arXiv subjects

Yoyo Hinuma

Publications and source records attributed to Yoyo Hinuma.

12 recordsLinked to original sources

arXiv2025

Direct derivation of anisotropic atomic displacement parameters from molecular dynamics simulations in extended solids with substitutional disorder using a neural network potential

Atomic displacement parameters (ADPs) are crystallographic information that describe the statistical distribution of atoms around an atom site. Anisotropic ADPs by atom were directly derived from classical molecular dynamics (MD) simulations using a universal machine-learned potential. The (co)valences of atom positions were taken over recordings at different time steps in a single MD simulation. The procedure was demonstrated on extended solids, namely rocksalt structure MgO and three thermoelectric materials, Ag8SnSe6, Na2In2Sn4, and BaCu1.14In0.86P2. Unlike the very frequently used lattice dynamics approach, the MD approach can obtain ADPs in crystals with substitutional disorder and explicitly at finite temperature, but not under conditions where atoms migrate in the crystal. The calculated ADP becomes ->0 at temperature ->0 and the ADP is proportional to the temperature when the atom is in a harmonic potential and the sole contribution to the actual non-zero ADP is from the zero-point motion. The zero-point motion contribution can be estimated from the proportionality constant assuming this Einstein model. ADPs from MD simulations would act as a tool complementing experimental efforts to understand the crystal structure including the distribution of atoms around atom sites.

cond-mat.mtrl-sci↗

arXiv2025

Neural network potential molecular dynamics simulations of (La,Ce,Pr,Nd)0.95(Mg,Zn,Pb,Cd,Ca,Sr,Ba)0.05F2.95

Tysonite structure fluorides doped with divalent cations, represented by Ce0.95Ca0.05F2.95, are a class of good F- ion conductors together with fluorite-structured compounds. Computational understanding of the F- conduction process is difficult because of the complicated interactions between three symmetrically distinct F sites and the experimentally observed change in the F diffusion mechanism slightly above room temperature, effectively making first principles molecular dynamics (FP-MD) simulations, which are often conducted well above the transition temperature, useless when analyzing behavior below the transition point. Neural network potential (NNP) MD simulations showed that the F diffusion coefficient is higher when the divalent dopant cation size is similar to the trivalent cation size. The diffusion behavior of F in different sites changes at roughly 500 K in Ce0.95Ca0.05F2.95 because only the F1 site sublattice contributes to F diffusion below this temperature but the remaining F2 and F3 sublattices becomes gradually active above this temperature. The paradox of higher diffusion coefficients in CeF3-based compounds than similar LaF3-based compounds even though the lattice parameters are larger in the latter may be caused by a shallower potential of Ce and F in CeF3 compared to the LaF3 counterparts.

cond-mat.mtrl-sci↗

arXiv2024

Effect of very slow O diffusion at high temperature on very fast H diffusion in the hydride ion conductor LaH2.75O0.125

Neural network potential based molecular dynamics (MD) simulations on the excellent H conductor LaH2.75O0.125 show that O starts diffusing above a critical temperature of Tc~550 K, according to the variance of atom positions regardless of the time step. The original diffusion process at temperatures below Tc has an activation barrier of 0.25 eV. Use of MD simulations with various O and La mass revealed, at above Tc, the coexistence of the 0.25 eV process and an additional diffusion process with an activation barrier of 0.20 eV. The O and La have strongly anharmonic characters.

cond-mat.mtrl-sci↗

arXiv2023

Surface activation by electron scavenger metal nanorod adsorption on TiH2, TiC, TiN, and Ti2O3

Metal/oxide support perimeter sites are known to provide unique properties because the nearby metal changes the local environment on the support surface. In particular, the electron scavenger effect reduces the energy necessary for surface anion desorption, thereby contributes to activation of the (reverse) Mars-van Krevelen mechanism. This study investigated the possibility of such activation in hydrides, carbides, nitrides, and sulfides. The work functions (WFs) of known hydrides, carbides, nitrides, oxides, and sulfides with group 3, 4, or 5 cations (Sc, Y, La, Ti, Zr, Hf, V, Nb, and Ta) were calculated. The WFs of most hydrides, carbides, and nitrides are smaller than the WF of Ag, implying that the electron scavenger effect may occur when late transition metal nanoparticles are adsorbed on the surface. The WF of oxides and sulfides decrease when reduced. The surface anion vacancy formation energy correlates well with the bulk formation energy in carbides and nitrides, while almost no correlation is found in hydrides because of the small range of surface hydrogen vacancy formation energy values. The electron scavenger effect is explicitly observed in nanorods adsorbed on TiH2 and Ti2O3; the surface vacancy formation energy decreases at anion sites near the nanorod, and charge transfer to the nanorod happens when an anion is removed at such sites. Activation of hydrides, carbides, and nitrides by nanorod adsorption and screening support materials through WF calculation are expected to open up a new category of supported catalysts.

cond-mat.mtrl-sci↗

arXiv2023

Factors determining surface oxygen vacancy formation energy in ternary spinel structure oxides with zinc

Spinel oxides are an important class of materials for heterogeneous catalysis including photocatalysis and electrocatalysis. The surface O vacancy formation energy (EOvac) is a critical quantity on catalyst performance because the surface of metal oxide catalysts often acts as reaction sites, for example, in the Mars-van Krevelen mechanism. However, experimental evaluation of EOvac is very challenging. We obtained the EOvac for (100), (110), and (111) surfaces of normal zinc-based spinel oxides ZnAl2O4, ZnGa2O4, ZnIn2O4, ZnV2O4, ZnCr2O4, ZnMn2O4, ZnFe2O4, and ZnCo2O4. The most stable surface is (100) for all compounds. The smallest EOvac for a surface is the largest in the (100) surface except for ZnCo2O4. For (100) and (110) surfaces, there is a good correlation, over all spinels, between the smallest EOvac for the surface and bulk formation energy, while the ionization potential correlates well in (111) surfaces. Machine learning over EOvac of all surface sites in all orientations and all compounds to find the important factors, or descriptors, that decide the EOvac revealed that bulk and surface-dependent descriptors are the most important, namely the bulk formation energy, a Boolean descriptor on whether the surface is (111), and the ionization potential, followed by geometrical descriptors that are different in each O site.

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arXiv2023

Boundary Plane-Oriented Grain Boundary Model Generation

This study proposes algorithms for building tilt grain boundary (GB) models with a boundary plane-oriented approach that does not rely on existence of a coincidence site lattice (CSL). As conventional GB model generation uses the CSL of superimposed grains as the starting point, our totally different approach allows systematic treatment of diverse grain boundary systems that was previously not possible. Candidates of a pair of GB planes for a selected rotation axis, constituting a symmetrical or asymmetrical tilt GB, are thoroughly obtained by computational search that is applicable to any crystal structure. A GB interface for feasible computational analysis would have two-dimensional (2D) periodicity shared by the 2D lattices of the two GB planes, hence surface-slab supercells (slab-and-vacuum models) with common in-plane basis vectors of the shared 2D lattice are obtained. Finally, a procedure to obtain a GB-model supercell with alternately stacking such slabs is given. Symmetry operations of each slab may be considered such that the iterated interfaces are symmetrically equivalent, which is beneficial in ab initio calculations. The proposed algorithms allow streamlined generation of GB models, both symmetric and asymmetric, with or without an exact 3D-CSL relation.

cond-mat.mtrl-sci↗

arXiv2023

Comparison of Matlantis and VASP bulk formation and surface energies in metal hydrides, carbides, nitrides, oxides, and sulfides

Generic neural network potentials without forcing users to train potentials could result in significantly acceleration of total energy calculations. Takamoto et al. [Nat. Commun. (2022), 13, 2991] developed such a deep neural network potential (NNP) and made it available in their Matlantis package. We compared the Matlantis bulk formation, surface, and surface O vacancy formation energies of metal hydrides, carbides, nitrides, oxides, and sulfides with our previously calculated VASP values obtained from first-principles with the PBEsol(+U) functional. Matlantis bulk formation energies were consistently ~0.1 eV/atom larger and the surface energies were typically ~10 meV/Å^2 smaller than the VASP counterpart. Surface O vacancy formation energies were generally underestimated within ~0.8 eV. These results suggest that Matlantis energies could serve as a relatively good descriptor of the VASP bulk formation and surface energies.

cond-mat.mtrl-sci↗

arXiv2018

Finding a junction partner for candidate solar cell absorbers enargite and bournonite from electronic band and lattice matching

An essential step in the development of a new photovoltaic (PV) technology is choosing appropriate electron and hole extraction layers to make an efficient device. We recently proposed the minerals enargite (\enargite) and bournonite (\bournonite) as materials that are chemically stable with desirable optoelectronic properties for use as the absorber layer in a thin-film PV device. For these compounds, spontaneous lattice polarization with internal electric fields --- and potential ferroelectricity --- may allow for enhanced carrier separation and novel photophysical effects. In this work, we calculate the ionization potentials for non-polar surface terminations and propose suitable partners for forming solar cell heterojunctions by matching the electronic band edges to a set of candidate electrical contact materials. We then further screen these candidates by matching the lattice constants and identify those that are likely to minimise strain and achieve epitaxy. This two-step screening procedure identified a range of unconventional candidate contact materials including SnS2, ZnTe, WO3, and Bi2O3.

cond-mat.mtrl-sci↗

arXiv2016

Band structure diagram paths based on crystallography

Systematic and automatic calculations of the electronic band structure are a crucial component of computationally-driven high-throughput materials screening. An algorithm, for any crystal, to derive a unique description of the crystal structure together with a recommended band path is indispensable for this task. The electronic band structure is typically sampled along a path within the first Brillouin zone including the surface in reciprocal space. Some points in reciprocal space have higher site symmetries and/or have higher constraints than other points regarding the electronic band structure and therefore are likely to be more important than other points. This work categorizes points in reciprocal space according to their symmetry and provides recommended band paths that cover all special wavevector (k-vector) points and lines necessarily and sufficiently. Points in reciprocal space are labeled such that there is no conflict with the crystallographic convention. The k-vector coefficients of labeled points, which are located at Brillouin zone face and edge centers as well as vertices, are derived based on a primitive cell compatible with the crystallographic convention, including those with axial ratio-dependent coordinates. Furthermore, we provide an open-source implementation of the algorithms within our SeeK-path python code, to allow researchers to obtain k-vector coefficients and recommended band paths in an automated fashion. Finally, we created a free online service to compute and visualise Brillouin Zone, labeled k-points and suggested band paths for any crystal structure, that we made available at http://www.materialscloud.org/tools/seekpath/ .

cond-mat.mtrl-sci↗

arXiv2015

Categorization of surface polarity from a crystallographic approach

With ab initio codes that employ three-dimensional periodic boundary conditions, the slab-and-vacuum model has proven invaluable for the derivation of energetic, atomistic, and electronic properties of materials. Within this approach, polar and nonpolar slabs require different levels of treatment, as any polar instability must be compensated on a case-by-case basis in the former. This article proposes an efficient algorithm based on isometries to identify whether a slab with the given surface orientation would be intrinsically polar, and if not, to obtain information on where to cleave the bulk crystal to obtain a stoichiometric nonpolar slab and whether reconstruction is necessary to generate a stoichiometric slab that is not polar.

cond-mat.mtrl-sci↗

arXiv2015

Choice of basis vectors for conventional unit cells revisited

Band diagrams often pass through special $\mathbf{k}$-vector points with "irrational" fractional coordinates such as some Brillouin zone vertices and centers of edges. Use of "standard" primitive cells as defined by Setyawan and Curtarolo [Comp. Mater. Sci. 49, 299] is convenient for band diagram and effective mass calculations because the definitions and coordinates of special $\mathbf{k}$-vector points including "irrational" fractional points are provided, but their basis vectors are taken differently and/or special $\mathbf{k}$-vector point definitions differ from the crystallographic convention in many cases. On the other hand, the Bilbao Crystallographic Server [Bulg. Chem. Commun. 43, 183] defines special $\mathbf{k}$-vector points based on crystallographic convention; however, symbols for "irrational" special $\mathbf{k}$-vector points are not defined. Obviously there is a need for a crystallographic convention-friendly scheme to describe such "irrational" special $\mathbf{k}$-vector points. This paper outlines an algorithm that is relatively straightforward to implement in software to bridge between crystallographic conventional cells and "standard" primitive cells by retaking basis vectors. The procedure is expected to ease systematic electronic and phonon band calculations.

cond-mat.mtrl-sci↗

arXiv2011

Lithium Diffusion in Graphitic Carbon

Graphitic carbon is currently considered the state-of-the-art material for the negative electrode in lithium-ion cells, mainly due to its high reversibility and low operating potential. However, carbon anodes exhibit mediocre charge/discharge rate performance, which contributes to severe transport-induced surface-structural damage upon prolonged cycling, and limits the lifetime of the cell. Lithium bulk diffusion in graphitic carbon is not yet completely understood, partly due to the complexity of measuring bulk transport properties in finite-sized, non-isotropic particles. To solve this problem for graphite, we use the Devanathan-Stachurski electrochemical methodology combined with ab-initio computations to deconvolute, and quantify the mechanism of lithium-ion diffusion in highly oriented pyrolytic graphite (HOPG). The results reveal inherent high lithium-ion diffusivity in the direction parallel to the graphene plane (ca. 10^-7 - 10^-6 cm2 s-1), as compared to sluggish lithium-ion transport along grain boundaries (ca. 10^-11 cm^2 s^-1), indicating the possibility of rational design of carbonaceous materials and composite electrodes with very high rate capability.

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