traditional implicit or explicit central difference time-stepping schemes for shock-like loadings. Here, shock viscosity is added to the mixture momentum balance equation to regularize the shock front, and a stabilization term is added to the mixture mass balance equation to stabilize equal order interpolation finite elements for the coupled finite element solution of multiphase materials.

Engineering↗
DOE OSTI2020

A least-squares finite element method based on the Helmholtz decomposition for hyperbolic balance laws

In this paper, a least-squares finite element method for scalar nonlinear hyperbolic balance laws is proposed and studied. The approach is based on a formulation that utilizes an appropriate Helmholtz decomposition of the flux vector and is related to the standard notion of a weak solution. This relationship, together with a corresponding connection to negative-norm least-squares, is described in detail. As a consequence, an important numerical conservation theorem is obtained, similar to the famous Lax–Wendroff theorem. The numerical conservation properties of the method in this paper do not fall precisely in the framework introduced by Lax and Wendroff, but they are similar in spirit as they guarantee that when L 2 convergence holds, the resulting approximations approach a weak solution to the hyperbolic problem. The least-squares functional is continuous and coercive in an H -1 -type norm, but not L 2 -coercive. Nevertheless, the L 2 convergence properties of the method are discussed. Convergence can be obtained either by an explicit regularization of the functional, that provides control of the L 2 norm, or by properly choosing the finite element spaces, providing implicit control of the L 2 norm. Numerical results for the inviscid Burgers equation with discontinuous source terms are shown, demonstrating the L 2 convergence of the obtained approximations to the physically admissible solution. The numerical method utilizes a least-squares functional, minimized on finite element spaces, and a Gauss–Newton technique with nested iteration. Finally, we believe that the linear systems encountered with this formulation are amenable to multigrid techniques and combining the method with adaptive mesh refinement would make this approach an efficient tool for solving balance laws (this is the focus of a future study).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Coupling between radiative flux divergence and turbulence near the surface

Near‐surface turbulent flux and radiation divergence field observations are analysed over a grass‐covered surface located at the Wageningen observatory, the Netherlands. Net radiative flux divergence appears to be a large component of the energy budget near the surface, accounting for a cooling rate of several tens of degrees per day. Long‐wave radiation divergence dominates this radiation divergence flux. We show here that long‐wave flux divergence near the surface is strongly coupled to sensible heat flux, except in high relative humidity (>90%) and foggy conditions. The net long‐wave radiative flux divergence exhibits a sharp gradient within the first 20 m above the surface. This flux divergence is itself strongly coupled to sensible heat flux through adjustments in surface‐layer profiles. Nonetheless, no systematic effect of radiation is witnessed on the turbulent temperature spectrum so that the main effect of near‐surface radiation is on the mean heat budget. As typical flux‐gradient relationships are derived based on observations taken in the near‐surface boundary‐layer region where sharp long‐wave divergence is present, we suspect that those relationships implicitly represent some of the long‐wave divergence term. A modification of Monin–Obukhov Similarity Theory to include the effect of radiative divergence is proposed and discussed. This calls for independent measurements of turbulent fluxes and radiative flux divergence near the surface to re‐derive turbulent flux‐gradient relationships independently of radiative effects.

Gentine, Pierre↗