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At least 397 records · Page 22

Sierra/SolidMechanics 5.6 User's Manual

Sierra/SolidMechanics (Sierra/SM) is a three-dimensional solid mechanics code with a versatile element library, nonlinear material models, large deformation capabilities, and contact. It is built on the SIERRA Framework. SIERRA provides a data management framework in a parallel computing environment that allows the addition of capabilities in a modular fashion. Contact capabilities are parallel and scalable. This document provides information about the functionality in Sierra/SM and the command structure required to access this functionality in a user input file. This document is divided into chapters based primarily on functionality. For example, the command structure related to the use of various element types is grouped in one chapter; descriptions of material models are grouped in another chapter. Sierra/SM provides both explicit transient dynamics and implicit quasistatics and dynamics capabilities. Both the explicit and implicit modules are highly scalable in a parallel computing environment. In the past, the explicit and implicit capabilities were provided by two separate codes, known as Presto and Adagio, respectively. These capabilities have been consolidated into a single code. The executable is named Adagio, but it provides the full suite of solid mechanics capabilities, for both implicit and explicit. The Presto executable has been disabled as a consequence of this consolidation.

97 MATHEMATICS AND COMPUTING↗

A cubic spline approximation for problems in fluid mechanics

A cubic spline approximation is presented which is suited for many fluid-mechanics problems. This procedure provides a high degree of accuracy, even with a nonuniform mesh, and leads to an accurate treatment of derivative boundary conditions. The truncation errors and stability limitations of several implicit and explicit integration schemes are presented. For two-dimensional flows, a spline-alternating-direction-implicit method is evaluated. The spline procedure is assessed, and results are presented for the one-dimensional nonlinear Burgers' equation, as well as the two-dimensional diffusion equation and the vorticity-stream function system describing the viscous flow in a driven cavity. Comparisons are made with analytic solutions for the first two problems and with finite-difference calculations for the cavity flow.

Rubin, S. G.↗

Kalman filter estimation of human pilot-model parameters

The parameters of a human pilot-model transfer function are estimated by applying the extended Kalman filter to the corresponding retarded differential-difference equations in the time domain. Use of computer-generated data indicates that most of the parameters, including the implicit time delay, may be reasonably estimated in this way. When applied to two sets of experimental data obtained from a closed-loop tracking task performed by a human, the Kalman filter generated diverging residuals for one of the measurement types, apparently because of model assumption errors. Application of a modified adaptive technique was found to overcome the divergence and to produce reasonable estimates of most of the parameters.

Schiess, J. R.↗

A two dimensional model of viscous slot flow

The effects of viscosity on flows through slots are investigated. Using Briley's formulation of the Alternating Direction Implicit method together with the Thompson transformation, numerical solution of viscous incompressible flow through a slot is simulated, for Reynolds number 1000 and openness ratio one tenth. The problem is formulated in terms of stream function and vorticity. A wall iteration of Israeli type is employed to iteratively induce the no slip condition on velocity.

Cooke, C. H.↗

Reaction Dynamics of Cyanohydrins with Hydrosulfide in Water

We studied the reaction dynamics of a proposed prebiotic reaction theoretically. The chemical process involves acetone cyanohydrin or formalcyanohydrin reacting with hydrosulfide in an aqueous environment. Rate constants and populations of reactant and product bimolecular geometric orientations for the reactions were obtained by using density functional theory for the energies, transition-state theory for the rates, and matrix exponentiation as well as the hybrid tau-leaping algorithm for the population dynamics. The role of including the solvent explicitly versus implicitly was also investigated. We found that adding explicit water or hydrogen sulfide molecules lowers the activation energy barrier and leads to a more efficient reaction pathway. In particular, hydrogen sulfide was a better proton donor. Lastly, we studied the role of including more than one reactant and product bimolecular orientation geometry in the dynamics. Including all initial pathways, reactant to reactant, product to product, reactant to product, and product to reactant led to a larger reaction rate constant compared to the single minimum energy pathway approach. Overall, we found that most reactions which involve formalcyanohydrin occur more rapidly or at the same speed as reactions which involve acetone cyanohydrin at room temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Viscous flow solutions with a cubic spline approximation

A cubic spline approximation is used for the solution of several problems in fluid mechanics. This procedure provides a high degree of accuracy even with a nonuniform mesh, and leads to a more accurate treatment of derivative boundary conditions. The truncation errors and stability limitations of several typical integration schemes are presented. For two-dimensional flows a spline-alternating-direction-implicit (SADI) method is evaluated. The spline procedure is assessed and results are presented for the one-dimensional nonlinear Burgers' equation, as well as the two-dimensional diffusion equation and the vorticity-stream function system describing the viscous flow in a driven cavity. Comparisons are made with analytic solutions for the first two problems and with finite-difference calculations for the cavity flow.

Rubin, S. G.↗

Accuracy and convergence of a finite element algorithm for turbulent boundary layer flow

The Galerkin-Weighted Residuals formulation is employed to derive an implicit finite element solution algorithm for the nonlinear parabolic partial differential equation system governing turbulent boundary layer flow. Solution accuracy and convergence with discretization refinement are quantized in several error norms using linear and quadratic basis functions. Richardson extrapolation is used to isolate integration truncation error in all norms, and Newton iteration is employed for all equation solutions performed in double-precision. The mathematical theory supporting accuracy and convergence concepts for linear elliptic equations appears extensible to the nonlinear equations characteristic of turbulent boundary layer flow.

Soliman, M. O.↗

Interplanetary Program to Optimize Simulated Trajectories (IPOST). Volume 1: User's guide

IPOST is intended to support many analysis phases, from early interplanetary feasibility studies through spacecraft development and operations. The IPOST output provides information for sizing and understanding mission impacts related to propulsion, guidance, communications, sensor/actuators, payload, and other dynamic and geometric environments. IPOST models three degree of freedom trajectory events, such as launch/ascent, orbital coast, propulsive maneuvering (impulsive and finite burn), gravity assist, and atmospheric entry. Trajectory propagation is performed using a choice of Cowell, Encke, Multiconic, Onestep, or Conic methods. The user identifies a desired sequence fo trajectory events, and selects which parameters are independent (controls) and dependent (targets), as well as other constraints and the coat function. Targeting and optimization is performed using the Stanford NPSOL algorithm. IPOST structure allows sub-problems within a master optimization problem to aid in the general constrained parameter optimization solution. An alternate optimization method uses implicit simulation and collocation techniques.

Hong, P. E.↗

Correction to “Toward Chemical Accuracy for Chemi- and Physisorption with an Efficient Density Functional”

In the original manuscript, the value of parameter c was not explicitly provided. We wish to clarify that c was refitted to the hydrogen atom exchange energy, using the updated value of κ. With the updated κ = 0.2501, the optimized value of the parameter is c = 0.391596228. These values supersede any implicit assumptions about c in the original manuscript, and readers are encouraged to use these parameters for reproducing the results presented therein.

Adsorption↗

Accurate Modeling of Bromide and Iodide Hydration with Data-Driven Many-Body Potentials

Ion–water interactions play a central role in determining the properties of aqueous systems in a wide range of environments. However, a quantitative understanding of how the hydration properties of ions evolve from small aqueous clusters to bulk solutions and interfaces remains elusive. Here, we introduce the second generation of data-driven many-body energy (MBnrg) potential energy functions (PEFs) representing bromide–water and iodide–water interactions. The MB-nrg PEFs use permutationally invariant polynomials to reproduce two-body and three-body energies calculated at the coupled cluster level of theory, and implicitly represent all higher-body energies using classical many-body polarization. Further, a systematic analysis of the hydration structure of small Br - (H 2 O) n and I - (H 2 O) n clusters demonstrates that the MBnrg PEFs predict interaction energies in quantitative agreement with “gold standard” coupled cluster reference values. Importantly, when used in molecular dynamics simulations carried out in the isothermal-isobaric ensemble for single bromide and iodide ions in liquid water, the MB-nrg PEFs predict extended X-ray absorption fine structure (EXAFS) spectra that accurately reproduce the experimental spectra, which thus allows for characterizing the hydration structure of the two ions with high level of confidence.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microwave backscattering theory and active remote sensing of the ocean surface

The status is reviewed of electromagnetic scattering theory relative to the interpretation of microwave remote sensing data acquired from spaceborne platforms over the ocean surface. Particular emphasis is given to the assumptions which are either implicit or explicit in the theory. The multiple scale scattering theory developed during this investigation is extended to non-Gaussian surface statistics. It is shown that the important statistic for the case is the probability density function of the small scale heights conditioned on the large scale slopes; this dependence may explain the anisotropic scattering measurements recently obtained with the AAFE Radscat. It is noted that present surface measurements are inadequate to verify or reject the existing scattering theories. Surface measurements are recommended for qualifying sensor data from radar altimeters and scatterometers. Additional scattering investigations are suggested for imaging type radars employing synthetically generated apertures.

Brown, G. S.↗

Interplanetary program to optimize simulated trajectories (IPOST). Volume 4: Sample cases

The Interplanetary Program to Optimize Simulated Trajectories (IPOST) is intended to support many analysis phases, from early interplanetary feasibility studies through spacecraft development and operations. The IPOST output provides information for sizing and understanding mission impacts related to propulsion, guidance, communications, sensor/actuators, payload, and other dynamic and geometric environments. IPOST models three degree of freedom trajectory events, such as launch/ascent, orbital coast, propulsive maneuvering (impulsive and finite burn), gravity assist, and atmospheric entry. Trajectory propagation is performed using a choice of Cowell, Encke, Multiconic, Onestep, or Conic methods. The user identifies a desired sequence of trajectory events, and selects which parameters are independent (controls) and dependent (targets), as well as other constraints and the cost function. Targeting and optimization are performed using the Standard NPSOL algorithm. The IPOST structure allows sub-problems within a master optimization problem to aid in the general constrained parameter optimization solution. An alternate optimization method uses implicit simulation and collocation techniques.

Hong, P. E.↗

Efficient 3D Molecular Design with an E(3) Invariant Transformer VAE

This work introduces a three-dimensional (3D) invariant graph-to-string transformer variational autoencoders (VAE) (Vagrant) for generating molecules with accurate density functional theory (DFT)-level properties. Vagrant learns to model the joint probability distribution of a 3D molecular structure and its properties by encoding molecular structures into a 3D-aware latent space. Directed navigation through this latent space implicitly optimizes the 3D structure of a molecule, and the latent embedding can be used to condition a generative transformer to predict the candidate structure as a one-dimensional (1D) sequence. Additionally, we introduce two novel sampling methods that exploit the latent characteristics of a VAE to improve performance. Here, we show that our method outperforms comparable 3D autoregressive and diffusion methods for predicting quantum chemical property values of novel molecules in terms of both sample quality and computational efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transitioning GlideinWMS, a multi domain distributed workload manager, from GSI proxies to tokens and other granular credentials

GlideinWMS is a distributed workload manager that has been used in production for many years to provision resources for experiments like CERN’s CMS, many Neutrino experiments, and the OSG. Its security model was based mainly on GSI (Grid Security Infrastructure), using X.509 certificate proxies and VOMS (Virtual Organization Membership Service) extensions. Even when other credentials, like SSH keys, were used to authenticate with resources, proxies were also added all the time, to establish the identity of the requestor and the associated memberships or privileges. This single credential was used for everything and was, often implicitly, forwarded wherever needed. The addition of identity and access tokens and the phase-out of GSI forced us to reconsider the security model of GlideinWMS, to handle multiple credentials which can differ in type, technology, and functionality. Both identity tokens and access tokens are supported. GSI proxies even if no more mandatory, are still used, together with various JWT (JSON Web Token) based tokens and other certificates. The functionality of the credentials, defined by issuer, audience, and scope, also differ: a credential can allow access to a computing resource, or can protect the GlideinWMS framework from tampering, or can grant read or write access to storage, can provide an identity for accounting or auditing, or can provide a combination of any the formers. Furthermore, the tools in use do not include automatic forwarding and renewal of the new credentials so credential lifetime and renewal requirements became part of the discussion as well. In this paper, we will present how GlideinWMS was able to change its design and code to respond to all these changes.

97 MATHEMATICS AND COMPUTING↗

Comparison of dynamical approximation schemes for non-linear gravitational clustering

We have recently conducted a controlled comparison of a number of approximations for gravitational clustering against the same n-body simulations. These include ordinary linear perturbation theory (Eulerian), the adhesion approximation, the frozen-flow approximation, the Zel'dovich approximation (describable as first-order Lagrangian perturbation theory), and its second-order generalization. In the last two cases we also created new versions of approximation by truncation, i.e., smoothing the initial conditions by various smoothing window shapes and varying their sizes. The primary tool for comparing simulations to approximation schemes was crosscorrelation of the evolved mass density fields, testing the extent to which mass was moved to the right place. The Zel'dovich approximation, with initial convolution with a Gaussian e(exp -k(exp 2)/k(exp 2, sub G)) where k(sub G) is adjusted to be just into the nonlinear regime of the evolved model (details in text) worked extremely well. Its second-order generalization worked slightly better. All other schemes, including those proposed as generalizations of the Zel'dovich approximation created by adding forces, were in fact generally worse by this measure. By explicitly checking, we verified that the success of our best-choice was a result of the best treatment of the phases of nonlinear Fourier components. Of all schemes tested, the adhesion approximation produced the most accurate nonlinear power spectrum and density distribution, but its phase errors suggest mass condensations were moved to slightly the wrong location. Due to its better reproduction of the mass density distribution function and power spectrum, it might be preferred for some uses. We recommend either n-body simulations or our modified versions of the Zel'dovich approximation, depending upon the purpose. The theoretical implication is that pancaking is implicit in all cosmological gravitational clustering, at least from Gaussian initial conditions, even when subcondensations are present.

Melott, Adrian L.↗

A Framework for Distributed Approximation of Moments with Higher-Order Derivatives through Automatic Differentiation

We present a framework for the distributed approximation of moments, enabling the evaluation of the uncertainty in a dynamical system. The first and second moment, mean, and variance are computed with up to third-order Taylor series expansion. The required derivatives for the expansion are generated automatically by automatic differentiation and propagated through an implicit time stepper. The computational kernels are the accumulation of the derivatives (Jacobian, Hessian, tensor) and the covariance matrix. We apply distributed parallelism to the Hessian or third-order tensor, and the user merely has to provide a function for the differential equation, thus achieving similar ease of use as Monte Carlo-based methods. We demonstrate our approach using with benchmarks on Theta, a KNL-based system at the Argonne Leadership Computing Facility.

Automatic Differentiation↗

On the effect of using the Shapiro filter to smooth winds on a sphere

Spatial differencing schemes which are not enstrophy conserving nor implicitly damping require global filtering of short waves to eliminate the build-up of energy in the shortest wavelengths due to aliasing. Takacs and Balgovind (1983) have shown that filtering on a sphere with a latitude dependent damping function will cause spurious vorticity and divergence source terms to occur if care is not taken to ensure the irrotationality of the gradients of the stream function and velocity potential. Using a shallow water model with fourth-order energy-conserving spatial differencing, it is found that using a 16th-order Shapiro (1979) filter on the winds and heights to control nonlinear instability also creates spurious source terms when the winds are filtered in the meridional direction.

Takacs, L. L.↗

Beyond Mechanism Design

The field of mechanism design is concerned with setting (incentives superimposed on) the utility functions of a group of players so as to induce desirable joint behavior of those players. It arose in the context of traditional equilibrium game theory applied to games involving human players. This has led it to have many implicit restrictions, which strongly limits its scope. In particular, it ignores many issues that are crucial for systems that are large (and therefore far off-equilibrium in general) and/or composed of non-human players (e.g., computer-based agents). This also means it has concentrated on issues that are often irrelevant in those broader domains (e.g., incentive compatibility). This paper illustrates these shortcomings by reviewing some of the recent theoretical work on the design of collectives, a body of work that constitutes a substantial broadening of mechanism design. It then presents computer experiments based on a recently suggested nanotechnology testbed that demonstrates the power of that extended version of mechanism design.

Wolpert, David H.↗