Searcharxiv⌕ Search

arXiv subjects

Tsuyoshi Miyazaki

Publications and source records attributed to Tsuyoshi Miyazaki.

33 records · Page 2Linked to original sources
arXiv2017

Efficient calculation of electronic structure using O(N) density functional theory

We propose an efficient way to calculate the electronic structure of large systems by combining a large-scale first-principles density functional theory code, Conquest, and an efficient interior eigenproblem solver, the Sakurai-Sugiura method. The electronic Hamiltonian and charge density of large systems are obtained by \conquest and the eigenstates of the Hamiltonians are then obtained by the Sakurai-Sugiura method. Applications to a hydrated DNA system, and adsorbed P2 molecules and Ge hut clusters on large Si substrates demonstrate the applicability of this combination on systems with 10,000+ atoms with high accuracy and efficiency.

cond-mat.mtrl-sci↗
arXiv2016

Machine Learning for Atomic Forces in a Crystalline Solid: Transferability to Various Temperatures

Recently, machine learning has emerged as an alternative, powerful approach for predicting quantum-mechanical properties of molecules and solids. Here, using kernel ridge regression and atomic fingerprints representing local environments of atoms, we trained a machine-learning model on a crystalline silicon system in order to directly predict the atomic forces at a wide range of temperatures. Our idea is to construct a machine-learning model using a quantum-mechanical data set taken from canonical-ensemble simulations at a higher temperature, or an upper bound of the temperature range. With our model, the force prediction errors were about 2% or smaller with respect to the corresponding force ranges, in the temperature region between 300 and 1650 K. We also verified the applicability to a larger system, ensuring the transferability with respect to system size.

cond-mat.mtrl-sci↗
arXiv2015

A linear scaling DFT study of the growth of a new \{105\} facet layer on a Ge hut cluster

Ge hut clusters, which appear during heteroepitaxy of Ge on Si(001), are prototypical examples of islands formed through strain. Experimentally, complete facets are observed to form rapidly, though the mechanism is unknown. We model the growth of new faces on Ge hut clusters, using linear scaling DFT. We build realistic small huts on substrates, and show that the growth of \{105\} facets proceeds from top-to-bottom, even for these small huts. The growth of the facet is driven by the reconstruction on the \{105\} facet, and nucleates at the boundaries of the facet. We thus resolve any ambiguities in kinetic models of hut cluster growth.

cond-mat.mtrl-sci↗
arXiv2015

First-principles study of hydrogen-bonded molecular conductor $κ$-H$_3$(Cat-EDT-TTF/ST)$_2$

We theoretically study hydrogen-bonded molecular conductors synthesized recently, $κ$-H$_3$(Cat-EDT-TTF)$_2$ and its diselena analog, $κ$-H$_3$(Cat-EDT-ST)$_2$, by first-principles density-functional theory calculations. In these crystals, two H(Cat-EDT-TTF/ST) units share a hydrogen atom with a short O--H--O hydrogen bond. The calculated band structure near the Fermi level shows a quasi-two-dimensional character, with a rather large interlayer dispersion due to the absence of insulating layers in contrast with conventional molecular conductors. We discuss effective low-energy models based on H(Cat-EDT-TTF/ST) units and its dimers, respectively, where the microscopic character of the orbitals composing them are analyzed. Furthermore, we find a stable structure which is different from the experimentally determined structure, where the shared hydrogen atom becomes localized to one of the oxygen atoms, in which charge disproportionation between the two types of H(Cat-EDT-TTF) units is associated. The calculated potential energy surface for the H atom is very shallow near the minimum points, therefore the probability of the H atom can be delocalized between the two O atoms.

cond-mat.str-el↗
arXiv2015

Fragment Model Study of Molecular Multi-Orbital System $X$[Pd(dmit)$_2$]$_2$

Electronic properties of quasi-two-dimensional molecular conductors $X$[Pd(dmit)$_2$]$_2$ are studied theoretically. We construct an effective model based on the fragment molecular orbital scheme developed recently, which can describe the multi-orbital degree of freedom in this system. The tight-binding parameters for a series of $β'$-type compounds with different cations $X$ are evaluated by fitting to first-principles band calculations. We find that the transfer integrals within the dimers of Pd(dmit)$_2$ molecules, along the intramolecular and intermolecular bonds including the diagonal ones, are the same order, leading to hybridization between different molecular orbitals. This results in charge disproportionation within each molecule, as seen in our previous ab initio study [T. Tsumuraya et al, J. Phys. Soc. Jpn. 82, 033709 (2013)], and also to a revised picture of an effective dimer model. Furthermore, we discuss broken-symmetry insulating states triggered by interaction effects, which show characteristic features owing to the multi-orbital nature. The on-site Coulomb interaction induces antiferromagnetic states with intramolecular antiparallel spin pattern, while electron-lattice couplings stabilize non-magnetic charge-lattice ordered states where two kinds of dimers with different charge occupation arrange periodically. These states showing different spatial patterns compete with each other as well as with the paramagnetic metallic state.

cond-mat.str-el↗
arXiv2015

Optimized multi-site local orbitals in the large-scale DFT program CONQUEST

We introduce numerical optimization of multi-site support functions in the linear-scaling DFT code CONQUEST. Multi-site support functions, which are linear combinations of pseudo-atomic orbitals on a target atom and those neighbours within a cutoff, have been recently proposed to reduce the number of support functions to the minimal basis while keeping the accuracy of a large basis [J. Chem. Theory Comput., 2014, 10, 4813]. The coefficients were determined by using the local filter diagonalization (LFD) method [Phys. Rev. B, 2009, 80, 205104]. We analyse the effect of numerical optimization of the coefficients produced by the LFD method. Tests on crystalline silicon, a benzene molecule and hydrated DNA systems show that the optimization improves the accuracy of the multi-site support functions with small cutoffs. It is also confirmed that the optimization guarantees the variational energy minimizations with multi-site support functions.

cond-mat.mtrl-sci↗
arXiv2014

Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10,000+ atoms

The recent progress of linear-scaling or O(N) methods in the density functional theory (DFT) is remarkable. We expect that first-principles molecular dynamics (FPMD) simulations based on DFT can now treat more realistic and complex systems using the O(N) technique. However, very few examples of O(N) FPMD simulations exist so far and the information for the accuracy or reliability of the simulations is very limited. In this paper, we show that efficient and robust O(N) FPMD simulations are now possible by the combination of the extended Lagrangian Born-Oppenheimer molecular dynamics method, which was recently proposed by Niklasson et al (Phys. Rev. Lett. 100, 123004 (2008)), and the density matrix method as an O(N) technique. Using our linear-scaling DFT code Conquest, we investigate the reliable calculation conditions for the accurate O(N) FPMD and demonstrate that we are now able to do actual and reliable self-consistent FPMD simulation of a very large system containing 32,768 atoms.

cond-mat.mtrl-sci↗
arXiv2014

Efficient Calculations with Multisite Local Orbitals in the large-scale DFT Code CONQUEST

Multisite local orbitals, which are formed from linear combinations of pseudo-atomic orbitals from a target atom and its neighbor atoms, have been introduced in the large-scale density functional theory calculation code CONQUEST. Multisite local orbitals correspond to local molecular orbitals so that the number of required local orbitals can be minimal. The multisite support functions are determined by using the localized filter diagonalization (LFD) method [Phys. Rev. B 2009, 80, 205104]. Two new methods, the double cutoff method and the smoothing method, are introduced to the LFD method to improve efficiency and stability. The Hamiltonian and overlap matrices with multisite local orbitals are constructed by efficient sparse-matrix multiplications in CONQUEST. The investigation of the calculated energetic and geometrical properties and band structures of bulk Si, Al and DNA systems demonstrate the accuracy and the computational efficiency of the present method. The representability of both occupied and unoccupied band structures with the present method has been also confirmed.

cond-mat.mtrl-sci↗
arXiv2013

Density-functional theory study of gramicidin A ion channel geometry and electronic properties

Understanding the mechanisms underlying ion channel function from the atomic-scale requires accurate ab initio modelling as well as careful experiments. Here, we present a density functional theory (DFT) study of the ion channel gramicidin A, whose inner pore conducts only monovalent cations and whose conductance has been shown to depend on the side chains of the amino acids in the channel. We investigate the ground-state geometry and electronic properties of the channel in vacuum, focusing on their dependence on the side chains of the amino acids. We find that the side chains affect the ground state geometry, while the electrostatic potential of the pore is independent of the side chains. This study is also in preparation for a full, linear scaling DFT study of gramicidin A in a lipid bilayer with surrounding water. We demonstrate that linear scaling DFT methods can accurately model the system with reasonable computational cost. Linear scaling DFT allows ab initio calculations with 10,000 to 100,000 atoms and beyond, and will be an important new tool for biomolecular simulations.

q-bio.BM↗
arXiv2013

Effect of magnetic field on the superconducting phase in the electron-doped metallic double-chain compound Pr$_{2}$Ba$_{4}$Cu$_{7}$O$_{15-δ}$

We report the magnetotransport and $dc$ magnetic susceptibility of the polycrystalline samples of Pr$_{2}$Ba$_{4}$Cu$_{7}$O$_{15-δ}$, to examine the effect of magnetic field on the superconducting phase of the metallic CuO double chain. The resistive critical magnetic field is estimated to be about 21 T at low temperatures from the resistive transition data. On the other hand, the corresponding critical field determined from the magnetization measurements gives rise to a very low value of $\sim 0.3$T at 2 K. These discrepancies in the magnetic response between the resistivity and magnetization data are caused by disappearance of the magnetically shielding effect even in relatively lower fields. In spite of the observation of the resistive drop associated with the superconducting transport currents, the suppression of the diamagnetic signal is probably related to the superconductivity of quasi one-dimensional CuO double-chain. The behavior of Seebeck coefficient in the superconducting Pr$_{2}$Ba$_{4}$Cu$_{7}$O$_{15-δ}$ is discussed on the basis of the double chain model from the density functional band calculation.

cond-mat.supr-con↗
arXiv2013

Cation Dependence of the Electronic States in Molecular Triangular Lattice System β'-X[Pd(dmit)_2]_2: A First-principles study

The electronic structure of an isostructural series of molecular conductors, β'-X[Pd(dmit)_2]_2 is systematically studied by a first-principles method based on the density-functional theory. The calculated band structures are fitted to the tight-binding model based on Pd(dmit)_2 dimers on the triangular lattice. We find systematic variation in the anisotropy of the transfer integrals along the three directions of the triangular lattice taking different values. The transfer integral along the face-to-face stacking direction of Pd(dmit)_2 dimers is always the largest. Around the quantum spin liquid, X = EtMe_3Sb, the other two transfer integrals become comparable. We also report sensible differences in the distribution of wavefunctions near the Fermi level between the two dmit ligands of the Pd(dmit)_2 molecule.

cond-mat.str-el↗
arXiv2012

Linear-scaling implementation of exact exchange using localized numerical orbitals and contraction reduction integrals

We present enhancements to the computational efficiency of exact exchange calculations using the density matrix and local support functions. We introduce a numerical method which avoids the explicit calculation the four-center two-electron repulsion integrals and reduces the prefactor scaling by a factor N, where N is the number of atoms within the range of the exact exchange Hamiltonian. This approach is based on a contraction-reduction scheme, and takes advantage of the discretization space which enables the direct summation over the support functions in a localized space. Using the sparsity property of the density matrix, the scaling of the prefactor can be further reduced to reach asymptotically O(N).

physics.chem-ph↗
arXiv2006

First-Principles Study of Electronic Structure in $α$-(BEDT-TTF)$_2$I$_3$ at Ambient Pressure and with Uniaxial Strain

Within the framework of the density functional theory, we calculate the electronic structure of $α$-(BEDT-TTF)$_2$I$_3$ at 8K and room temperature at ambient pressure and with uniaxial strain along the $a$- and $b$-axes. We confirm the existence of anisotropic Dirac cone dispersion near the chemical potential. We also extract the orthogonal tight-binding parameters to analyze physical properties. An investigation of the electronic structure near the chemical potential clarifies that effects of uniaxial strain along the a-axis is different from that along the b-axis. The carrier densities show $T^2$ dependence at low temperatures, which may explain the experimental findings not only qualitatively but also quantitatively.

cond-mat.str-el↗
arXiv2003

Phase Diagram of $β'$-(BEDT-TTF)$_2$ICl$_2$ under High Pressure Based on the First-Principles Electronic Structure

We present a theoretical study on the superconductivity of $β'$-(BEDT-TTF)$_2$ICl$_2$ at $T_{\rm c}=$14.2 K under a high hydrostatic pressure recently found, which is the highest among organic superconductors. In the present work, we study an effective model using the fluctuation-exchange (FLEX) approximation based on the results of first-principles calculation. In the obtained phase diagram, the superconductivity with $d_{xy}$-like symmetry is realized next to the antiferromagnetic phase, as a result of the one-dimensional to two-dimensional crossover driven by the pressure.

cond-mat.supr-con↗