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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

A Verified Conformal Decomposition Finite Element Method for Implicit, Many-Material Geometries

As computing power rapidly increases, quickly creating a representative and accurate discretization of complex geometries arises as a major hurdle towards achieving a next generation simulation capability. Component definitions may be in the form of solid (CAD) models or derived from 3D computed tomography (CT) data, and creating a surface-conformal discretization may be required to resolve complex interfacial physics. Furthermore, the Conformal Decomposition Finite Element Methods (CDFEM) has been shown to be an efficient algorithm for creating conformal tetrahedral discretizations of these implicit geometries without manual mesh generation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

An implicit, sharp numerical treatment of viscous terms at arbitrarily shaped liquid-gas interfaces in evaporative flows

We report a novel methodology for accurate treatment of viscous terms in evaporation problems. The proposed scheme is an extension of the sharp viscous treatment of Kang et al. (2000) [7] to 3D phase change problems. To ensure accuracy and grid converging solutions, a new implicit approach to computing viscous fluxes across the phase interfaces is proposed, which was previously unavailable in fixed grid numerical schemes. Analytical relations were derived for the jump in velocity gradients across the 2D and 3D phase interfaces, an important constituent of the proposed scheme. The relations show a non-vanishing jump in the tangential gradients across the phase interface that are associated with evaporative flux and interfacial curvature. The proposed methodology demonstrated first order accuracy in canonical test cases. It is general and applicable to arbitrarily oriented interfaces, and can be readily implemented in existing evaporation flow solvers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

An implicit particle code with exact energy and charge conservation for studies of dense plasmas in axisymmetric geometries

A collisional particle code based on implicit energy- and charge-conserving methods in axisymmetric geometries is presented. A new particle pusher for axisymmetric systems is introduced that is compatible with exact energy and charge conservation and yields improved accuracy compared to other methods. How to appropriately treat all aspects of the algorithm near the r = 0 axis of symmetry is described in detail. Here, the axisymmetric model is verified by simulating the free expansion of a plasma sphere in 2D cylindrical and 1D spherical geometries. The algorithm's ability to study the dynamic compression of a dense plasma is illustrated by simulating the dynamic Z-pinch in 1D cylindrical geometry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Spatiotemporally dynamic implicit large eddy simulation using machine learning classifiers

In this article, we utilize machine learning to dynamically determine if a point on the computational grid requires implicit numerical dissipation for large eddy simulation (LES). The decision making process is learnt through a priori training on quantities derived from direct numerical simulation (DNS) data. In particular, we compute eddy-viscosities obtained through the coarse-graining of DNS quantities and utilize their projection onto a Gaussian distribution to categorize areas that may require dissipation. If our learning determines that closure is necessary, an upwinded scheme is utilized for computing the non-linear Jacobian. In contrast, if it is determined that closure is unnecessary, a symmetric and second-order accurate energy and enstrophy preserving Arakawa scheme is utilized instead. This results in a closure framework that precludes the specification of any model-form for the small scale contributions of turbulence but deploys an appropriate numerical dissipation from explicit closure driven hypotheses. Here, this methodology is deployed for the Kraichnan turbulence test-case and assessed through various statistical quantities such as angle-averaged kinetic energy spectra and vorticity structure functions. Our framework thus establishes a link between the use of explicit LES ideologies for closure and numerical dissipation-based modeling of turbulence leading to improved statistical fidelity of a posteriori simulations.

42 ENGINEERING↗
DOE OSTI2022

An unconditionally stable, time-implicit algorithm for solving the one-dimensional Vlasov–Poisson system

The development of an implicit, unconditionally stable, numerical method for solving the Vlasov–Poisson system in one dimension using a phase-space grid is presented. The algorithm uses the Crank–Nicolson discretization scheme and operator splitting allowing for direct solution of the finite difference equations. This method exactly conserves particle number, enstrophy and momentum. A variant of the algorithm which does not use splitting also exactly conserves energy but requires the use of iterative solvers. This algorithm has no dissipation and thus fine-scale variations can lead to oscillations and the production of negative values of the distribution function. We find that overall, the effects of negative values of the distribution function are relatively benign. We consider a variety of test cases that have been used extensively in the literature where numerical results can be compared with analytical solutions or growth rates. We examine higher-order differencing and construct higher-order temporal updates using standard composition methods.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Implementation of INDO/SCI with COSMO Implicit Solvation and Benchmarking for Solvatochromic Shifts

Accurate and rapid quantum mechanical prediction of solvatochromic shifts, particularly in systems where charge transfer plays a significant role, is important for many aspects of molecular and material design. Although the semiempirical INDO/SCI approach is computationally efficient and performs well for charge-transfer states, the availability of implicit solvent approaches has been limited. As such, we implement the COSMO solvent model with a perturbative state-specific correction to the excited-state energies with the INDO/SCI method. We show that for a series of prototypical π-conjugated molecules, our newly implemented INDO/SCI/COSMO model yields more accurate absorption energies and comparably accurate solvatochromic shifts to those computed using TD-ωB97XD and CIS with COSMO solvation at a substantially lower computational cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Capturing dynamical correlations using implicit neural representations

Abstract Understanding the nature and origin of collective excitations in materials is of fundamental importance for unraveling the underlying physics of a many-body system. Excitation spectra are usually obtained by measuring the dynamical structure factor, S ( Q , ω ), using inelastic neutron or x-ray scattering techniques and are analyzed by comparing the experimental results against calculated predictions. We introduce a data-driven analysis tool which leverages ‘neural implicit representations’ that are specifically tailored for handling spectrographic measurements and are able to efficiently obtain unknown parameters from experimental data via automatic differentiation. In this work, we employ linear spin wave theory simulations to train a machine learning platform, enabling precise exchange parameter extraction from inelastic neutron scattering data on the square-lattice spin-1 antiferromagnet La 2 NiO 4 , showcasing a viable pathway towards automatic refinement of advanced models for ordered magnetic systems.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Improved AlphaFold modeling with implicit experimental information

Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Multidimensional low-Mach number time-implicit hydrodynamic simulations of convective helium shell burning in a massive star

A realistic parametrization of convection and convective boundary mixing in conventional stellar evolution codes is still the subject of ongoing research. Furthermore, to improve the current situation, multidimensional hydrodynamic simulations are used to study convection in stellar interiors. Such simulations are numerically challenging, especially for flows at low Mach numbers which are typical for convection during early evolutionary stages. We explore the benefits of using a low-Mach hydrodynamic flux solver and demonstrate its usability for simulations in the astrophysical context. Simulations of convection for a realistic stellar profile are analyzed regarding the properties of convective boundary mixing. The time-implicit Seven-League Hydro (SLH) code was used to perform multidimensional simulations of convective helium shell burning based on a 25 M ⊙ star model. The results obtained with the low-Mach AUSM + -up solver were compared to results when using its non low-Mach variant AUSM B + -up. We applied well-balancing of the gravitational source term to maintain the initial hydrostatic background stratification. The computational grids have resolutions ranging from 180 × 90 2 to 810 × 540 2 cells and the nuclear energy release was boosted by factors of 3 × 10 3 , 1 × 10 4 , and 3 × 10 4 to study the dependence of the results on these parameters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

A generalized implicit algorithm for multi-dimensional particle-in-cell simulations in Cartesian geometry

An implicit multi-dimensional particle-in-cell (PIC) code is developed to study the interaction of ultrashort pulse lasers with matter. The algorithm is based on current density decomposition and is only marginally more complicated compared to explicit PIC codes, but it completely eliminates grid heating and possesses good energy conserving properties with relaxed time step and grid resolution. This is demonstrated in a test case study, in which high-energy protons are generated from a thin carbon foil at solid density using linear and circular polarizations. The grid heating rate is estimated to be 1-10 eV/ps.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Spacecraft charging analysis with the implicit particle-in-cell code iPic3D

We present the first results on the analysis of spacecraft charging with the implicit particle-in-cell code iPic3D, designed for running on massively parallel supercomputers. The numerical algorithm is presented, highlighting the implementation of the electrostatic solver and the immersed boundary algorithm; the latter which creates the possibility to handle complex spacecraft geometries. As a first step in the verification process, a comparison is made between the floating potential obtained with iPic3D and with Orbital Motion Limited theory for a spherical particle in a uniform stationary plasma. Second, the numerical model is verified for a CubeSat benchmark by comparing simulation results with those of PTetra for space environment conditions with increasing levels of complexity. In particular, we consider spacecraft charging from plasma particle collection, photoelectron and secondary electron emission. The influence of a background magnetic field on the floating potential profile near the spacecraft is also considered. Although the numerical approaches in iPic3D and PTetra are rather different, good agreement is found between the two models, raising the level of confidence in both codes to predict and evaluate the complex plasma environment around spacecraft.

42 ENGINEERING↗
DOE OSTI2014

A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect

To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability, and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (≤45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 Å and an overall minimum RMSD of 1.9 Å from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ∼ 1.0 °C of melting temperatures, as compared with the extensive experimental data. In addition, the model could provide the ensemble of possible 3D structures for a short RNA at a given temperature/salt condition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Thermal equilibrium properties of surface hopping with an implicit Langevin bath

The ability of fewest switches surface hopping (FSSH) approach, where the classical degrees of freedom are coupled to an implicit Langevin bath, to establish and maintain an appropriate thermal equilibrium was evaluated in the context of a three site model for electron transfer. The electron transfer model consisted of three coupled diabatic states that each depends harmonically on the collective bath coordinate. This results in three states with increasing energy in the adiabatic representation. The adiabatic populations and distributions of the collective solvent coordinate were monitored during the course of 250 ns FSSH-Langevin (FSSH-L) simulations performed at a broad range of temperatures and for three different nonadiabatic coupling strengths. The agreement between the FSSH-L simulations and numerically exact results for the adiabatic population ratios and solvent coordinate distributions was generally favorable. The FSSH-L method produces a correct Boltzmann distribution of the solvent coordinate on each of the adiabats, but the integrated populations are slightly incorrect because FSSH does not rigorously obey detailed balance. The overall agreement is better at high temperatures and for high nonadiabatic coupling, which agrees with a previously reported analytical and simulation analysis [J. R. Schmidt, P. V. Parandekar, and J. C. Tully, J. Chem. Phys. 129, 044104 (2008)] on a two-level system coupled to a classical bath.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

An implicit divalent counterion force field for RNA molecular dynamics

How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg{sup 2+} screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

The Poisson–Boltzmann model for implicit solvation of electrolyte solutions: Quantum chemical implementation and assessment via Sechenov coefficients

Here, we present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the solute. A hierarchy of approximations for this model includes a linear approximation for weak electrostatic potentials, finite size of the mobile electrolyte ions, and a Stern-layer correction. Recasting the Poisson-Boltzmann equations into Euler-Lagrange equations then significantly simplifies the derivation of the free energy of solvation for these approximate models. The parameters of the model are either fit directly to experimental observables-e.g., the finite ion size-or optimized for agreement with experimental results. Experimental data for this optimization are available in the form of Sechenov coefficients that describe the linear dependence of the salting-out effect of solutes with respect to the electrolyte concentration. In the final part, we rationalize the qualitative disagreement of the finite ion size modification to the Poisson-Boltzmann model with experimental observations by taking into account the electrolyte concentration dependence of the Stern layer. A route toward a revised model that captures the experimental observations while including the finite ion size effects is then outlined. This implementation paves the way for the study of electrochemical and electrocatalytic processes of molecules and cluster models with accurate electronic structure methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

An implicit solution for Asay foil trajectories generated by separable, sustained-production ejecta source models

We present a simple implicit solution for the time-dependent trajectory of a thin Asay foil ejecta diagnostic for the general case where the impinging ejecta cloud is generated by a source function characterized by an arbitrary (sustained) time dependence and a time-independent (stationary) particle velocity distribution. In the limit that the source function time dependence becomes a delta function, this solution—which is amenable to rapid numerical calculations of arbitrary accuracy—exactly recovers a previously published solution for the special case of instantaneous ejecta production. We also derive simple expressions for the free-surface arrival (catch-up) time as well as the true ejecta areal mass accumulation on the accelerating foil and place bounds on the level of error incurred when applying instant-production mass solutions to a sustained-production trajectory. We demonstrate these solutions with example calculations for hypothetical source functions spanning a wide range of ejecta production durations, velocity distributions, and temporal behaviors. These calculations demonstrate how the foil trajectory is often insensitive to the temporal dependence of the source function, instead being dominated by the velocity distribution. We quantify this insensitivity using a “compatibility score” metric. Under certain conditions, one may capitalize upon this insensitivity to obtain a good approximation of the second integral of the velocity distribution from the observed foil trajectory.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Semi-implicit continuum kinetic modeling of weakly collisional parallel transport in a magnetic mirror

We present implicit-explicit (IMEX) kinetic simulations of weakly collisional parallel plasma transport in magnetic mirror configurations using the continuum code COGENT. The numerical scheme employs a Jacobian-free Newton–Krylov method with algebraic multigrid preconditioning to overcome the severe time step limitations imposed by strong mirror forces in fully explicit schemes. Applied to parameters relevant to the Wisconsin HTS Axisymmetric Mirror experiment, the IMEX approach enables time steps up to 2.5×10 4 times larger than those permitted by explicit methods, resulting in a 2500× speedup in 1D–2V simulations of parallel transport with kinetic ions and Boltzmann electrons. Additionally, a reduced bounce-averaged model for a square mirror is implemented to support the computationally intensive fully kinetic simulations. The bounce-averaged formulation is used to evaluate the numerical convergence of the velocity-space discretization algorithms and to assess the role of the collision model by comparing simulations employing the nonlinear Fokker–Planck and the simplified Lenard–Bernstein–Dougherty collision operators.

Collision theories↗