Activity Reports ofMaterials Design through Computics:
Complex Correlation andNon-equilibrium Dynamics
July, 2015

Scientific Research on Innovative Areas by MEXT
during July 2010 and March 2015

PREFACE

This booklet is a report of a research project ``Materials Design through Computics: Complex
Correlation and Non-equilibrium Dynamics” conducted as a ``Scientific Research on InnovativeAreas” supported by Ministry of Education, Culture, Sports, Science and Technology (MEXT),
Japan. The project started in July of 2010 and successfully ended in March of 2015. The research
project was conducted by 45 research groups including 135 researchers in total.
Computational approach to science was started around 1960s. An approximation called HartreeFock approximation in describing the electron-electron interaction was developed and applied to avariety of molecules in 60s with the aid of computers.1 Density-functional theory (DFT) innovatedby Walter Kohn, Pierre Hohenberg and Lu Sham in 1964 had been developed in 60s and 70s andprovided a firm theoretical framework and actual prescriptions to calculate electron states of not
only molecules but also condensed matters. 2 Today, computational science is recognized as thethird approach which complements the previous two approaches, experimental and theoretical, andallows us to access new aspects of phenomena in nature.
One of the typical stances of people in the field of computational science has been solving the basicequations with the aid of computers. Computers themselves have been black boxes for scientists inphysics and chemistry. Collaboration between physical/chemical science and computer science orinformation technology has been very rare.
Current dramatic change in computer architecture is awakening scientists with this happy and oldstance. The performance of a single CPU or a compute core is already saturated, corresponding tothe limitation of Moore’s scaling law on the device integration. Then the only way to make asupercomputer is gathering a huge number of compute cores and nodes and connecting them withhigh speed networks. The K computer at Kobe, Japan, for instance, which shows the peak
performance of 10.62 PetaFLOPS is composed of 640 thousands compute cores connected by the6-dimensional Tofu (Torus Fusion) networks. In the coming supercomputers, in addition to suchmany-core massively parallel architecture, some hardware accelerators should be introduced. 3
Owing to this complexity in the current and next computer architecture, it is almost impossible toexploit potential power of the supercomputers, unless we tune our application codes progressively.
The tuning in this context means not only improvements of the existing application codes but also
1The ``super”-computer in those days has the performance of only 1 MFLOPS (Mega FLoating-pointOperations Per Second) [CDC 6600, (1964)], being much slower than the current personal computers.
2 A systematic calculations for the structural characteristics and energy bands for simple metals are
performed and documented in 1978 (V. L. Moruzzi, J. F. Janak, and A. R. Williams, CalculatedElectronic Properties of Metals, Pergamon Press)
3 Top500 supercomputing sites: http://www.top500.org/i

developments of new algorithms suitable to the parallel architecture. The algorithms to solve theissues rely on mathematical methods. Hence the tuning includes innovation of new mathematicalmethodology to tackle most important scientific issues and then its implementation on the newcomputer architecture. This requires an effort to analyze basic equations describing phenomena innature and innovate new algorithms. These efforts we call compuics. Mathematics has contributed
a lot to progress in science since Principia by Isaac Newton. Computics in this century may be a
new approach to clarify underlying principles in nature.
This project focuses complex correlation and non-equilibrium dynamics in phenomena in materials.
Properties of materials are determined by competition of various physical and chemicalinteractions: Covalency, ionicity and metallicity are typical ingredients to determine properties ofmaterials. Electron Correlation is also an important factor. In nano-materials and structures,nanoscale shape decisively affects the relevant wave-functions and then induces new properties
hidden in bulk structures. We call this complex correlation. Femtosecond laser irradiation onmaterials, for instance, causes electron excitation and then ionic motions. It occasionally induces
structural transformation. This is a new way of materials design by utilizing non-equilibriumdynamics.
In order to reveal complex correlation and non-equilibrium dynamics, developments ofcomputational schemes along three axes are required. First, in the nanometer scale objects,
quantum effects are important. On the other hand, 10-cube-nanometer objects are composed of 100
thousands atoms. Quantum mechanical electronic structure calculations for 100-thousands atoms
are certainly unprecedented. This is a challenge along the space axis. Second, the electron
excitation followed by the ionic motions is a multi-scale phenomena: Electron excitation takes
place in femtosecond timescale and ionic motions are in picoseconds; structural transformation
requires nano-, micro, or even mili-seconds. We are challenged along the time axis. Thirdly,
materials are composed of many electrons and nuclei. In describing their electronic properties,materials are regarded as interacting electron systems. Accurate calculations based on quantum
mechanical many-body theory are indispensable. This is a challenge along the accuracy axis. In
our projects, many efforts have been done on these lines.
This report consists of three parts. In Part I, activities in ``Architecture and Algorithms of High
Performance Computing” are reported. They are mainly in the field of computer science and/orapplied mathematics. But the collaborations between this field and the field of computational
materials physics are also reported. Principal investigators in this Part are Mary Inaba (Universityof Tokyo), Daisuke Takahashi (University of Tsukuba) and S.-L. Zhang (Nagoya University).
Activities of other two research groups performed during 2013-2014 are also reported in Part I.
Part II is devoted to the activities in ``New Development in Density-Functional Theory”. Densityii

functional theory (DFT) has been contributing tremendously to reveal materials properties in thesedecades. The exchange-correlation functional which describes many-body effects is still improvedand widens a set of the target materials which are described by DFT. Efforts along the space axis
and time axis are also documented in Part II. Principal investigators in this Part are AtsushiOshiyama (University of Tokyo), Shinji Tsuneyuki (University of Tokyo), Satoshi Watanabe(University of Tokyo), Hiroshi Nakanishi (Osaka University) and Takahisa Yamato (NagoyaUniversity). Activities of other nine research groups including experimental works performed
during 2013-2014 are also reported in Part II.
In Part III, activities in `` Beyond Density-Functional Theory” are reported. Current DFT has
certainly limitation. In particular, materials with strong electron correlation are difficult to betreated by the current DFT. Theory and computational schemes which are beyond DFT are certainlyimportant. In our project, several efforts based on the perturbation theory, a new down-folding
approach and so forth have been done. Principal investigators in this Part are Masatoshi Imada(University of Tokyo), Yasutami Takada (University of Tokyo) and Kazunori Sato (OsakaUniversity). Activities of other seven research groups including experimental works performed
during 2013-2014 are also reported in Part III.
Research activities achieved by other ten research groups during the period of 2011 – 2012 are notincluded in this booklet due to the limitation of the pages. The activities are accessible on thecomputics web page, http://computics-material.jp/index-e.html. The researchers in the ten projects
include I. Hamada (NIMS), M. Hase (University of Tsukuba), H. Hirayama (Tokyo Institute ofTechnology), H. Ono (Kyushu University), F. Shimojo (Kumamoto University), M. Kitajima(National Defense Academy), M. Saito (Kanazawa University), H. Tanaka (Osaka University), Y.
K. Zhou (Osaka University) and T. Kotani (Tottori University).
The online version of this report is available thorough http://computics-material.jp/index-e.html. I
wish this booklet contributes to the progress in a new growing field, computics.
Tokyo, July 2015

Atsushi Oshiyama
LeaderMaterials Design through Computics:
Complex Correlation and Non-equilibrium Dynamics

iii

CONTENTS

Part I

Architecture and Algorithms of High Performance Computing

High-Speed Ultra-Low-Power Simulation Methodology for Material Science
M. Inaba, H. Imai, R. Suda, K. Hiraki····························································································· 1
Numerical Computation Algorithms for Large-Scale Parallel Environment
D. Takahashi, T. Imamura, H. Tadano ··························································································· 11
Fast Solution for Ultra-Large Scale Systems as a Basis of Computational Materials ScienceS.-L. Zhang, T. Sogabe, I. Imahori, T. Miyata, Y. Yamamoto························································· 22
Development of High Performance Parallel Eigensolvers for the Needs in Computational Quantum
ScienceT. Sakurai ······································································································································ 33
Hybrid Mathematical Principles for Ultra-Large-Scale Massively Parallel Electronic Structure
Calculations
T. Hoshi ········································································································································· 37

Pat IINew Development in Density-Functional Theory

Density-Functional Approach to Atomic and Electronic Structures and their Dynamics in NanoStructures
A. Oshiyama, J.-I. Iwata, T. Ozaki, T. Miyazaki, E. Tsuchida ······················································· 45
Studies on Structure Sampling and Non-Equilibrium Dynamics Using Ab-Initio MolecularDynamics Methods
S. Tsuneyuki, Y. Yoshimoto, J. Yamauchi, M. Otani ···················································· 59
Nanoscale Non-Equilibrium Electric Transport Dynamics Based on Density Functional Theory
S. Watanabe, K. Watanabe, S. Souma, T. Ono ··············································································· 71
New Properties of Materials Probed by Proton and Muon, and their Quantum Dynamics
H. Nakanishi, H. Goto, M. Geshi, M. Wilde, W. Dino,
H. Kasai, K. Fukutani, H. Kikuji ································································································· 85iv

Reaction Analysis and Conformational Sampling for Multidimensional Large Scale Systems
T. Yamato, A. Mitsutake ················································································································· 99
Developments of First-Principles Multiscale Simulation for Coupled Dynamics of Light-Wave andElectrons in Dielectrics
K. Yabana ····································································································································· 111
Hybrid-Density-Functional Theory for Magnetic Materials
Y. Gohda ······································································································································· 117
Dynamics of Electron, Spin and Heat Transport through Single Atomic and Molecular Junctions
M. Kiguchi ··································································································································· 121
Electron-Phonon Coupling Dynamics and High-Sensitive Detection of Nano-Scale Phonon
Wavepackets in Carbon-Based Materials
J. Takeda .................................................................................................................................... 125
First-principle molecular dynamics analyses on nonlinear optical properties change of Si nano-dot
Y. Shigeta, K. Shiraishi, M. Nakano ···························································································· 129
De novo design of the functional transition metal proteins using a coiled-coil scaffold
Y. Takano ····································································································································· 134
Construction of Material Design System on Next-Generation Density Functional Theory
Y. Imamura ·································································································································· 141
First Principles Simulation of Nonequilibrim Transport at Nano-contact and Design of FunctionalMaterials
H. Nakamura ······························································································································· 145
Reactions Analysis of Plasma with Self-Assembled Monolayer
M. Shinohara ······························································································································· 152

Part III

Beyond Density-Functional Theory

Frontiers of Ab-Initio Effective Models and Correlation ScienceM. Imada, T. Miyake, K. Nakamura, T. Oguchi, R. Arita, S. Ishibashi,
A. Fujimori, S. Shin ····················································································································· 156v

Many-Body Theory from First Principles
Y. Takada, K. Shirai, R. Maezono, H. Maebashi, M. Sakurai······················································ 170
Computational Design and Realization of Spintronics Materials
K. Sato, T. Oda T. Nozaki, M. Ogura··························································································· 182
MBE Growth and Magnetic Properties of Diluted Magnetic Semiconductors Based on II-VI andIV-VI Compounds
K. Zhang, S. Ishitsuka, T. Domon, R. Sakurai, R. Akiyama,
K. Kanazawa, S. Kuroda ············································································································· 194
Surface Plasmons and Magneto-Optics in Metal/Magnetic Quantum Wells
H. Matsui ····································································································································· 198
Development of Nonequilibrium Dynamical Mean-Feld Theory and its Application to LowDimensional Strongly Correlated SystemsN. Tsuji ········································································································································ 202
Effect of Electron-Phonon Couplings on Electronic Structures and Material Design
T. Koretsune, S. Saito ·················································································································· 206
Development of Computational Code of Electron Excitation Dynamics in Green’s Function
MethodK. Ohno, S. Ono, R. Kuwahara ··································································································· 210
Large Scale First-Principles Calculations on Transition Metal Oxide Superlattices
F. Ishii, M. Saito ·························································································································· 214
Development of Quantum Multi-Component Molecular Theory and its Application to Material
DesignM. Tachikawa ······························································································································ 217vi