arXiv subjects

Tsuyoshi Miyazaki

Publications and source records attributed to Tsuyoshi Miyazaki.

At least 19 recordsLinked to original sources

arXiv2026

SevenNet-Polar for MultiTask Prediction of Energy, Forces, Stress, and Born Effective Charges: Development and Application to ZrO$_2$, Li$_3$PO$_4$, and Perovskites

Accurate prediction of the Born effective charge (BEC) tensor is crucial for modeling materials under electric fields but remains computationally expensive. To bridge this gap, we present SevenNet-Polar, an equivariant graph neural network framework based on the SevenNet architecture for fast and accurate BEC predictions. Our BEC-only predictors can achieve an RMSE as low as 0.0043 e on ZrO$_2$, Li$_3$PO$_4$, and perovskites, despite the presence of high-temperature (up to 2,000 K) and defect-laden training data. Our all-in-one multitask models for predicting energy, forces, stress, and BEC in ZrO$_2$ and Li$_3$PO$_4$ achieve high accuracy with an RMSE of 1.0 meV/atom for energy, 12 meV/angstrom for forces, 0.05 GPa for stress, and 0.0029 e for BEC. BEC accuracy is not degraded by multitask training. Scaling analysis reveals distinct exponents for diagonal and off-diagonal BEC components, both of which exhibit less favorable scaling than energy, force and stress errors. SevenNet-Polar generalizes robustly when tested on scenarios containing structural environments absent from the training set, such as along nudged elastic band (NEB) trajectories or grain boundaries in ZrO$_2$. Accelerated by FlashTP, SevenNet-Polar enables simulations containing up to 1.5 million atoms on multi-GPU supercomputers and up to approximately 15,000 atoms on a single consumer-grade GPU. This makes charge-aware molecular dynamics simulations under electric fields more accessible.

cond-mat.mtrl-sci↗

arXiv2026

Stress calculation in linear scaling DFT: convergence and dynamics

We present the approach needed to calculate stress within density functional theory (DFT) using a localised orbital basis, both for exact diagonalisation and linear scaling approaches, and demonstrate our implementation within the large scale DFT code Conquest. For the linear scaling approach, we test the rate of convergence of stress with density matrix range, and compare it to the convergence of energy and forces for different materials with a range of band gaps. We show that excellent convergence is found for modest cutoffs, and show that large-scale isothermal-isobaric molecular dynamics is stable and accurate.

cond-mat.mtrl-sci↗

arXiv2025

Nonrelativistic Piezomagnetic Effect in an Organic Altermagnet

We theoretically study the piezomagnetic effect on the altermagnetic state in $κ$-type molecular conductors, focusing on its nonrelativistic mechanism. By introducing shear stress as a monoclinic distortion, we evaluate variations in the effective tight-binding model using first-principles calculations. Using the derived parameters, we investigate the Hubbard model and its effective Heisenberg model on the two-dimensional (distorted) $κ$-type lattice within mean-field approximation. We show that the system exhibits the piezomagnetic effect, i.e., a net magnetization induced at finite temperatures in the undoped insulating state and both in the ground state and at finite temperatures upon doping. In a real-space picture, this uniform magnetization arises from the ferrimagnetic spin structure due to inequivalent spin sites induced by lattice distortion. Meanwhile, in a momentum-space picture, it stems from the {\it s}-wave spin splitting of the electron and magnon bands, independent of spin-orbit coupling. We find that this nonrelativistic piezomagnetism remains finite, but becomes smaller in the limit of strong dimerization where the energy gap between the bonding and antibonding orbitals is infinitely large and the {\it d}-wave altermagnetic spin splitting is absent, highlighting the importance of the multi-orbital nature.

cond-mat.str-el↗

arXiv2025

Development of the Timing System for the X-Ray Imaging and Spectroscopy Mission

This paper describes the development, design, ground verification, and in-orbit verification, performance measurement, and calibration of the timing system for the X-Ray Imaging and Spectroscopy Mission (XRISM). The scientific goals of the mission require an absolute timing accuracy of 1.0~ms. All components of the timing system were designed and verified to be within the timing error budgets, which were assigned by component to meet the requirements. After the launch of XRISM, the timing capability of the ground-tuned timing system was verified using the millisecond pulsar PSR~B1937+21 during the commissioning period, and the timing jitter of the bus and the ground component were found to be below $15~μ$s compared to the NICER (Neutron star Interior Composition ExploreR) profile. During the performance verification and calibration period, simultaneous observations of the Crab pulsar by XRISM, NuSTAR (Nuclear Spectroscopic Telescope Array), and NICER were made to measure the absolute timing offset of the system, showing that the arrival time of the main pulse with XRISM was aligned with that of NICER and NuSTAR to within $200~μ$s. In conclusion, the absolute timing accuracy of the bus and the ground component of the XRISM timing system meets the timing error budget of $500~μ$s.

astro-ph.IM↗

arXiv2024

Stability of correlated insulating states in molecular conductors from first-principles calculation

Electronic properties of molecular conductors exhibiting antiferromagnetic (AFM) spin order and charge order (CO) owing to electron correlation are studied using first-principles density functional theory calculations. We investigate two systems, a quasi-two-dimensional Mott insulator $β^\prime$-(BEDT-TTF)$_{2}$ICl$_{2}$ with an AFM ground state, and several members of quasi-one-dimensional (TMTTF)$_2$$X$ showing CO. The stabilities of the AFM and CO states are compared between the use of a standard exchange-correlation functional based on the generalized gradient approximation and that of a range-separated hybrid functional; we find that the latter describes these states better. For $β^\prime$-(BEDT-TTF)$_{2}$ICl$_{2}$, the AFM order is much stabilized with a wider band gap. For (TMTTF)$_2$$X$, only by using the hybrid functional, the AFM insulating state is realized and the CO states coexisting with AFM order are stable under structural optimization, whose stability among different \textit{X} shows the tendency consistent with experiments.

cond-mat.str-el↗

arXiv2024

Quasi-one-dimensional Spin Dynamics in a Molecular Spin Liquid System

The molecular triangular lattice system, beta'-EtMe3Sb[Pd(dmit)2]2, is considered as a candidate material for the quantum spin liquid (QSL) state, although ongoing debates arise from recent controversial results. Here, the results of electron spin resonance (ESR) and muon spin relaxation (muSR) measurements on beta'-EtMe3Sb[Pd(dmit)2]2 are presented. Both results indicate characteristic behaviors related to quasi-one-dimensional (q1D) spin dynamics, whereas the direction of anisotropy found in ESR is in contradiction with previous theories. We succeed in interpreting the experiments by combining density-functional theory calculations and analysis of the effective model taking into account the multi-orbital nature of the system. While the QSL-like origin of beta'-EtMe3Sb[Pd(dmit)2]2 was initially attributed to the magnetic frustration of the triangular lattice, it appears that the primary origin is a 1D spin liquid resulting from the dimensional reduction effect.

cond-mat.str-el↗

arXiv2022

Roadmap on Electronic Structure Codes in the Exascale Era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.

cond-mat.mtrl-sci↗

arXiv2022

Large-scale DFT methods for calculations of materials with complex structures

Large-scale density functional theory (DFT) calculations provide a powerful tool to investigate the atomic and electronic structure of materials with complex structures. This article reviews a large-scale DFT calculation method, the multi-site support function (MSSF) method, in the CONQUEST code. MSSFs are linear combinations of the basis functions which belong to a group of atoms in a local region. The method can reduce the computational time while preserving accuracy. The accuracy of MSSFs has been assessed for bulk Si, Al, Fe and NiO and hydrated DNA, which demonstrate the applicability of the MSSFs for varied materials. The applications of MSSFs on large systems with several thousand atoms, which have complex interfaces and non-periodic structures, indicate that the MSSF method is promising for precise investigations of materials with complex structures.

cond-mat.mtrl-sci↗

arXiv2021

Unsupervised learning-based structural analysis: Search for a characteristic low-dimensional space by local structures in atomistic simulations

Owing to the advances in computational techniques and the increase in computational power, atomistic simulations of materials can simulate large systems with higher accuracy. Complex phenomena can be observed in such state-of-the-art atomistic simulations. However, it has become increasingly difficult to understand what is actually happening and mechanisms, for example, in molecular dynamics (MD) simulations. We propose an unsupervised machine learning method to analyze the local structure around a target atom. The proposed method, which uses the two-step locality preserving projections (TS-LPP), can find a low-dimensional space wherein the distributions of datapoints for each atom or groups of atoms can be properly captured. We demonstrate that the method is effective for analyzing the MD simulations of crystalline, liquid, and amorphous states and the melt-quench process from the perspective of local structures. The proposed method is demonstrated on a silicon single-component system, a silicon-germanium binary system, and a copper single-component system.

cond-mat.mtrl-sci↗

arXiv2020

Large scale and linear scaling DFT with the CONQUEST code

We survey the underlying theory behind the large-scale and linear scaling DFT code, Conquest, which shows excellent parallel scaling and can be applied to thousands of atoms with exact solutions, and millions of atoms with linear scaling. We give details of the representation of the density matrix and the approach to finding the electronic ground state, and discuss the implementation of molecular dynamics with linear scaling. We give an overview of the performance of the code, focussing in particular on the parallel scaling, and provide examples of recent developments and applications.

physics.comp-ph↗

arXiv2020

Blue moon ensemble simulation of aquation free energy profiles applied to mono and bifunctional platinum anticancer drugs

Aquation free energy profiles of neutral cisplatin and cationic monofunctional derivatives, including triaminochloroplatinum(II) and cis-diammine(pyridine)chloroplatinum(II), were computed using state of the art thermodynamic integration, for which temperature and solvent were accounted for explicitly using density functional theory based canonical molecular dynamics (DFT-MD). For all the systems the "inverse-hydration" where the metal center acts as an acceptor of hydrogen bond has been observed. This has motivated to consider the inversely bonded solvent molecule in the definition of the reaction coordinate required to initiate the constrained DFT-MD trajectories. We found that there exists little difference in free enthalpies of activations, such that these platinum-based anticancer drugs are likely to behave the same way in aqueous media. Detailed analysis of the microsolvation structure of the square-planar complexes, along with the key steps of the aquation mechanism are discussed.

physics.chem-ph↗

arXiv2020

First-principles study of the charge ordered phase in $κ$-D$_3$(Cat-EDT-TTF/ST)$_2$: Stability of $π$-electron deuterium coupled ordering in hydrogen-bonded molecular conductors

We study the electronic and structural properties of the low-temperature ordered phase of hydrogen-bonded molecular conductors, $κ$-D$_3$(Cat-EDT-TTF)$_2$ and its selenium-substituted analog $κ$-D$_3$(Cat-EDT-ST)$_2$, by means of first-principles density functional theory~(DFT) calculations. In these compounds, the charge ordering in the $π$-electron system is coupled with the ordering of the displacements in the deuteriums forming the hydrogen-bond, equally shared by two oxygens in the high-temperature phase. While the structural optimization within the standard DFT method based on the generalized gradient approximation fails to reproduce the structural stability of the charge-ordered (CO) phase, we show that a hybrid functional of Heyd, Scuseria, and Ernzerhof can reproduce structural characters of the CO phase, owing to the more localized nature of the wave functions. Furthermore, using the ability of the hybrid functional to predict the electronic and structural properties, we find a stable noncentrosymmetric CO phase with another pattern of deuterium ordering.

cond-mat.str-el↗

arXiv2019

Highly accurate local basis sets for large-scale DFT calculations in CONQUEST

Given the widespread use of density functional theory (DFT), there is an increasing need for the ability to model large systems (beyond 1,000 atoms). We present a brief overview of the large-scale DFT code Conquest, which is capable of modelling such large systems, and discuss approaches to the generation of consistent, well-converged pseudo-atomic basis sets which will allow such large scale calculations. We present tests of these basis sets for a variety of materials, comparing to fully converged plane wave results using the same pseudopotentials and grids.

cond-mat.mtrl-sci↗

arXiv2019

Gate controlled quantum interference: direct observation of anti-resonances in single molecule charge transport

Quantum interference can profoundly affect charge transport in single molecules, but experiments can usually measure only the conductance at the Fermi energy. Because in general the most pronounced features of the quantum interference are not located at the Fermi energy, it is highly desirable to probe charge transport in a broader energy range. Here by the method of electrochemical gating, we measure the conductance and map the transmission functions of single molecules at and around the Fermi energy, and study signatures associated with constructive and destructive interference. With the electrochemical gate control, we tune the quantum interference between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), and directly observe anti-resonance, a distinct feature of destructive interference. By tuning the molecule in and out of anti-resonance, we achieve continuous control of the conductance over 2 orders of magnitude with a subthreshold swing of ~17 mV/dec, features relevant to high-speed and low-power electronics.

cond-mat.mes-hall↗

arXiv2018

Machine learning forces trained by Gaussian process in liquid states: Transferability to temperature and pressure

We study a generalization performance of the machine learning (ML) model to predict the atomic forces within the density functional theory (DFT). The targets are the Si and Ge single component systems in the liquid state. To train the machine learning model, Gaussian process regression is performed with the atomic fingerprints which express the local structure around the target atom. The training and test data are generated by the molecular dynamics (MD) based on DFT. We first report the accuracy of ML forces when both test and training data are generated from the DFT-MD simulations at a same temperature. By comparing the accuracy of ML forces at various temperatures, it is found that the accuracy becomes the lowest around the phase boundary between the solid and the liquid states. Furthermore, we investigate the transferability of ML models trained in the liquid state to temperature and pressure. We demonstrate that, if the training is performed at a high temperature and if the volume change is not so large, the transferability of ML forces in the liquid state is high enough, while its transferability to the solid state is very low.

physics.comp-ph↗

arXiv2018

Structural properties of Silicon-Germanium and Germanium-Silicon Core-Shell Nanowires

Core-shell nanowires made of Si and Ge can be grown experimentally with excellent control for different sizes of both core and shell. We have studied the structural properties of Si/Ge and Ge/Si core-shell nanowires aligned along the $[110]$ direction, with diameters up to 10.2~nm and varying core to shell ratios, using linear scaling Density Functional Theory (DFT). We show that Vegard's law, which is often used to predict the axial lattice constant, can lead to an error of up to 1\%, underlining the need for a detailed \emph{ab initio} atomistic treatment of the nanowire structure. We analyse the character of the intrinsic strain distribution and show that, regardless of the composition or bond direction, the Si core or shell always expands. In contrast, the strain patterns in the Ge shell or core are highly sensitive to the location, composition and bond direction. The highest strains are found at heterojunction interfaces and the surfaces of the nanowires. This detailed understanding of the atomistic structure and strain paves the way for studies of the electronic properties of core-shell nanowires and investigations of doping and structure defects.

cond-mat.mtrl-sci↗

arXiv2018

High-accuracy large-scale DFT calculations using localized orbitals in complex electronic systems: The case of graphene-metal interfaces

Over many years, computational simulations based on Density Functional Theory (DFT) have been used extensively to study many different materials at the atomic scale. However, its application is restricted by system size, leaving a number of interesting systems without a high-accuracy quantum description. In this work, we calculate the electronic and structural properties of a graphene-metal system significantly larger than in previous plane-wave calculations with the same accuracy. For this task we use a localised basis set with the \textsc{Conquest} code, both in their primitive, pseudo-atomic orbital form, and using a recent multi-site approach. This multi-site scheme allows us to maintain accuracy while saving computational time and memory requirements, even in our exemplar complex system of graphene grown on Rh(111) with and without intercalated atomic oxygen. This system offers a rich scenario that will serve as a benchmark, demonstrating that highly accurate simulations in cells with over 3000 atoms are feasible with modest computational resources.

cond-mat.mes-hall↗

arXiv2017

Canonical-ensemble extended Lagrangian Born-Oppenheimer molecular dynamics for the linear scaling density functional theory

We discuss the development and implementation of a constant temperature (NVT) molecular dynamics scheme that combines the Nosé-Hoover chain thermostat with the extended Lagrangian Born-Oppenheimer molecular dynamics (BOMD) scheme, using a linear scaling density functional theory (DFT) approach. An integration scheme for this canonical-ensemble extended Lagrangian BOMD is developed and discussed in the context of the Liouville operator formulation. Linear scaling DFT canonical-ensemble extended Lagrangian BOMD simulations are tested on bulk silicon and silicon carbide systems to evaluate our integration scheme. The results show that the conserved quantity remains stable with no systematic drift even in the presence of the thermostat.

cond-mat.mtrl-sci↗