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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Bergman-type medium range order in amorphous Zr77Rh23 alloy studied by ab initio molecular dynamics simulations

In recent years, some arguments about the existence of medium-range order (MRO) in the Zr-Rh system have been put forward. However, research on the structural features of the Zr-Rh binary alloy at the atomic level is still lacking. This study uses ab initio molecular dynamics simulations to systematically study the local structures of Zr77Rh23 from the liquid to the glassy states. Pair correlation function (PCF), coordination number (CN), Honeycutt–Anderson(HA) index, bond-angle distribution functions, and the Voronoi tessellation method are used to reveal a clear icosahedral-like configuration in the amorphous Zr77Rh23 alloy. It is noteworthy that the splitting in the second peak of the partial PDF implies the existence of a medium range order (MRO) in the Zr77Rh23 system. We obtain the local order in three-dimensional atomic density distributions by using a new atomistic cluster alignment (ACA) method. Interestingly, a Bergman-type MRO is observed in the glassy Zr77Rh23. Furthermore, the spatial distribution and connections of icosahedral-like clusters are shown to further demonstrate the MRO network. Our findings shed light on the nature of atomic local structures of amorphous Zr77Rh23 alloy and have important implications to understanding the formation of various MROs in metallic glasses.

Guo, Y. R.↗
DOE OSTI2020

Ab initio molecular dynamics simulation of Nd3+ incorporation in calcite

Trivalent rare-earth elements (REEs) readily incorporate in Ca-bearing minerals such as calcite (CaCO3), a phenomenon with important implications for the use of REEs as biogeochemical tracers as well as for environmental remediation. Despite substantial efforts, determining the incorporation modes of trivalent REEs in calcite has remained challenging due to their presence in multiple coordination environments. This is particularly problematic for the interpretation of extended X-ray absorption fine structure (EXAFS) spectroscopy. In this work, ab initio molecular dynamics (AIMD) simulations of Nd3+ incorporated in calcite were performed to resolve its incorporation modes. Nd3+ and Ca2+ have very similar ionic radii but the additional positive charge requires a charge compensation scheme (CCS). Five CCSs were considered in AIMD simulations, and the resulting atomic trajectories were then used to compute EXAFS spectra for direct fitting to a published experimental spectrum. The results of the fits indicated that Nd3+ incorporates at the Ca2+ site in calcite in a mixture of six- and seven-fold coordination environments and through three main incorporation modes: associated with a protonated nearest-neighbor Ca2+ vacancy, incorporated as NdOH2+, and charge compensated by a remote species (on the spatial scale probed by EXAFS). The incorporation of Nd3+ in calcite via multiple modes was consistent with previous work, but the AIMD-EXAFS approach allowed for resolving the nature, proportion, and structure of the different coordination environments.

Kerisit, Sebastien N.↗
DOE OSTI2021

Ab Initio Molecular Dynamics Simulations of Amorphous Calcium Carbonate: Interpretation of Pair Distribution Function and X-Ray Absorption Spectroscopy Data

The structure and transformation of hydrous amorphous calcium carbonate (ACC) are key to understanding biomineralization pathways and their relationship with the properties of the resulting material. Quantitative interpretation of scattering experiments aimed at elucidating the structure of ACC is challenging, due to the amorphous nature of this material, and, therefore, requires models for the structure and the scattering physics. Here, we generate physically realistic ensembles of hydrated ACC structures and their vibrational disorder from ab initio molecular dynamics (AIMD) simulations with an emphasis on enabling the consistent interpretation of the finer details of three complementary structural probes: neutron and x-ray pair distribution experiments and x-ray absorption spectroscopy (XAS). In each case, we simulate the signal directly in reciprocal space and then manipulate it into the real-space pair distribution function (PDF) or spectrum using the same procedures for the experimental and theoretical data. Good agreement with experiment was obtained across the three techniques with the simulations accounting well for all features in the spectra. Remaining small discrepancies pointed to differences between real samples and the idealized simulated systems such as deviations from the nominal CaCO3·nH2O stoichiometry. Additionally, the simulations offered a more accurate description of the local coordination environment of calcium than previous shell-by-shell fits to spectra of synthetic ACC and classical molecular dynamics simulations. This work demonstrates that AIMD is a powerful approach for extracting detailed structural information from neutron PDF, x-ray PDF, and XAS of amorphous carbonate phases.

Prange, Micah P.↗
DOE OSTI2019

Effects of electron-phonon coupling and electronic thermal conductivity in high energy molecular dynamics simulations of irradiation cascades in nickel

The two-temperature model has been applied to investigate the effects of the electronic subsystem on 150 keV Ni ion cascades in nickel using molecular dynamics simulation. We explore the effects of the magnitude of the electron-phonon coupling and the electronic thermal conductivity on defect production and cluster formation. It has been found that stronger electron-phonon coupling allows larger and more rapid energy feedback to the atomic subsystem, leading to reduction of number of point defects and suppression of the formation of larger defect clusters. It was observed that larger electronic thermal conductivity results in slightly increased number of point defects and larger size vacancy clusters. The latter takes place because of suppression of point defects recombination in faster cooling areas of initial damage.

Zarkadoula, Eva↗
DOE OSTI2019

Dynamical properties of a room temperature ionic liquid: Using molecular dynamics simulations to implement a dynamic ion cage model [plus supplemental information]

The transport behavior of ionic liquids (ILs) is pivotal for a variety of applications, especially when ILs are used as electrolytes. Many aspects of the transport dynamics of ILs remain to be understood. Here, a common ionic liquid, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimNTf 2 ), was studied with molecular dynamics simulations. The results show that BmimNTf 2 displays typical structural relaxation, subdiffusive behavior, and a breakdown of the Stokes-Einstein diffusion relation as in glass-forming liquids. In addition, the simulations show that the translational dynamics, reorientation dynamics, and structural relaxation dynamics are well described by the Vogel-Fulcher-Tammann equation like fragile glass forming liquids. Building on previous work that employed ion cage models, it was found that the diffusion dynamics of the cations and anions were well described by a hopping process random walk where the step time is the ion cage lifetime obtained from the cage correlation function. Detailed analysis of the ion cage structures indicated that the electrostatic potential energy of the ion cage dominates the diffusion dynamics of the caged ion. The ion orientational relaxation dynamics showed that ion reorientation is a necessary step for ion cage restructuring. The dynamic ion cage model description of ion diffusion presented here may have implications for designing ILs to control their transport behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Predicting the Dissolution Rate of Borosilicate Glasses using QSPR analysis based on molecular dynamics simulations

Quantitative Structure Property Relationship (QSPR) analysis based on molecular dynamics (MD) simulations is a promising approach for establishing the composition-property relationships of glass and other materials with complex structures. A series of 20 borosilicate and boroaluminosilicate glasses have been modeled by using MD simulations with recently developed effective potentials. Short- and medium-range structures of these glasses were analyzed and, based on these structural information, QSPR analysis of the initial dissolution rate (r0) was made and compared with measured r0 at 90°C and pH 9 using various structural descriptors such as percentage of bridging oxygen species, network connectivity and average ring size. The structural descriptors, Fnet, containing energetic information such as single bond strength and other structural information were also used. It was found that overall network connectivity, average ring size and Fnet give reasonable predictions of the r0 of studied glasses, given the conditions that the glasses are homogeneous and dissolve congruently. Modifying glass compositions to account preferential release of modifiers gives a better prediction for incongruently dissolving glasses. The results were compared with our recent work of predicting glass dissolution behavior from compositions using the topological-constraints-based models.

Du, Jincheng↗
DOE OSTI2017

Error correction in multi-fidelity molecular dynamics simulations using functional uncertainty quantification

We use functional, Fréchet, derivatives to quantify how thermodynamic outputs of a molecular dynamics (MD) simulation depend on the potential used to compute atomic interactions. Our approach quantifies the sensitivity of the quantities of interest with respect to the input functions as opposed to its parameters as is done in typical uncertainty quantification methods. We show that the functional sensitivity of the average potential energy and pressure in isothermal, isochoric MD simulations using Lennard–Jones two-body interactions can be used to accurately predict those properties for other interatomic potentials (with different functional forms) without re-running the simulations. This is demonstrated under three different thermodynamic conditions, namely a crystal at room temperature, a liquid at ambient pressure, and a high pressure liquid. The method provides accurate predictions as long as the change in potential can be reasonably described to first order and does not significantly affect the region in phase space explored by the simulation. The functional uncertainty quantification approach can be used to estimate the uncertainties associated with constitutive models used in the simulation and to correct predictions if a more accurate representation becomes available.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Enhancing the formation of ionic defects to study the ice Ih/XI transition with molecular dynamics simulations

Ice Ih, the common form of ice in the biosphere, contains proton disorder. Its proton-ordered counterpart, ice XI, is thermodynamically stable below 72 K. However, the formation of ice XI is kinetically hindered, and experimentally it is obtained by doping with KOH. Doping creates ionic defects that promote the migration of protons and the associated change in proton configuration. In this article, we mimic the effect of doping with a bias potential that enhances the formation of ionic defects in molecular dynamics simulations. The recombination of the ions thus formed proceeds through fast migration of the hydroxide along hydrogen bond loops, providing a physical and expedite way to change the proton configuration. Here, a key ingredient of this approach is a machine learning potential trained with density functional theory data and capable of modelling molecular dissociation. We exemplify the usefulness of this idea by studying the order-disorder transition using an appropriate order parameter that distinguishes the proton environments in ice Ih and XI. We calculate the changes in free energy, enthalpy, and entropy associated with the transition. Our estimated entropy agrees with experiment within the error bars of the calculation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Domain-specific compilers for dynamic simulations of quantum materials on quantum computers

Abstract Simulation of the dynamics of quantum materials is emerging as a promising scientific application for noisy intermediate-scale quantum (NISQ) computers. Due to their high gate-error rates and short decoherence times, however, NISQ computers can only produce high-fidelity results for those quantum circuits smaller than some given circuit size. Dynamic simulations, therefore, pose a challenge as current algorithms produce circuits that grow in size with each subsequent time-step of the simulation. This underscores the crucial role of quantum circuit compilers to produce executable quantum circuits of minimal size, thereby maximizing the range of physical phenomena that can be studied within the NISQ fidelity budget. Here, we present two domain-specific (DS) quantum circuit compilers for the Rigetti and IBM quantum computers, specifically designed to compile circuits simulating dynamics under a special class of time-dependent Hamiltonians. The compilers outperform state-of-the-art general-purpose compilers in terms of circuit size reduction by around 25%–30% as well as wall-clock compilation time by around 40% (dependent on system size and simulation time-step). Drawing on heuristic techniques commonly used in artificial intelligence, both compilers scale well with simulation time-step and system size. Code for both compilers is open-source and packaged into a full-stack quantum simulation software with tutorials included for ease of use for future researchers wishing to perform dynamic simulations of quantum materials on quantum computers. As our DS compilers provide significant improvements in both compilation time and simulation fidelity, they provide a building block for accelerating progress toward physical quantum supremacy.

Physics↗
DOE OSTI2017

Aggregation of cyclic polypeptoids bearing zwitterionic end-groups with attractive dipole–dipole and solvophobic interactions: a study by small-angle neutron scattering and molecular dynamics simulation

Aggregation behavior of cyclic polypeptoids bearing zwitterionic end-groups in methanol has been studied using a combination of experimental and simulation techniques. Here, the data from SANS and cryo-TEM indicate that the solution contains small clusters of these cyclic polypeptoids, ranging from a single polypeptoid chain to small oligomers, while the linear counterpart shows no cluster formation. Atomistic molecular dynamics simulations reveal that the driving force for this clustering behavior is due to the interplay between the effective repulsion due to the solvation of the dipoles formed by the charged end-groups in each polypeptoid chain and the attractive forces due to dipole–dipole interactions and the solvophobic effect.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Reactive Molecular Dynamics Simulations and Quantum Chemistry Calculations To Investigate Soot-Relevant Reaction Pathways for Hexylamine Isomers

Sooting tendencies of a series of nitrogen-containing hydrocarbons (NHCs) have been recently characterized experimentally using the yield sooting index (YSI) methodology. This work aims to identify soot-relevant reaction pathways for three selected C6H15N amines, namely, dipropylamine (DPA), diisopropylamine (DIPA), and 3,3-dimethylbutylamine (DMBA) using ReaxFF molecular dynamics (MD) simulations and quantum mechanical (QM) calculations and to interpret the experimentally observed trends. ReaxFF MD simulations are performed to determine the important intermediate species and radicals involved in the fuel decomposition and soot formation processes. QM calculations are employed to extensively search for chemical reactions involving these species and radicals based on the ReaxFF MD results and also to quantitatively characterize the potential energy surfaces. Specifically, ReaxFF simulations are carried out in the NVT ensemble at 1400, 1600, and 1800 K, where soot has been identified to form in the YSI experiment. These simulations account for the interactions among test fuel molecules and pre-existing radicals and intermediate species generated from rich methane combustion, using a recently proposed simulation framework. ReaxFF simulations predict that the reactivity of the amines decrease in the order DIPA > DPA > DMBA, independent of temperature. Both QM calculations and ReaxFF simulations predict that C2H4, C3H6, and C4H8 are the main nonaromatic soot precursors formed during the decomposition of DPA, DIPA, and DMBA, respectively, and the associated reaction pathways are identified for each amine. Both theoretical methods predict that sooting tendency increases in the order DPA, DIPA, and DMBA, consistent with the experimentally measured trend in YSI. This work demonstrates that sooting tendencies and soot-relevant reaction pathways of fuels with unknown chemical kinetics can be identified efficiently through combined ReaxFF and QM simulations. Overall, predictions from ReaxFF simulations and QM calculations are consistent, in terms of fuel reactivity, major intermediates, and major nonaromatic soot precursors.

fuel decomposition↗
DOE OSTI2017

A novel energy conversion based method for velocity correction in molecular dynamics simulations

Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations

The Tersoff potential is one of the empirical many-body potentials that has been widely used in simulation studies at atomic scales. Unlike pair-wise potentials, the Tersoff potential involves three-body terms, which require much more arithmetic operations and data dependency. In this contribution, we have implemented the GPU-accelerated version of several variants of the Tersoff potential for LAMMPS, an open-source massively parallel Molecular Dynamics code. Compared to the existing MPI implementation in LAMMPS, the GPU implementation exhibits a better scalability and offers a speedup of 2.2X when run on 1000 compute nodes on the Titan supercomputer. On a single node, the speedup ranges from 2.0 to 8.0 times, depending on the number of atoms per GPU and hardware configurations. The most notable features of our GPU-accelerated version include its design for MPI/accelerator heterogeneous parallelism, its compatibility with other functionalities in LAMMPS, its ability to give deterministic results and to support both NVIDIA CUDA- and OpenCL-enabled accelerators. Our implementation is now part of the GPU package in LAMMPS and accessible for public use.

Computer Science↗