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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Advanced time integration algorithms for dislocation dynamics simulations of work hardening

Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relative to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Effects of Surface Orientation and Termination Plane on Glass‐to‐Crystal Transformation of Lithium Disilicate by Molecular Dynamics Simulations

Glass‐to‐crystal transformation of lithium disilicate is studied using molecular dynamics simulations using an effective partial charge potential. The structural evolution of the interface between glassy and crystalline lithium disilicate is analyzed to simulate crystallization of glass on pre‐existing crystal seeds. Besides previously used atomic number density, the distribution of Q n species (Si tetrahedra with n bridging oxygen) is shown to be an effective parameter for following this transformation quantitatively. The early stages of crystal growth are significantly affected by the orientation and termination of the surface of adjacent crystal, as indicated by calculated atomic density, partial ordering, atomic segregation, and an increase in Q 3 concentration. In particular, under‐coordinated Si within the outer crystal layer is found to be most effective in transforming the amorphous structure toward crystallinity. The increase in Q 3 in the glass close to interface region most clearly shows the initial stage of lithium disilicate crystal growth.

Sun, Wei↗
DOE OSTI2018

Model Evaluation Report for LNG Dispersion on Fire Dynamics Simulator Version 6.5.3

This report is an assessment of the computational fluid dynamics (CFD) code Fire Dynamics Simulator (FDS), version 6.5.3, using the Model Evaluation Protocol (MEP) for Liquefied Natural Gas (LNG). The MEP consists of model validation and a scientific assessment that encompasses model information and model verification activities. Model validation entails comparison against various field and wind-tunnel trials for LNG and other dense gases with and without obstructions. The results indicate that FDS is generally over-predictive for most of the field scale dense gas releases and cases involving obstructions without requiring a safety factor of 2, however, since there are uncertainties in extrapolating to accident scales a safety factor of 2 (1/2 LFL criteria) may be appropriate. The results of this scientific assessment and prior verification efforts demonstrate the soundness of the numerical techniques and robustness of FDS. The validation results indicate that FDS is suitable for modeling dense gas dispersion with and without obstructions.

03 NATURAL GAS↗
DOE OSTI2015

Direct molecular dynamics simulation of Ge deposition on amorphous SiO 2 at experimentally relevant conditions

Molecular dynamics simulations were used to study Ge island nucleation and growth on amorphous SiO 2 substrates. This process is relevant in selective epitaxial growth of Ge on Si, for which SiO 2 is often used as a template mask. The islanding process was studied over a wide range of temperatures and fluxes, using a recently proposed empirical potential model for the Si–SiO 2 –Ge system. The simulations provide an excellent quantitative picture of the Ge islanding and compare well with detailed experimental measurements. These quantitative comparisons were enabled by an analytical rate model as a bridge between simulations and experiments despite the fact that deposition fluxes accessible in simulations and experiments are necessarily different by many orders of magnitude. In particular, the simulations led to accurate predictions of the critical island size and the scaling of island density as a function of temperature. Lastly, the overall approach used here should be useful not just for future studies in this particular system, but also for molecular simulations of deposition in other materials.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Diffusion of Selective Penetrants in Interfacially Modified Block Copolymers from Molecular Dynamics Simulations

In order to show the influence of the interface on structure and dynamics of microphase separated polymer systems, we study interfacially modified AB block copolymers with small molecule penetrants. The polymers have a random midblock or tapered midblock whose composition varies from pure A to pure B (or from pure B to pure A for an inverse taper) between two pure blocks of A and B. We perform simple coarse-grained molecular dynamics simulations of symmetric polymers that form lamellae. With normal tapering, both polymer and penetrant diffusion parallel to the lamellae increases as taper length increases. Inverse tapered polymers exist in different conformational states (e.g. stretched versus folded back and forth across the interface) with different dynamic behavior, leading to non-monotonic trends in their diffusion. However, the local mixing of monomers (rather than polymer conformation) appears to be the most important factor in determining penetrant diffusion.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Scalable Reactive Molecular Dynamics Simulations for Computational Synthesis

Reactive molecular dynamics (MD) simulation is a powerful research tool for describing chemical reactions. We eliminate the speed-limiting charge iteration in MD with a novel extended-Lagrangian scheme. The extended-Lagrangian reactive MD (XRMD) code drastically improves energy conservation while substantially reducing time-to-solution. Furthermore, we introduce a new polarizable charge equilibration (PQEq) model to accurately predict atomic charges and polarization. The XRMD code based on hybrid message passing+multithreading achieves a weak-scaling parallel efficiency of 0.977 on 786 432 IBM Blue Gene/Q cores for a 67.6 billion-atom system. The performance is portable to the second-generation Intel Xeon Phi, Knights Landing. Blue Gene/Q simulations for the computational synthesis of materials via novel exfoliation mechanisms for synthesizing atomically thin transition metal dichalcogenide layers will dominate nanomaterials science in this century.

Simulation, Modeling, Performance, and Visualizati↗
DOE OSTI2025

Machine learning-accelerated path integral molecular dynamics simulations of reactive organic electrolytes

Hydrogen bonded electrolytes that exhibit accelerated proton transport via sequential reactive hops have drawn interest for their promise in clean energy applications. Molecular dynamics simulations of these electrolytes offer the opportunity to uncover microscopic mechanistic details that could be used to design and tune the properties of candidate electrolyte technologies. However, accurately modeling the proton transfer reactions and transport properties that give rise to high charge conductivites in these electrolytes proves computationally challenging because of the need to perform lengthy condensed phase simulations, treating both the electronic and nuclear degrees of freedom quantum mechanically. In this paper, we demonstrate that such a modeling task can be efficiently achieved with the use of density functional theory (DFT)-trained machine learning potentials (MLP) to accelerate path integral molecular dynamics (PIMD) simulations. We highlight the practical utility of this approach by using it to benchmark how closely PIMD simulations employing different DFT exchange–correlation functionals reproduce the composition-dependent densities, diffusion coefficients, and electrical conductivities of mixtures consisting of imidazole and levulinic acid. Even with the speedup afforded by our MLPs, PIMD simulations remain quite expensive. Furthermore, in order to render PIMD more computationally tractable, we introduce and benchmark the accuracy of a ring polymer contraction approach that leverages a computationally efficient short-range MLP to accelerate our PIMD simulations by an additional factor of four.

Chemical bonding↗
DOE OSTI2013

Molecular Dynamics Simulation of Cascade-Induced Ballistic Helium Resolutioning from Bubbles in Iron

Molecular dynamics simulations have been used to assess the ability of atomic displacement cascades to eject helium from small bubbles in iron. This study of the ballistic resolutioning mechanism employed a recently-developed Fe-He interatomic potential in concert with an iron potential developed by Ackland and co-workers. The primary variables examined were: irradiation temperature (100 and 600K), cascade energy (5 and 20 keV), bubble radius (0.5 and 1.0 nm), and He-to-vacancy ratio in the bubble (0.25, 0.5 and 1.0). Systematic trends were observed for each of these variables. For example, ballistic resolutioning leads to a greater number of helium atoms being displaced from larger bubbles and from bubbles that have a higher He/vacancy ratio (bubble pressure). He resolutioning was reduced at 600K relative to 100K, and for 20 keV cascades relative to 5 keV cascades. Overall, the results indicate a modest level of He removal by ballistic resolutioning. The results can be used to provide guidance in selection of a resolution parameter that can be employed in cluster dynamics models to predict the bubble size distribution that evolves under irradiation.

displacement cascades↗
DOE OSTI2025

Acceleration of Power System Dynamic Simulations Using a Deep Equilibrium Layer and Neural ODE Surrogate

The dominant paradigm for power system dynamic simulation is to build system-level simulations by combining physics-based models of individual components. The sheer size of the system along with the rapid integration of inverter-based resources exacerbates the computational burden of running time domain simulations. Here, in this paper, we propose a data-driven surrogate model based on implicit machine learningspecifically deep equilibrium layers and neural ordinary differential equationsto learn a reduced order model of a portion of the full underlying system. The data-driven surrogate achieves similar accuracy and reduction in simulation time compared to a physics-based surrogate, without the constraint of requiring detailed knowledge of the underlying dynamic models. This work also establishes key requirements needed to integrate the surrogate into existing simulation workflows; the proposed surrogate is initialized to a steady state operating point that matches the power flow solution by design.

Neural ordinary differential equations↗
DOE OSTI2015

Molecular dynamics simulation of radiation damage cascades in diamond

Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Accelerating dissipative particle dynamics simulations on GPUs: Algorithms, numerics and applications

We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores and almost linear weak scaling across a thousand nodes. A unified framework is developed within which the efficient generation of the neighbor list and maintaining particle data locality are addressed. Our algorithm generates strictly ordered neighbor lists in parallel, while the construction is deterministic and makes no use of atomic operations or sorting. Such neighbor list leads to optimal data loading efficiency when combined with a two-level particle reordering scheme. A faster in situ generation scheme for Gaussian random numbers is proposed using precomputed binary signatures. We designed custom transcendental functions that are fast and accurate for evaluating the pairwise interaction. The correctness and accuracy of the code is verified through a set of test cases simulating Poiseuille flow and spontaneous vesicle formation. Computer benchmarks demonstrate the speedup of our implementation over the CPU implementation as well as strong and weak scalability. A large-scale simulation of spontaneous vesicle formation consisting of 128 million particles was conducted to further illustrate the practicality of our code in real-world applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Thermodynamic analysis of the Livermore molecular-dynamics simulations of dislocation-mediated plasticity

Results of recent large-scale molecular dynamics simulations of dislocation-mediated solid plasticity are compared with predictions of the statistical thermodynamic theory of these phenomena. These computational and theoretical analyses are in substantial agreement with each other in both their descriptions of strain-rate-dependent steady plastic flows and of transient stress peaks associated with initially small densities of dislocations. Lastly, the comparisons between the numerical simulations and basic theory reveal inconsistencies in some conventional phenomenological descriptions of solid plasticity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Large-scale molecular dynamics simulations of bubble collapse in water: Effects of system size, water model, and nitrogen

Molecular dynamics simulations in the microcanonical ensemble are performed to study the collapse of a bubble in liquid water using the single-site mW and the four-site TIP4P/2005 water models. To study system size effects, simulations for pure water systems are performed using periodically replicated simulation boxes with linear dimensions, L, ranging from 32 to 512 nm with the largest systems containing 8.7 × 10 6 and 4.5 × 10 9 molecules for the TIP4P/2005 and mW water models, respectively. The computationally more efficient mW water model allows us to reach converging behavior when the bubble dynamics results are plotted in reduced units, and the limiting behavior can be obtained through linear extrapolation in L –1 . Qualitative differences are observed between simulations with the mW and TIP4P/2005 water models, but they can be explained by the models’ differences in predicted viscosity and surface tension. Although bubble collapse occurs on time scales of only hundreds of picoseconds, the system sizes used here are sufficiently large to obtain bubble dynamics consistent with the Rayleigh–Plesset equation when using the models’ thermophysical properties as input. For the conditions explored here, extreme heating of the interfacial water molecules near the time of collapse is observed for the larger mW water systems (but the model underpredicts the viscosity), whereas heating is less pronounced for the TIP4P/2005 water systems because its larger viscosity contribution slows the collapse dynamics. The presence of nitrogen within the bubble only starts to affect bubble dynamics near the very end of the initial collapse, leading to an incomplete collapse and strong rebound for the mW water model. Although nitrogen is non-condensable at 300 K, it becomes highly compressed and reaches a liquid-like density near the collapse point. We find that the dissolution of nitrogen is much slower than the movement of the collapsing water front, and the re-expansion of the dense nitrogen droplet gives rise to bubble rebound. The incompatibility of the collapse and dissolution time scales should be considered for continuum-scale modeling of bubble dynamics. Finally, we also confirm that the diffusion coefficient for dissolved nitrogen is insensitive to pressure as the liquid transitions from a compressed to a stretched state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Molecular Dynamics Simulation and Analysis of Interfacial Water at Selected Sulfide Mineral Surfaces under Anaerobic Conditions

In this paper, we report on a molecular dynamics simulation (MDS) study of the behavior of interfacial water at selected sulfide mineral surfaces under anaerobic conditions. The study revealed the interfacial water structure and wetting characteristics of the pyrite (100) surface, galena (100) surface, chalcopyrite (012) surface, sphalerite (110) surface, and molybdenite surfaces (i.e., the face, armchair-edge, and zigzag-edge surfaces), including simulated contact angles, relative number density profiles, water dipole orientations, hydrogen-bonding, and residence times. For force fields of the metal and sulfur atoms in selected sulfide minerals used in the MDS, we used the universal force field (UFF) and another set of force fields optimized by quantum chemical calculations for interactions with interfacial water molecules at selected sulfide mineral surfaces. Simulation results for the structural and dynamic properties of interfacial water molecules indicate the natural hydrophobic character for the selected sulfide mineral surfaces under anaerobic conditions as well as the relatively weak hydrophobicity for the sphalerite (110) surface and two molybdenite edge surfaces. Part of the financial support for this study was provided by the U.S. Department of Energy (DOE) under Basic Science Grant No. DE-FG-03-93ER14315. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE, funded work performed by Liem X. Dang. Battelle operates Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES. The authors are grateful to Professor Tsun-Mei Chang for valuable discussions.

Jin, Jiaqi↗
DOE OSTI2013

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf{sub 2}N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 {mu}mol/m{sup 2} at 300 K. For [bmim][Tf{sub 2}N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are {+-}0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf{sub 2}N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

36 MATERIALS SCIENCE↗
DOE OSTI2014

PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

The structure of PX{sub 3} (X = Cl, Br, I) molecular liquids from X-ray diffraction, molecular dynamics simulations, and reverse Monte Carlo modeling

Synchrotron X-ray diffraction measurements have been conducted on liquid phosphorus trichloride, tribromide, and triiodide. Molecular Dynamics simulations for these molecular liquids were performed with a dual purpose: (1) to establish whether existing intermolecular potential functions can provide a picture that is consistent with diffraction data and (2) to generate reliable starting configurations for subsequent Reverse Monte Carlo modelling. Structural models (i.e., sets of coordinates of thousands of atoms) that were fully consistent with experimental diffraction information, within errors, have been prepared by means of the Reverse Monte Carlo method. Comparison with reference systems, generated by hard sphere-like Monte Carlo simulations, was also carried out to demonstrate the extent to which simple space filling effects determine the structure of the liquids (and thus, also estimating the information content of measured data). Total scattering structure factors, partial radial distribution functions and orientational correlations as a function of distances between the molecular centres have been calculated from the models. In general, more or less antiparallel arrangements of the primary molecular axes that are found to be the most favourable orientation of two neighbouring molecules. In liquid PBr{sub 3} electrostatic interactions seem to play a more important role in determining intermolecular correlations than in the other two liquids; molecular arrangements in both PCl{sub 3} and PI{sub 3} are largely driven by steric effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗