Atomistic level simulation of the nanostructure properties
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A molecular dynamics study of laser-excited gold
The structural evolution of laser-excited systems of gold has previously been measured through ultrafast MeV electron diffraction. However, there has been a long-standing inability of atomistic simulations to provide a consistent picture of the melting process, leading to large discrepancies between the predicted threshold energy density for complete melting, as well as the transition between heterogeneous and homogeneous melting. We make use of two-temperature classical molecular dynamics simulations utilizing three highly successful interatomic potentials and reproduce electron diffraction data presented by Mo et al. [Science 360, 1451–1455 (2018)]. We recreate the experimental electron diffraction data, employing both a constant and temperature-dependent electron–ion equilibration rate. In all cases, we are able to match time-resolved electron diffraction data, and find consistency between atomistic simulations and experiments, only by allowing laser energy to be transported away from the interaction region. This additional energy-loss pathway, which scales strongly with laser fluence, we attribute to hot electrons leaving the target on a timescale commensurate with melting.
36 MATERIALS SCIENCE↗
Effect of hydrogen on plasticity of $α$-Fe: A multi-scale assessment
A multi-scale study was carried out to quantify the effect of interstitial hydrogen concentration on plasticity in $α$-Fe. Here, in this work, the influence of hydrogen on the screw dislocation glide behavior was examined across several length-scales. The insights obtained were integrated to provide an accurate continuum description for the effect of hydrogen on the dislocation based plasticity in polycrystalline $α$-Fe. At the outset of this work, a new Fe—H interatomic potential was formulated that enhanced the atomistic estimation of the variation in dislocation glide behavior in presence of hydrogen. Next, the dislocation core reconstruction observed due to the addition of hydrogen using atomistic simulations was validated with the help of large-scale DFT calculations based on the DFT-FE framework. Several atomistic simulations were carried out to comprehensively quantify the effect of hydrogen on the non-Schmid behavior exhibited during the dislocation glide in $α$-Fe. Finally, crystal plasticity simulations were carried out to understand the effect of hydrogen on the meso-scale deformation behavior of polycrystalline $α$-Fe.
36 MATERIALS SCIENCE↗
Multiscale Modeling of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2: Application to Lattice Thermal Conductivity
We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.
Lawson, John W.↗
Multiscale Modeling of UHTC: Thermal Conductivity
We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.
Lawson, John W.↗
eReaxFF force field development for BaZr 0.8 Y 0.2 O 3-δ solid oxide electrolysis cells applications
The use of solid-oxide materials in electrocatalysis applications, especially in hydrogen-evolution reactions, is promising. However, further improvements are warranted to overcome the fundamental bottlenecks to enhancing the performance of solid-oxide electrolysis cells (SOECs), which is directly linked to the more-refined fundamental understanding of complex physical and chemical phenomena and mass exchanges that take place at the surfaces and in the bulk of electrocatalysis materials. Here, we developed an eReaxFF force field for barium zirconate doped with 20 mol% of yttrium, BaZr 0.8 Y 0.2 O 3-δ (BZY20) to enable a systematic, large-length-scale, and longer-timescale atomistic simulation of solid-oxide electrocatalysis for hydrogen generation. All parameters for the eReaxFF were optimized to reproduce quantum-mechanical (QM) calculations on relevant condensed phase and cluster systems describing oxygen vacancies, vacancy migrations, electron localization, water adsorption, water splitting, and hydrogen generation on the surfaces of the BZY20 solid oxide. Using the developed force field, we performed both zero-voltage (excess electrons absent) and non-zero-voltage (excess electrons present) molecular dynamics simulations to observe water adsorption, water splitting, proton migration, oxygen-vacancy migrations, and eventual hydrogen-production reactions. Based on investigations offered in the present study, we conclude that the eReaxFF force field-based approach can enable computationally efficient simulations for electron conductivity, electron leakage, and other non-zero-voltage effects on the solid oxide materials using the explicit-electron concept. Moreover, we demonstrate how the eReaxFF force field-based atomistic-simulation approach can enhance our understanding of processes in SOEC applications and potentially other renewable-energy applications.
08 HYDROGEN↗
A high-performance implementation of atomistic spin dynamics simulations on x86 CPUs
Atomistic spin dynamics simulations provide valuable information about the energy spectrum of magnetic materials in different phases, allowing one to identify instabilities and the nature of their excitations. However, the time cost of evaluating the dynamical correlation function S(q,t) increases quadratically as the number of spins N, leading to significant computational effort, making the simulation of large spin systems very challenging. In this work, here, we propose to use a highly optimized general matrix multiply (GEMM) subroutine to calculate the dynamical spin-spin correlation function that can achieve near-optimal hardware utilization. Furthermore, we fuse the element-wise operations in the calculation of S(q,t) into the in-house GEMM kernel, which results in further performance improvements of 44\% - 71\% on several relatively large lattice sizes when compared to the implementation that uses the GEMM subroutine in OpenBLAS, which is the state-of-the-art open source library for Basic Linear Algebra Subroutine (BLAS).
97 MATHEMATICS AND COMPUTING↗
An intrinsic ductility parameter derived from anisotropic linear elasticity theory
A new indicator of intrinsic ductility (κ) is introduced based on linear elasticity. In the limit of elastic isotropy this parameter is equal to the Pugh ratio ( B / G ) plus a constant; but unlike the Pugh ratio, κ incorporates anisotropy and crystallography to improve predictive value. We identify a single ductile-to-brittle transition setpoint for κ that predicts crack-tip plasticity in atomistic simulations, experimental elongation to failure of polycrystalline elemental metals pulled in tension, and fracture energy measurements of glasses, suggesting commonality in the relationship between plasticity and fracture across all three of these cases. Statistical analysis supports the superiority of κ over B / G at predicting crack-tip plasticity in atomistic simulations and elongation to failure of polycrystalline elemental metals.
Winter, Ian S.↗
Score-based denoising for atomic structure identification
We propose an effective method for removing thermal vibrations that complicate the task of analyzing complex dynamics in atomistic simulation of condensed matter. Our method iteratively subtracts thermal noises or perturbations in atomic positions using a denoising score function trained on synthetically noised but otherwise perfect crystal lattices. The resulting denoised structures clearly reveal underlying crystal order while retaining disorder associated with crystal defects. Purely geometric, agnostic to interatomic potentials, and trained without inputs from explicit simulations, our denoiser can be applied to simulation data generated from vastly different interatomic interactions. The denoiser is shown to improve existing classification methods, such as common neighbor analysis and polyhedral template matching, reaching perfect classification accuracy on a recent benchmark dataset of thermally perturbed structures up to the melting point. Demonstrated here in a wide variety of atomistic simulation contexts, the denoiser is general, robust, and readily extendable to delineate order from disorder in structurally and chemically complex materials.
36 MATERIALS SCIENCE↗
Skyrmion formation in Ni-based Janus dihalide monolayers: Interplay between magnetic frustration and Dzyaloshinskii-Moriya interaction
Here we present a comprehensive theory of the magnetic phases in monolayer nickel-based Janus dihalides (NiIBr, NiICl, NiBrCl) through a combination of first-principles calculations and atomistic simulations. Phonon band structure calculations and finite-temperature molecular dynamics simulations show that Ni-dihalide Janus monolayers are stable. The parameters of the interacting spin Hamiltonian extracted from ab initio calculations show that nickel-dihalide Janus monolayers exhibit varying degrees of magnetic frustration together with a large Dzyaloshinskii-Moriya interaction due to their inherent inversion symmetry breaking. The atomistic simulations reveal a delicate interplay between these two competing magnetic interactions in giving rise to skyrmion formation.
36 MATERIALS SCIENCE↗
Investigation into the transport properties of planetary interiors through inelastic X-ray scattering experiments and quantum molecular dynamics (Final Technical Report)
This was a two-year research project for the period 08/15/2018 - 08/14/2020 conducted at the University of Nevada, Reno using Pronghorn, a newly built high-performance cluster located at the University. The short-term project goal was to provide computational support for the experimental campaigns at LCLS through data analysis of previous and upcoming scheduled experiments, along with performing state-of-the-art atomistic simulations of dense plasmas. The longer-term goal was to create a new computational high energy density physics group located at the University of Nevada, Reno. Guided by results from past and future high-resolution scattering experiments, we aimed to research and develop non-equilibrium and non-adiabatic atomistic simulations of dense plasmas that went beyond the Born-Oppenheimer approximation
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Channelrhodopsin C1C2: Photocycle kinetics and interactions near the central gate
Channelrhodopsins (ChR) are light-sensitive cation channels used in optogenetics, a technique that applies light to control cells (e.g., neurons) that have been modified genetically to express those channels. Although mutations are known to affect pore kinetics, little is known about how mutations induce changes at the molecular scale. To address this issue, we first measured channel opening and closing rates of a ChR chimera (C1C2) and selected variants (N297D, N297V, and V125L). Then, we used atomistic simulations to correlate those rates with changes in pore structure, hydration, and chemical interactions among key gating residues of C1C2 in both closed and open states. Overall, the experimental results show that C1C2 and its mutants do not behave like ChR2 or its analogous variants, except V125L, making C1C2 a unique channel. Furthermore, our atomistic simulations confirmed that opening of the channel and initial hydration of the gating regions between helices I, II, III, and VII of the channel occurs with 1) the presence of 13-cis retinal; 2) deprotonation of a glutamic acid gating residue, E129; and 3) subsequent weakening of the central gate hydrogen bond between the same glutamic acid E129 and asparagine N297 in the central region of the pore. Also, an aspartate (D292) is the unambiguous primary proton acceptor for the retinal Schiff base in the hydrated channel.
59 BASIC BIOLOGICAL SCIENCES↗
Performant implementation of the atomic cluster expansion (PACE) and application to copper and silicon
The atomic cluster expansion is a general polynomial expansion of the atomic energy in multi-atom basis functions. Here we implement the atomic cluster expansion in the performant C++ code that is suitable for use in large-scale atomistic simulations. We briefly review the atomic cluster expansion and give detailed expressions for energies and forces as well as efficient algorithms for their evaluation. We demonstrate that the atomic cluster expansion as implemented in shifts a previously established Pareto front for machine learning interatomic potentials toward faster and more accurate calculations. Moreover, general purpose parameterizations are presented for copper and silicon and evaluated in detail. We show that the Cu and Si potentials significantly improve on the best available potentials for highly accurate large-scale atomistic simulations.
36 MATERIALS SCIENCE↗
Topological grain boundary segregation transitions
Engineering the structure of grain boundaries (GBs) by solute segregation is a promising strategy to tailor the properties of polycrystalline materials. Solute segregation triggering phase transitions at GBs has been suggested theoretically to offer different pathways to design interfaces, but an understanding of their intrinsic atomistic nature is missing. Here, we combined atomic resolution electron microscopy and atomistic simulations to discover that iron segregation to GBs in titanium stabilizes icosahedral units (“cages”) that form robust building blocks of distinct GB phases. Owing to their five-fold symmetry, the iron cages cluster and assemble into hierarchical GB phases characterized by a different number and arrangement of the constituent icosahedral units. Our advanced GB structure prediction algorithms and atomistic simulations validate the stability of these observed phases and the high excess of iron at the GB that is accommodated by the phase transitions.
36 MATERIALS SCIENCE↗
Dynamic embedding of effective harmonic normal mode vibrations in all-atomistic energy gap fluctuations: Case study of light harvesting 2 complex
Environmental effects in excitation energy transfer have mostly been modeled by baths of harmonic oscillators, but to what extent such modeling provides a reliable description of actual interactions between molecular systems and environments remains an open issue. Here, we address this issue by investigating fluctuations in the excitation energies of the light harvesting 2 complex using a realistic all-atomistic simulation of the potential energy surface. Our analyses reveal that molecular motions exhibit significant anharmonic features, even for underdamped intramolecular vibrations. In particular, we find that the anharmonicity contributes to the broadening of spectral densities and substantial overlaps between neighboring peaks, which complicates the meaning of mode frequencies constituting a bath model. Thus, we develop a strategy to construct a minimally underdamped harmonic bath that has a clear connection to all-atomistic dynamics by utilizing actual normal modes of molecules but optimizing their frequencies such that the resulting bath model can best reproduce the all-atomistic simulation results. By subtracting the underdamped contribution from the entire fluctuations, we also show that identifying a residual spectral density representing all other contributions with overdamped behavior is possible. We find that this can be fitted well with a well-established analytic form of a spectral density function or, alternatively, modeled as explicit time dependent fluctuations with muti-exponential or power law type correlation functions. We provide an assessment and the implications of these possibilities. The approach presented here can also serve as a general strategy to construct a simplified bath model that can effectively represent the underlying all-atomistic bath dynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Neural-network model for force prediction in multi-principal-element alloys
Atomistic simulations can provide useful insights into the physical properties of multi-principal-element alloys. However, classical potentials mostly fail to capture key quantum (electronic-structure) effects. Here we present a deep 3D convolutional neural network (3D CNN) based framework combined with a voxelization technique to design interatomic potentials for chemically complex alloys. We highlight the performance of the 3D CNN model and its efficacy in computing potentials using the medium-entropy alloy TaNbMo. In order to provide insights into the effect of voxel resolution, we implemented two approaches based on the inner and outer bounding boxes. An efficient 3D CNN model, which is as accurate as the density-functional theory (DFT) approach, for calculating potentials will provide a promising schema for accurate atomistic simulations of structure and dynamics of general multi-principle element alloys.
36 MATERIALS SCIENCE↗
Performant implementation of the atomic cluster expansion
The atomic cluster expansion is a general polynomial expansion of the atomic energy in multi-atom basis functions. Here we implement the atomic cluster expansion in the performant C++ code PACE that is suitable for use in large scale atomistic simulations. We briefly review the atomic cluster expansion and give detailed expressions for energies and forces as well as efficient algorithms for their evaluation. We demonstrate that the atomic cluster expansion as implemented in PACE shifts a previously established Pareto front for machine learning interatomic potentials towards faster and more accurate calculations. Moreover, general purpose parameterizations are presented for copper and silicon and evaluated in detail. We show that the new Cu and Si potentials significantly improve on the best available potentials for highly accurate large-scale atomistic simulations.
74 ATOMIC AND MOLECULAR PHYSICS↗
Coexisting paramagnetic spins and long-range magnetic order in Ba4(Ru0.92Ir0.08)3O10
We investigate the effect of dilute Ir substitution on the magnetism of the trimer-based ruthenate Ba4Ru3O10 using neutron diffraction, magnetic susceptibility measurements, first-principles calculations, and atomistic simulations. Neutron diffraction shows that Ir doping preserves the zigzag antiferromagnetic structure and the ordered-moment magnitude of the parent compound, in which the moments reside exclusively on the two outer Ru(2) sites of each Ru3O12 trimer, while the central Ru(1) site remains nonmagnetic. The Néel temperature is reduced from ∼105 to 84.0(1) K upon 8% Ir substitution, while magnetic susceptibility reveals a pronounced low-temperature Curie-like upturn, indicating the coexistence of paramagnetic spins with long-range antiferromagnetic order. Density-functional calculations show that Ir preferentially occupies the central Ru(1) site, which disrupts the exchange pathways of the affected Ru3O12 trimer state. Atomistic simulations incorporating this paramagnetic dilution reproduce the suppressed ordering temperature and the coexistence of ordered and paramagnetic components.
Islam, Farhan [Ames Laboratory]↗