Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

3.2

First-Principles Calculationof Material Properties

44

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical study on dynamical processes inheterogeneous catalysis using density functional
theory and machine learning methods
H. H. HALIM, T. N. PHAM,Y.-L. WANG, T. OTA, S. E. M. PUTRA
Y. HAMAMOTO, K. INAGAKI, I. HAMADA, and Y. MORIKAWA
Department of Precision Engineering, Graduate School of Engineering,Osaka University, 2-1 Yamadaoka Suita, Osaka 565-0871

In 2022-2023, we carried out theoretical investigation of chemical processes at surfaces
and interfaces, Cu-Zn surface alloy formation on Cu(997), Hydrogenation of formate
species using atomic hydrogen on a Cu(111)model catalyst, oxygen vacancy migrationin SrFeO3−δ and Sr3 Fe2 O7−δ , NO-H2O coadsorption on Cu(111), and activity and selectivity of N2 ﬁxation on B doped g-C9 N10 .
In this report, we report Cu-Zn surface alloy formation on Cu(997)[1]. The catalysts
based on metal-alloys are well recognized in
the ﬁeld of heterogenous catalysis considering
the emerging of unique properties upon alloying. Given the optimal composition and environment, these catalysts can oﬀer high catalytic performance that outperform their alloy
constituents. There have been notorious examples on the application of metal-alloy based
catalysts in heterogenous catalysis. In thepresent study, we focus on Cu-Zn surface alloy
which has been reported to be very active formethanol synthesis by hydrogenation of CO2 .
Experimental studies have shown that the deposition of Zn on Cu(111) promotes the activity of methanol production by an order ofmagnitude at Zn coverage of 0.197. In addition, the Cu-Zn alloy has been reported as agood model of Cu/ZnO/Al2 O3 (CZA), the industrial catalyst used to synthesize methanol
by hydrogenation of CO2 . Thus, this alloy has
been extensively involved in the investigationof the true active site of CZA which remains
under controversy.
Recently, it was reported that by coupling
Molecular Dynamics (MD), active-learning,
and automated event detection, Lim et al.
have successfully reveal the restructuring
mechanisms of Pd deposited on Ag. By adopting similar methodologies, we performed MD
simulation of Zn depositions on Cu(997) surface to explicitly capture the mechanisms thatare responsible to the Cu-Zn surface alloying.
The MD simulations were implemented basedon force-ﬁeld that was trained by means ofGaussian Process (GP). The database, containing information of atomic forces acting
on various environments, were obtained from
DFT calculations. The task of training wasdone by using Fast Learning of Atomistic Rare
Events (FLARE) code which utilizes the uncertainty information from GP, together withactive on-the-ﬂy learning scheme to build theforce-ﬁeld eﬃciently.
We used DFT calculations to provide forcesof the central atom on each atomic environment. All DFT calculations were performed
using the STATE code. The electron-ion
interaction was described by ultrasoft pseudopotentials. We took into account the vander Waals (vdW) interactions by applying
optB86b-vdW exchange correlation functional
as implemented in the STATE code.
To construct GP force-ﬁeld, we used FLARE

45

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

code with two- and three-body multispecies
kernels. The interaction cutoﬀs for two- andthree-body kernels are set to 7.0 Å and 4.5 Å,respectively. The hyperparameters embedded
to these kernels, namely two-body signal variances (σ2 ), two-body length scale (l2 ), threebody signal variances (σ3 ), three-body lengthscale (l3 ), and noise hyperparameter (σn ) was
optimized by maximizing the log marginal likelihood using BFGS algorithm as implemented
in SciPy used inside the FLARE code. The
database is constructed by employing active
and on-the-ﬂy learning scheme that update thedatabase based on uncertainty information calculated by GP. In order to provide new atomic
environments to be candidate for the database,
MD code internal to FLARE is used to evolve
atomic structures with 1 fs timestep within
canonical (NVT) ensemble. The temperature
is set up at 700 K with all atoms are allowed to
move. To obtain more diverse atomic environments, we manually changed the initial structure after certain MD steps during the on-theﬂy learning when no signiﬁcance improvementin the Mean Absolute Error (MAE) was found.
The details of this procedure and the resulting
database are reported in the next section.
To observe the alloying process of Cu-Zn,
we performed MD simulations within NVT ensemble at temperature 700 K for up to 6.25
µs. Figure 1 shows the evolution of deposited
Zn atoms on Cu(997) until the Cu-Zn surface
alloy is formed. To clearly observed the number of Zn atoms that substituted at the terrace, we also plotted the composition of Cu
and Zn atoms as a function of rows for every
certain timesteps. Such plots accompany each
MD snapshots in Figure 1. The snapshots of
the MD simulation are also presented as video
in the Supporting Information. In the beginning (Figure 6a), the Zn atoms are found to
localize at the step edge, covering the original Cu step adatoms. The proﬁle of boundary
between Cu and Zn is still fairly linear. After
1.25 µs, some of the Zn atoms are incorporated

Figure 1: The snapshots of MD simulations
showing the evolution of deposited Zn atoms
on Cu(997). The green to yellow atom indicates the Cu atom, the red atom indicates
Zn as adatom, and blue atom indicates substituted Zn atom. The two plots accompanied
each snapshot show the composition of atom as
a function of row. In each plot, the red, blue,
light green, and dark green bars indicate thenumber of Zn as adatom, Zn as incorporated
atom, Cu as surface atom, and Cu atom whichis covered by additional Cu or Zn layer.
at the upper and lower terrace near the stepedge (Figure 1b). At this stage, almost no Zn
atoms are incorporated at the middle terrace.
We also noticed Zn atoms are dominantly incorporated to the upper terrace whereas only
few incorporated Zn atoms found at the lower
terrace. After 2.5 µs (Figure 1c), the distribution of the Zn on the surface and the number ofincorporated Zn atom are still relatively similar.

References[1] Harry Handoko Halim and Yoshitada
Morikawa: ACS Physical Chemistry Au
2, 430-447 (2022).

46

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Prediction of Material Properties using Density Functional
TheoryOsamu Sugino
Institute for Solid State Physics,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8581

We have studied properties of cuprate

The accuracy of the xc functionals issuperconductors and zirconia cathode materials

essential in providing reliable prediction ofusing the SCAN and PBE exchange-correlationmaterial properties. We tried to improve the(xc) functionals, respectively, of the density

accuracy using a machine learning method. We

functional theory (DFT). Our DFT calculations

used the accurate electronic structures of smallof cuprates reproduced lattice properties andmolecules provided by a quantum chemicalelectronic band structures consistent withcalculation together with the theoreticallyavailable experimental data and predicted

derived properties of the xc functionals [4].

properties of layered ones [1]. Our calculatedThose different data of molecules and theory

free energy landscape for the oxygen reduction

are found to play a complementary role inreaction occurring on the zirconia surface

increasing the accuracy and numerical stability

suggested that a high reactivity appears notof the functional as demonstrated by calculation

only when doped with nitrogen atoms andof various crystals.

oxygen vacancies also in the pristine conditions.
It is therefore possible that the role of defects

References

may be increase of the carrier conductivity[1] A. N. Tatan, et al., AIP Advances 12,

rather than enhancement of the reactivity [2].

105308 (2022).

We have used for the electronic structure[2] S. Muhammady, et al., J. Phys. Chem. C

calculations the packages VASP and Quantum

126, 15662 (2022).

Espresso

ISSP[3] https://www.pasums.issp.u-tokyo.ac.jp/abics

supercomputers. We have used for modeling[4] R. Nagai et al., Phys. Rev. Research 4,

the defective zirconia the abICS package

013106 (2022); Electron. Struct. 1, 37-38

developed by S. Kasamatsu [3].

(2022).

implemented

in

the

47

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Clarification of Microscopic Mechanisms of Semiconductor Epitaxial
Growth and Device-Interface Formation by Large-Scale Quantum-TheoryBased Computations
Atsushi Oshiyama
Institute of Materials and Systems for Sustainability, Nagoya University
Furo-cho, Chikusa-ku, Nagoya 464-8601
In the fiscal year of 2022, on the basis of theproperties. Several methods have been proposed

total-energy electronic-structure calculations andto produce graphene sheets. Among them, an

molecular

within theemerging technology consists in the thermal

density-functional theory (DFT), we have studied

decomposition of silicon carbide (SiC). The major

the epitaxial growth of wide-gap semiconductors

advantage of this technique is the possibility ofand graphene sheets, atomic and electronic struc-growing graphene directly on a semiconductingtures of semiconductor surfaces and their inter-

substrate, thus avoiding the difficult step offaces with insulators. The main computational

extracting and transferring graphene sheets on atools are our RSDFT (Real Space DFT) code andsubstrate. From a scientific standpoint, the forma-

RS-CPMD (Car-Parrinello Molecular Dynamics)

tion of graphene from a SiC crystal, possibly

dynamics

simulations

code as well as VASP code. Specifically, we havestudied 1) the atom-scale mechanism of GaN epitaxial growth [1,2], 2) the mechanism of graphene
growth on SiC surfaces [3], 3) atomic and electronic structures of stepped SiC surfaces [4] andGaN/AlSiO interfaces [5], and 5) the role of point
defects in SiN which have been speculated to be
the principal element of current flash memories.
The below is the explanation of the issues 2) and

Fig. 1: Free-energy profile of Si desorption
from the step edge and major relevant
configurations. The color code for the atoms isblue for Si and brown for C. The collective
variable (CV) used in the meta-dynamics isthe distance between a desorbing Si (redsphere) and the center of mass (black sphere)of the lower terrace site formed by three C
atoms.

5) above.

Initial stage of graphene formation on
SiC(0001) Surfaces
Graphene has a consolidated background as aninnovative

two-dimensional(2D)

material

because of the peculiar electronic and mechanical48

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyoof a graphene sheet. We have found that asubsequent Si desorption leaves behind undercoordinated C atoms and this, in turn, triggers theformation of three stable C-C bonds via an
exothermic reaction. This second step paves theroute to the formation of larger carbon structure at
the SiC(0001) surface. Following the guidelinesthat these simulations indicate, we focused on theprocesses occurring upon desorption of several Si
atoms. We have clarified how small C clusters

Fig. 2: Free-energy landscape (the bottom-left)
and minimum free-energy reaction pathway(path1 + path2 + path3: the dotted, solid anddashed lines) for the clustering of carbon
atoms. The labels from (I) to (VI) in thelandscape indicate the positions of the (meta)
stable configurations along the pathway. The
stable configurations (I) and (VI) are shown in
the top-left and the bottom-right, respectively.
In (I), C5 and C4 clusters are highlighted withmagenta and green spheres, respectively.
Those clusters become a single cluster C9 in
the final configuration (VI). The CV1 is the
distance between the COM of C5 (left black
sphere) and COM of C4 (right black sphere)
and the CV2 is the distance between the COM
of C5 and a C atom (yellow sphere).

formed at the exposed surface can merge into alarger structure presenting a C6 ring, the expected
seed of a graphene-like conformation (Fig. 2).
The extension of this carbon bond network
realized in this way is accompanied by aremarkable energy gain, leading to an exothermic
reaction and to a stable carbon structure precursorof an actual graphene flake.

Nitrogen Vacancy in Silicon Nitride:
Emergence of Floating Gap Statesaccompanied by a selective removal of Si atoms

Silicon nitride （SiN） thin films are fabricatedand subsequent condensation of C atoms, is stillnear interfaces of Si-MOS structures, and utilized

an unexplored issue.

as memory elements in non-volatile

flash

Based on the first principles molecular dyn-memories which sustain our energy-saving society.

amics empowered by free energy sampling

The microscopic mechanism of the memory

methods, we have clarified atomistic processes offunction

the initial stage of graphene formation on

performed

SiC(0001). Our simulations have shown that theapproximation

desorption of a Si atom from a step edge and its

functional and clarified the atomic and electronic

subsequent migration to a stable site on the

structures of nitrogen vacancy (VN) in SiN. The

nearby terrace is an endothermic reaction (Fig. 1).

results indicate that the floating electron state

Yet, this step is an essential initial trigger to theinherent to host SiN is localized near VN andprocess that eventually will lead to the formationinduce a gap state which is free from energy49

isunknown,DFT
tohowever.

calculations
the

We

with

have
hybridexchange-correlation

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

barriers upon electron capture and emission, thus
being a strong candidate for the memory unit.

Fig. 4: KS orbital of localized the floating statein the gap of SiN. Isovalue surface of theorbital from (a) a perpendicular and (b) aparallel directions to a plane consisting of 3neighbor Si atoms.

Fig. 3: KS orbital of the CBB of β-Si3N4
viewed from c axis (a) and from its
perpendicular direction (b). The isovalue
surface of the KS orbital is shown by theyellow (+) and bluegreen (-) blobs. The blueand gray balls depict Si and N atoms,
respectively.

the exchange splitting.
More interestingly, the floating state near CBB(Fig. 3) capture additional electrons and localizednear VN (Fig. 4). This is due to the ionicity of

Figure 3 shows the Kohn-Sham (KS) orbital of

SiN: The N atom in SiN is an anion so that VN isthe conduction-band bottom (CBB) of SiN (itscrystallineform

β-Si3N4).

The

orbitaleffectively positive, thus attracting electrons. Thisisgenerates additional gap states, making VN

distributed not near atomic sites but in the internal

multiply charged. The floating state localized inspace, showing the floating character. We havethe N-deficit region may be responsible for thefound from the DFT calculations that the floating

memory function.

state is ubiquitous in various sparse materials such

The group id codes for the achievements

as carbon nanomaterials and even in typicalabove are k0042 and m0037.

tetrahedral-symmetry semiconductors [Matsushita,
Oshiyama: PRL 2012, 2014, Nano Lett. 2017].

Related publications

When a single N atom is removed from SiN[1] M. Boero, K. M. Bui, K. Shiraishi, K. Ishisone,
Y. Kangawaa, and A. Oshiyama, Appl. Surf. Sci.
599, 153935 (2022).
[2] K. M. Bui, K. Shiraishi and A. Oshiyama,Appl. Surf. Sci. 613, 155840 (2023).
[3] M. Boero, F. Imoto and A. Oshiyama, Phys.
Rev. Materials 6, 093403 (2022).
[4] T. Kimura, K. Chokawa, K. Shiraishi, and A.
Oshiyama, Phys. Rev. B 106, 035309 (2022).
[5] K. Chokawa, K. Shiraishi and A. Oshiyama,(i.e., VN), the nearest neighbor three Si atoms lose
their partner, inducing 3 Si dangling bonds (DBs).
These DB states are linear combined and induce a
totally symmetric state in the valence band andremaining two states in the gap. Depending on theposition of the Fermi level in the gap, VN changes

J. Appl. Phys 133, 065301 (2023).
[6] F. Nanataki, K. Shiraishi, J.-I. Iwata, Y.-i.
Matsushita, and A. Oshiyama, Phys. Rev. B 106,155201 (2022)

its charge state from +1 to -3, showing interesting
competition between the Jahn-Teller splitting and50

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Understanding structure-property relationships of disorderedmaterials using first-principles based high-throughput
simulation framework
Shusuke KASAMATSU
Academic Assembly (Faculty of Science),
Yamagata University, Kojirakawa, Yamagata-shi, Yamagata 990-8560

Characterizing the order within disorder of

to learn energetics for varying compositions

atomic arrangements in materials is imperative

were discussed [2].

for predicting, understanding, and designing a

As a first application to an unsolved

wide variety of materials functionalities such as

materials science problem, abICS was used toelectronic,

thermalunderstand the hydration behavior of heavily

conductivity/insulation and catalytic activity.

Sc-doped BaZrO3, known as a promising

Recently, we have been focusing on developing

perovskite proton conductor for solid oxide fuelmethods

statisticalcells. Although this class of materials has beendisorderedknown as a good proton conductor for 40 years,

systems, and we have also started to consider

the local structure that activates the hydration

how to analyze such huge amounts of data toreaction, which is the key reaction to introduce

extract

protons into the system, remained unknown.

ionic,

toandperform

thermodynamics

sufficient

sampling

meaningfulinstructure-property

relationships.

Using abICS, we simulated the ratio of Sc-VO-

For sampling of disordered crystalline

Sc, Sc-VO-Zr, and Zr-VO-Zr that contribute tosystems, we had already introduced our abICS

hydration under experimental thermodynamic(ab Initio Configuration Sampling) framework

conditions. We also obtained a machine-for deriving an on-lattice neural network model

learning model for lattice volumes andfromfirst-principles

in

past

predicted

year,

we

lattice constants in excellent agreement withbenchmarked its performance on calculating

experiment. Careful comparison with in situ

temperature-dependent disorder in the cation

XAS and thermogravimetry measurements leadsublattice of three spinel oxides. The efficiency

to the conclusion that Sc-VO-Sc and Sc-VO-Zrof the approach in an active-learning setting

are the active sites for hydration [3].

Activity

Reports

calculations
[1].

This

was demonstrated clearly against random
sampling,andissuessuchasdoping and hydration-dependent

In the case of liquid and amorphous systems,

accuracy

we have been relying on available software fordegradation vs. lattice relaxation and the ability

neural network potential training such as

51

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Simple-NN [4]. Training a reliable model forcharacterize the subtle difference between

liquid and amorphous systems up to two

liquid and amorphous ZnCl2 in terms of thecomponents is now relatively easy to achieve,

intermediate-range order, which may be related

and for such systems, we have now started toto the exponential decay in viscosity at theconsider how to understand the order withinglass transition.

disorder. Towards this end, we have been
examining the applicability of topological data

References

analysis [5], which characterizes the structure[1] S. Kasamatsu, ISSP Supercomputer Centerin terms of the size and shapes of rings andActivity Report 2020, pp. 16-26.

cavities. Figure 1 shows the temperature-[2] S. Kasamatsu et al., J. Chem. Phys. 157,

dependent first order persistence diagram for104114 (2022).

liquid and amorphous ZnCl2, where each dot[3] K. Hoshino, S. Kasamatsu, et al., Chem.

corresponds to a ring of Zn atoms; the “birth”

Mater. 35, 2289-2301 (2023).

axis corresponds to the bond distance for[4] K. Lee et al., Comp. Phys. Comm. 242, 95

forming the rings, and the “death axis” roughly(2019).

corresponds to the roundness of the rings. A[5] I. Obayashi et al., J. Phys. Soc. Jpn., 91,

clear change is seen in the ring distribution vs.

091013 (2022).

temperature,suggesting

that

we

can

Fig. 1: First order persistence diagrams of liquid and amorphous ZnCl2.

52

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of first-principles calculation code
RSPACE and design of highly functional interface
Tomoya ONO
Graduate School of Engineering, Kobe University
Rokkodai-cho, Nada, Kobe 657-8501

surface. We considered the modification incorporating four Si vacancies (VSi s) and 16 N
atoms at C sites (NC s). The cases in which
VSi s were arranged parallel to the surface were
investigated to evaluate the anisotropy of theformation energy of the nitride layer. In ourmodel, the areal N-atom density was on theorder of 1014 cm−1 , which is consistent withthe experimental results. Although there are
two inequivalent lattice sites of 4H-SiC, i.e., h(hexagonal) and k (quasi-cubic) sites, our previous studies have shown that nitride layers
tend to grow at the k site. Thus, we consider
the cases in which VSi s are arranged at the ksite. We also investigated the interfaces with
the nitride layer at the second layer for all thefaces. For the first-principles calculation, weused the RSPACE code[1, 2], which is based on
the real-space finite-diﬀerence approach within
the frameworks of density functional theory(DFT) and is developed in this project. We
employed the local density approximation of
the DFT to describe the exchange and correlation eﬀects. Electron-ion interactions were approximated by the projector-augmented wave
method. The structural optimization was performed until the residual forces are smaller
than 0.001 Hartree/Bohr radius.

4H-silicon carbide (4H-SiC) is an IV-IV
type semiconductor with a wide band gap of
3.2 eV, and the 4H-SiC based metal-oxidesemiconductor field-eﬀect transistor (MOSFET) is expected to be used in next generation switching devices operating at high powerand high frequency applications. However, thepotential of 4H-SiC has not been fully utilized owing to the low on current of MOSFETs, which is caused by defects at the 4HSiC/SiO2 interface. The post-oxidation annealing process using N2 O, NO, or N2 gas has
been proposed to reduce the density of interface defects and increase the on current. In
our previous study, we investigated the totalenergies and electronic structures of the nitride layers by density functional theory (DFT)
calculation using the surface models, where
the 4H-SiC/SiO2 interfaces are modeled by the
OH terminated surfaces. However, the surface
models do not include the eﬀect of the SiO2
networks on the interface atomic structure. In
this project of 2022, we employ the models containing the SiO2 layers on the SiC substrate.
Figure 1 shows our computational models,
where the surface of the 4H-SiC substrate is
terminated with the SiO2 layer and the otherside of the substrate is terminated with H
atoms. The rectangular supercells of 10.1 Å ×
5.3 Å × 26.3 Å for the a-face model, 10.1
Å × 6.2 Å × 27.3 Å for the m-face model,
and 18.5 Å × 5.3 Å × 26.8 Å for the Siface model were employed. The z-axis was
taken to be the direction perpendicular to the

The formation energy of the above interaction for generating one VSi to insert a nitride
layer was obtained as(w/ mod)

Eform = Etotal/4 + E(SiO2 )(w/o mod)+4µCO + 2µN − Etotal

53/4 − 6µNO , (1)Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo(a)a face (1st)m face (1st)C face (1st)a face (2nd)m face (2nd)C face (2nd)PN (atm)
10-3
10-4
2

Eform (eV)

10-5

z
x

y

(b)

(c)

-5.6
-5.8
-6.0
-6.2
-6.4
-6.6
-6.8
-7.0
-7.2
-7.4 -5
10

10-4

10-3
PCO (atm)

10-2

10-2

10-1

Figure 2: Formation energies Eform defined
Eq. (1) for interface with CO bonds withrespect to partial pressures of CO and N2 .
Reprinted from Ref. 3.

z
z
y
x

those along the a, m, and Si faces. The formation energy of the nitride layer at the topmost
layer is smaller than that at the second layer,
resulting in the localization of the N atoms at
the interface. Note that the NO annealing generates the nitride layers immediately below the
SiO2 layers without any transition layers. It
was found that the eﬀect from the SiO2 layeron the interface atomic structure after the NO
annealing and our conclusions derived by thesurface models do not change when the SiO2
layers are attached to the substrates.

xyFigure 1: Interface atomic structures with CO
bonds for (a) a-, (b) m-, and (c) C-face models before N-atom incorporation. Blue, brown,
red, and gray spheres are Si, C, O, and H
atoms, respectively. Black lines are the boundaries of the supercell.
where E(SiO2 ) is the total energy of a SiO2
(w/o mod)unit in a bulk of quartz SiO2 . Etotal
and(w/ mod)
Etotalrepresent the total energies of theinterface without and with N-atom incorporation, respectively. In addition, µNO , µCO ,and µN are the chemical potentials of a NO
molecule, a CO molecule, and N atoms in a N2
molecule, respectively. We set the temperature
at 1000 K and the partial pressure of NO gas(pNO ) at 1 atm. The partial pressures of CO(pCO ) and N2 (pN2 ) gases were set at 10−5 atm
and 0.25 × 10−5 atm.
The formation energies of the nitride layers are shown in Fig. 2. All the reactions
are exothermic and the nitride layers growing
along the a face are the most stable among

References[1] T. Ono and K. Hirose, Phys. Rev. Lett.
82, 5016 (1999).
[2] K. Hirose, T. Ono, Y. Fujimoto, and
S. Tsukamoto, First Principles Calculations in Real-Space Formalism, Electronic
Configurations and Transport Propertiesof Nanostructures (Imperial College, London, 2005).
[3] N. Komatsu, M. Ohmoto, M. Uemoto,and T. Ono, J. Appl. Phys. 132, 155701(2022).

54

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-Principles Study on Carrier Mobility of SiC6
Nanoribbons
Yoshiyuki EGAMI
Division of Applied Physics, Faculty of Engineering, Hokkaido University
Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628

In recent years, as semiconductor electronic
devices have become smaller, a remarkable reduction in carrier mobility due to the thinningof silicon channels has become an important
issue. Therefore, two-dimensional materials
that can maintain high carrier mobility evenwith thin ﬁlms have been attracting attention.
A typical 2-dimensional material, graphene,
has a carrier mobility of about 100 times thatof silicon, and is therefore expected to becomea post-silicon material. However, since the energy band gap of graphene is zero, it is diﬃcult to apply it to semiconductor devices. So,
several studies have been performed to open
the gap. Among them, this work focuses onsiligraphene, in which graphene is doped withsilicon atoms. In particular, it is shown that
SiC6 siligraphene has a negative Poisson’s ratio
and a unique property that the carrier mobilitychanges signiﬁcantly with strain. On the other
hand, the carrier mobility of SiC6 nanoribbons
fabricated by cutting SiC6 siligraphene as achannel material has not yet been clariﬁed.
In this work, the carrier mobility of SiC6
nanoribbon considering acoustic phonon scattering at room temperature is evaluated using
the eﬀective mass, elastic modulus, and deformation potential obtained by ﬁrst-principles
calculations [1]. As a result, the electron
mobility of SiC6 nanoribbons is signiﬁcantly
lower than that of SiC6 siligraphene, but thehole mobility is suﬃciently improved to be applied to n-type transistor materials. For future
work, it is necessary to investigate the depen-

dence of carrier mobility on the width and edge
structure of the nanoribbon.
Ballistic electron transport properties in
SiC6 nanoribbons connected to semi-inﬁnite
electrodes consisting of graphene are also evaluated [1, 2]. There are two types of conduction channels: in the 1st channel, the scattering wave function is extended throughout thesystem via the delocalized π orbitals of carbon atoms (Fig. 1(a)), resulting in a conduction channel with high transmission. On theother hand, in the 2nd channel, the scatteringwave propagates via states consisting of sp3 orbitals of silicon atoms, but most of the wave is
reﬂected at nanoribbon region (Fig. 1(b)) andthe transmission is quite small.
This work has been performed on System Bof the Supercomputer Center, the Institute for
Solid State Physics, the University of Tokyo.
(a)

(b)

Figure 1: Charge density distribhutions of
scattering wave functions.

References[1] K. Hirose et al.: First-principles calculations in real-space formalism (Imperial
College Press, 2005).
[2] Y. Egami, S. Tsukamoto and T. Ono:
Phys. Rev. Res. 3, 013038 (2021).

55

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analyses related to atomic structures and atom
dynamics at complex structures such as surfaces,interfaces and defects
Satoshi WATANABE
Department of Materials Engineering, the University of Tokyo
7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656

1

Introduction

To deepen our understanding on atomic arrangements and dynamics in/at complex structures such as surfaces, interfaces and defects
is crucial for further development of novel
information and energy devices. We havebeen tackling this issue using various simulation methods including multi-scale or machinelearning approaches. In the following, two of
our results in fiscal year 2022 are described.

2

Defect structures in WS2
thin films

Investigations on WS2 aiming at electronic devices have been active recently. However, theperformance of prototype devices were much
lower than expected because of structural defects in fabricated WS2 thin films. We examined [1] defect structures of WS2 thin films using the high-dimiensional neural network potential (HDNNP). We successfully generated
HDNNP with the root mean square error ofenergy from density functional theory (DFT)
calculation of about 6 meV/atom. Molecular
dynamics (MD) simulations using the HDNNP
and WS2 slab models reveal that S vacancies introduced in the slab are transformed
into structures consisting of 5-memberd and 9membered rings or other structures including
rings diﬀerent from 6-membered one spontaneously.

3Electrical conductivity andSeebeck coeﬃcient of organic semiconductors

Organic semiconductors have attracted muchattention recently as thermoelectric materials.
However, their power generation eﬃcency is
still insuﬃcient for practical applications. We
developed [2] a realistic evaluation method of
the electrical conductivity and Seebeck coefficient of organic semiconductors using electronic structure calculations based on DFT.
In our method, many structures were obtainedusing MD simulations with an empirical force
field to consider thermal fluctuation in a crystal explicitly. The Seebeck coeﬃcient and carrier mobility were obtained from the averageof the density states and transfer integrals between adjacent moleculres calculated for eachstructure, respectively. We applied our scheme
to pentacene and rubrene. Our results agree
well with experimental data.

References[1] R. Otsuka, K. Shimizu, H. Wakabayashi,
S. Watanabe: 70th JPSJ Spring Meeting
2023, 16p-B414-7 (in Japanese).
[2] M. Ohno, K. Shimizu, and S. Watanabe:Appl. Phys. Express 16 (2023) 011005.

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Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical study of point defects invisible-light-driven semiconductor photocatalysts
using first-principles calculations
Seiichiro L. TEN-NO
Graduate School of System Informatics, Kobe University
Rokkodai-Cho, Nada-Ku, Kobe 657-8501

Point Defect in Layered Perovskite Photocatalyst Y2 Ti2 O5 S2
Layered perovskite Y2 Ti2 O5 S2 (YTOS) isa strong candidate for semiconductor photocatalysts for overall water splitting undervisible light. Although YTOS has a band
gap sutable for absorption of visible light andvalence/conduction band positions useful for
overall water splitting, structural defects during synthesis should be controlled to promote
photocatalytic performance [1, 2, 3].
We have investigated the point defects andelectronic structures using first-principles calculations based on the density functional theory (DFT). The DFT calculations were performed within the PBE+U (Perdew–Burke–
Ernzerhof functional with Hubbard U correction) functional using the projector augmented
wave (PAW) method, as implemented in the
Vienna ab initio simulation package (VASP).
We have evaluated the formation energy ofanion vacancies Eform using the chemical potentials ∆µi relative to bulk precipitate. ∆µiwere determined by the phase diagram of therelevant compounds in the synthesis of YTOS.
Fig. 1(a) shows the phase diagrams as functions of ∆µTi and ∆µY for S-rich conditions,in which YTOS is stable within the area of the
ABC triangle. In Fig. 1(b), Eform of VS , VOc ,and VOab for S-rich conditions is shown as afunction of the Fermi level EF measured fromthe valence band maximum EV . The evalu-

(a)

A

C

B
S-rich:ΔμS = 0 eV(b)+2/+1 +1/0
+1/0

+2/+1

+1/0

+2/+1

S-rich:ΔμS = 0 eV

Figure 1: (a) Quaternary phase diagram of
YTOS with respect to ∆µTi and ∆µY for Srich conditions. (b) Formation energy of anion
vacancies Eform against EF − EV .
ation of Eform suggests that the S-defect (Odefect) is easy to form when EF is near thevalence (conduction) band.
Chemical Doping in Perovskite Photocatalyst SrTiO3Perovskite SrTiO3 (STO) is a typical semiconductor photocatalyst for overall water split-

57

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

ting under ultraviolet. According to the recent
experiment [5], it is observed that Al-doped
STO can enable a quantum eﬃciency of almost
unity at wavelengths between 350 and 360 nm.
To explore more eﬃcient dopants for higherperformance photocatalysts, we have studied
the dopant eﬀects on the electronic structuresof STO using the first-principles analysis. The
DFT calculations were performed within the
PBE+U functional using PAW method as implemented in VASP. We treated the supercell
models including one VO and two XTi (oneMgTi ) with X being B, Al, Ga, In, Tl, Sc.

ABCD points.
Water oxidation reaction on BiVO4
Perovskite BiVO4 (BVO) is used as an O2 evolution photocatalyst for overall water splitting. We have investigated the reaction processes of the water oxidation on BVO using
the first-principles calculations. The DFT calculations were performed within PBE and revised PBE (RPBE) using the slab models with(110) facet. Fig. 3 shows the energy diagramof O2 - and H2 O2 -evolution on BVO (110) surface, which suggests that H2 O2 -evolution is expected to be favorable on the (110) facet compared to O2 -evolution.

(a)

(b)

Figure 2: (a) Ternary phase diagram of STO
with respect to ∆µSr and ∆µTi . (b) Dopant
formation energy of each dopnat Ef along
ABCD points.

Figure 3: Energy diagram of O2 - and H2 O2 evolution

References[1] Q. Wang et. al.: Nat. Mater. 18, 827(2019).

The supercell calculations showed that each
dopant except for Tl can cancel the defect levelarising from the VO . We have also evaluatedthe formation energy of each dopant Ef using
the chemical potentials ∆µi relative to bulk
precipitate. ∆µi were determined by the phase
diagram of the relevant compounds of STO.
Fig. 2(a) shows the phase diagrams as functions of ∆µSr and ∆µTi , in which STO is stable within the area of the ABCD square. In
Fig. 2(b), Ef of each dopant is shown along[2] Z. Pan et. al.: Res. Chem. Intermed. 47,
225 (2021).
[3] M. Nakabayashi, K. Nishiguchi et.
al.:
J. Phys. Chem. C (in press:
https://doi.org/10.1021/acs.jpcc.3c00820).
[4] M. Cococcioni et. al.: Phys. Rev. B 71,
035105 (2005).
[5] T. Takata et. al.: Nature 581, 413 (2020).

58

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of Thermal Functional Materials Based on First-principles
Simulations
Wenyang DING1, and Junichiro SHIOMI1,2
1. Department of Mechanical Engineering, The University of Tokyo, Japan
2. Institute of Engineering Innovation, The University of Tokyo, Japan
Manipulating thermal conductivity of crystalline materials by phonon engineering has attracted tremendous attention.
Van der Waals (vdW) heterostructures are an ideal candidate to realize low thermal conductivity in their throughthickness direction due to its weak interlayer interactions and prominent disorder by alternating stacking orders.1
However, previous studies have not been able to characterize phonon propagation thought vdW heterostructures in modewise fashion, which has limited the understanding and engineering of the heat conduction. Herein, for the first time, heat
conduction in vdW heterostructures are resolved to the level of individual phonon polarizations, whose incident angles
are utilized to elucidate the role that phonon interference and phonon tunneling play in vdW heterostructures.
First, we searched for vdW graphene-WS2 heterostructure with the ultralow thermal conductivity by combining
Bayesian optimization and non-equilibrium molecular dynamics (NEMD) including all the orders of anharmonicity. It isfound that the lowest thermal conductivity of optimized heterostructure is 0.04 W/m-K, only 5% of graphite thermal
conductivity and 13% of pristine WS2 thermal conductivity (Fig. 1). Interestingly, the thermal conductivity of optimized
heterostructure possesses only half of the thermal conductivity of the corresponding periodic superlattice. Moreover, thelattice thermal conductivity of pristine WS2, pristine graphite, periodic superlattice, and the optimized heterostructure arealso calculated by utilizing mode-resolved atomistic Green’s function (AGF) method. Since AGF only considers
harmonic interatomic force constants, it serves to probe the characteristics of elastic phonon scattering whose influenceon thermal conductivity is partial but significant as can be seen in the comparison with NEMD results (Fig. 1). To further
study the characteristics of elastic phonon scattering, the mode-resovled phonon transmissions are calculated using the
S-matrix analysis.2

References(1) Liu, Y.; Weiss, N. O.; Duan, X.; Cheng, H.-C.; Huang, Y.; Duan, X. Van
der Waals heterostructures and devices. Nature Reviews Materials 2016, 1(9), 16042.
(2) Ong, Z.-Y. Atomistic S-matrix method for numerical simulation ofphonon reflection, transmission, and boundary scattering. Physical Review B
2018, 98 (19), 195301.

Fig. 1 Comparison of the thermal conductivityof difference. structures and methods.

59Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study of energy and spintronics
materials
Fumiyuki ISHII, Naoya YAMAGUCHI, Rifky SYARIATI,
Hikaru SAWAHATA, Hana Pratiwi KADARISMAN, Kaiki SHIBATA,
Yaotang ZHANG, Vierta SARASWATI, Takahiro TOMINAGA,
Yedija Yusua Sibuea TEWENG, Juhri HENDRAWAN,
Yume MORISHIMA, Khusnul YAKIN, Wardah AMALIA,
Syifa Fauzia Hariyanti PUTURI, Ahmad GHIFFARI, Salsabila Amanda PUTRI
Nanomaterials Research Institute, Kanazawa University
Kanazawa, 920-1192, Japan

1. MnBi2 Te4 van der Waals layers[1]The transverse thermoelectric eﬀect, which
produces an electric ﬁeld in the direction of
the cross product of the temperature gradientand magnetization of magnetic materials, has
attracted much attention in recent years because of its potential applicability to a large
area. Since MnBi2 Te4 was predicted to haveantiferromagnetic order in the interlayer and to
be a ferrimagnetic semiconductor with quantized anomalous Hall conductivity in an odd
number of three or more septuple layers, it isexpected to generate a transverse thermoelectric eﬀect. We have performed ﬁrst-principles
calculations by using OpenMX code[2] for ultrathin MnBi2 Te4 ﬁlms and estimating thecoeﬃcient representing the magnitude of thetransverse thermoelectric eﬀect. The anomalous Hall and Nernst eﬀect were calculated byusing our developed eﬃcient methods by local Berry phase in momentum space[3]. A
large enhancement in transverse thermoelectric eﬀect, anomalous Nernst coeﬃcient, larger
than 20µV/K, was obtained by the Seebeck
term for a wide range of carrier concentrations.
The present results motivate further studies on
the anomalous Nernst eﬀect in intrinsically or
doped magnetic semiconductors.

2. Hapkeite Fe2 Si[4]In order to obtain a guideline for exploringnew inexpensive and high-performance thermoelectric materials, the ﬁrst-principles calculations were performed to clarify the thermoelectric properties of Fe-Si alloys, which
are the most abundant iron-based compounds.
As a result, we obtained a large transverse
thermoelectric transport coeﬃcient αxy of 2.06
A/mK for the model crystal structure of amineral Hapkeite Fe2 Si contained in a meteorite Dhofar 280, which is believed to originate from the Moon. Calculated results showthat the model structure, Hapkite Fe2 Si, exhibits a more signiﬁcant transverse thermoelectric transport coeﬃcient than bcc-Fe andhexagonal Fe2 Si. Detailed analysis of the electronic states and transport coeﬃcients indicates that the signiﬁcant transverse thermoelectric eﬀect is due to an anomaly in the density of states (DOS) at the interface between
the Fe layer and the Si-Fe alternating layer.
The band-edge type van Hove singularity contributed to the DOS at the Fermi level. Several previous studies have attempted to generate transverse thermoelectric eﬀect throughmulti-layered structures with each layer on theorder of 1 nm scale. A similar interfacial eﬀect
that enhances the transverse thermoelectric ef-

60

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

fect may be observed. Therefore, this ﬁnding
is promising for the design of new transverse
thermoelectric materials.

References[1] Y. Morishima, N. Yamaguchi, H. Sawahata, and F. Ishii, Appl. Phys. Express,
16 043003 (2023).

3. Persistent spin helix in diamond[5]Density functional theory (DFT) simulations
were performed to investigate the diamond(111) surface. We investigated how diﬀerent
terminations such as hydroxyl (OH) and hydrogen (H) aﬀect the strength of the spinorbit coupling on the diamond surface and thespin structure in momentum space. The calculation results reveal that the OH-terminatedstate contributes to the valence band maximum (VBM), while the H-terminated state
contributes to the conduction band minimum(CBM). Due to the OH termination, persistent spin helix spintexture is obtained and thespin-orbit coupling coeﬃcient is found to be
14.2 meV·Å at the valence band maximum(VBM). This is signiﬁcant compared to theZnO(101̄0) surface and slightly larger than various n-type sphalerite quantum wells. Moreover, it is larger than the 3.6 meV·Å resulting from the hydrogen termination of diamond.
Due to the large spin-orbit coupling coeﬃcient,
the wavelength of persistent spin helix is shortened, and miniaturization of spin ﬁeld eﬀect
transistors can be expected.

[2] H. Sawahata, N. Yamaguchi, S. Minami,
and F. Ishii, Phys. Rev. B 107, 024404(2023).
[3] T. Ozaki et al., http://www.openmxsquare.org/[4] T. Tominaga N. Yamaguchi, H. Sawahata, and F. Ishii, Jpn. J. Appl. Phys. 62
SD1019(2023).
[5] H.P. Kadarisman, N. Yamaguchi, and
F. Ishii, Appl. Phys. Express, 16023001(2023).

4. The Rashba eﬀect of PbS/Au(111)We have performed the ﬁrst-principles calculation of the PbS(111) which has buckled honeycomb structure on the Au(111) surfaces. The
broken inversion symmetry due to the bucklingof the system shifted the energy and caused the
Rashba eﬀect. The orientation or contact at
the interface highly controls the Rashba eﬀect
at heterostructures. For the metal-metal contact, Pb-Au, allows the Rashba eﬀect at theinterface, while metal-insulator contact, S-Au,
does not. The PbS(111) can be used to generate the Rashba eﬀect surface state of thin
noble metals.

61

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First Principles Studies on Spin Tranfer Torque Magnetic
Randum Access Memory (STT-MRAM)
Kenji SHIRAISHI
Institute for Materials and Systems for Sustainability,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601

Spin-transfer

torquemagnetic

random-magnetic anisotropy. In the DOS peaks in theaccess memory (STT-MRAM) is expected to be

down spin channel above Fermi energy in ideal

a non-volatile memory that replaces SRAM andmodel, the wave functions mainly form the

DRAM currently in use. MgO layer inbonding orbitals between interfacial Fe atoms

CoFeB/MgO/CoFeB

ofand second layer Fe atoms. Near grain

irregularly shaped grains with a diameter of 10

boundary, the in-plane symmetry is broken by

to 15 nm, and the presence of mainly the Σ5

the grain boundary and the hybridization(210) [001] grain boundaries was observed at

between interfacial Fe atoms and second layer

the interface between the grains. iPMA isFe

generally known to be sensitive to theunoccupied down spin states of “|m|=1” extend

cleanliness of the interface between theabove Fermi energy. We suggest that it isferromagnetic layer and the insulator [1]. In thisnecessary to keep the d orbital hybridization

study, we focus on the grain boundary whicharound Fe atoms for further microfabrication.

MTJ

consists

atoms

weakens.

It

causesthattheoccurred most frequently in MgO film andinvestigated the influence of the grain boundary
for iPMA by performing the first principles
calculations.
Near grain boundary (within a 4Å range
from the center line of grain boundary, theFig.1: Wave functions at Γ point in down spin

magnitude of iPMA strongly decreases. It is

statesbecause the DOS peaks in the down spinchannel for “|m|=1” above Fermi energy are

References

decreased. It causes the spin orbit coupling[1] A. Hallal, H. X. Yang, B. Dieny, and M.

hybridization

Chshiev, Phys. Rev. B 88, (2013) 184423.

of(|1|×|1|)changesfromperpendicular magnetic anisotropy to in-plane

62

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First Principles Studies on Si-rich a-SiN for Flash Memory
Application
Kenji SHIRAISHI
Institute for Materials and Systems for Sustainability,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601

SiN is a useful material under harshfound π state is unprecedented in the sense thatenvironments due to its high thermal stability

it has the origin of the floating state distributed

and toughness against fracture, and lately

not around atomic sites but in the internal space

utilized as passivation layer in Si solar cells. Toof the material. The multiple charge states weadvance our understanding of the memory

have found may be utilized as an active element

function in SiN, however, the most important

in information technology.

task never achieved so far is the determinationof the thermodynamic level (TD) induced by
VN. This TD level is responsible for theelectroncaptureandemissionandits

determination involves assessment of roles ofFig.1: π-like state appeared in VN in Si3N4

hybridization, spin polarization and ionicity of
VN in SiN. We find that the appearance of thisTD level is promoted by the spontaneous
structural transformation near VN, resulting in
multiple charge states of nitrogen vacancy.
We have performed the density-functional
calculations with the hybrid approximation thatclarify the atomic and electronic structures of
the N vacancy (VN) in Si3N4. We have foundFig.2: formation energy of VN in Si3N4.

that the floating state hidden in the conduction
bands create a new π-like state in collaboration

Referenceswith the dangling-bond states around the VN(,

[1] F. Nanataki, K. Shiraishi, J. Iwata, Y.

(Fig.1) thus rendering the VN being multiple

Matsushita, A. Oshiyama, Phys. Rev. B 88,

charge states from +1 to -5 (Fig.2). The newly(2013) 184423.

63

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Hydrogen production by water splitting on CeO2 (100) facet
Akira YOKO
Advanced Institute for Materials Research,
Tohoku University, Katahira 2-1-1,Aoba-ku, Sendai, Miyagi 980-8577
CeO2 nanocubes with (100) facet have

For the (100) facet model, half of the oxygen

been synthesized by supercritical method, andwas moved to the other side to exclude polarity

it was found to have high oxygen storage

keeping the CeO2 composition. When CeO2 iscapacity. In this study, the redox property of the

fully hydroxylated by water adsorption and(100) facet was studied by using first-principles

dissociation, the surface state is changed as

calculations.

Figure 1(b). Interestingly, the lattice expansion

In this study, first principles simulations

observed inside of the bare surface model (Fig.

based on density functional theory (DFT) was

1(a)) was relaxed with surface hydroxylation

conducted. Plane wave basis DFT simulations

owing to the surface stabilization.

were conducted using VASP code. Structures of
CeO2 at surface and bulk were calculated withgeneralized gradient approximation proposedby Perdew, Burke, and Ernzerhof (PBE) [1].
The

valenceconfigurations

of

the

pseudopotentials were 5s25p64f15d16s2 for Ce
and 2s22p6 for O. The DFT+U method
introduced by Dudarev et al. [2] was used totreat electron localization. The parameter U-J
was set to 5.0 eV for Ce4f and 5.5 eV for O2p
states, respectively, based on previous studies

Fig.

of CeO2 [3]. The Monkhorst-Pack k-point meshhydroxylated (100) surface.

of 4×4×4 was used for the unit cell of CeO2.

References

The slab model exposing (100) facet includes[1] J.P. Perdew, K. Burke, M. Ernzerhof, Phys. Rev.

60 atoms, and that for (111) facet includes 108

Lett., 77 (1996), p. 38650. [2] S. Dudarev, G. Botton, S.

atoms. The Monkhorst -Pack k-point mesh for

Savrasov, C. Humphreys, A. Sutton, Phys. Rev. B, 57

the slab model was 4×4×1.

(1998), p. 1505. [3] P.R. Keating, D.O. Scanlon, B.J.

Figure 1(a) and 1(b) show CeO2 (100) bare

1:

CeO2

(100)

bare

surfaceandMorgan, N.M. Galea, G.W. Watson, J. Phys. Chem. C,

surface and hydroxylated surface, respectively.

116 (2012), pp. 2443-2452

64

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Electronic structure analysis of SiC/SiO2 interface under gatedelectric field
Yu-ichiro MATSUSHITA
Laboratory for Materials and Structures, Institute of Innovative Research,
Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8552
SiC-MOS devices have attracted muchas the (11-20) plane. We found that thisattention as next-generation power devices due

is related to the structural channel nearto their excellent characteristics. However, thethe interface. Of particular importance,

device characteristics are at most 10% of thethe localization of the wavefunction attheoretical performance value of SiC, which is

this (0001) interface is distributed muchthought to be due to high-density interface

closer to the interface (<5 Å) thandefects. However, we have proposed a new

expected

type of mechanism for the generation of

approximationinterfacial levels, which originates from theexpected to be more sensitively scatteredpeculiarity of the wave function at the lower

by interface defects. This result may

end of the conduction band of SiC.

explain why the channel mobility of the

from

the

effective(EMA),

and

mass

thus

is

(0001) plane is particularly low comparedIn this study, we have performed atheelectronic

to the other planes (e.g., (1120)), which is

structure of the SiC/SiO2

interfaces

well known from experiments.

comparative

study

of

under a gated electric field by means oftheoretical calculations based on density
functional

theory,includingthedependence of the electronic structure on
the plane orientation. It is found [1] that

FIG 1. Isosurface at 38% of the peak value

the wavefunction at the conduction bandof wavefunction localized at outermost

minimum (CBM) at the SiC(0001)/SiO2

cubic site (F = 1.0 MV/cm, CBM). The blue,

interface tends to be localized at thebrown, red, and small white balls depict

cubic site closest to the interface. On the

Si, C, O, and H atoms, respectively.

other

hand,

we

found

that

such

localization of the wavefunction cannotWe

be observed on nonpolar interfaces such

65

have

also

clarified

that

the

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyodeviation from the EMA, which is a

succeeded in proposing a new way tofrequently used method to analyze theimprove SiC-MOS devices.

electronic structures in semiconducting
devices,isattributed

to

the

long

structural periodicity along the [0001]
direction in the SiC crystals.
Furthermore,in

actual

SiC-MOSinterfaces, the introduction of nitrogen isused to improve the interface properties.
However, its microscopic mechanism has
not

been

elucidated.

In

the

experimental

considering

recentFIG 2. Local density of states (LDOS) of

addition,

the CBM in slabs with di↵erent N-doped
regions. For clarity, averaging was done

results that the introduced nitrogen also

over the atomic layer thickness period.

diffuses to the SiC side. We study how

Applied electric fields are 0, 5, and 10

the electronic states at the SiC / SiO2

MV/cm, respectively.

interface are affected when nitrogen is
introduced as a dopant based on first-

References

principles calculations. As a result, we[1] K. Tachiki, Y. Nishiya, J.-I. Iwata, and Y.

found that the deep doping of nitrogen

Matsushita, arXiv:2303.08527 (2023).

relaxes the confinement potential near[2] H. Yoshioka, J.-I. Iwata, and Y. Matsushita,

the interface and the localization of the
wavefunction,

which

is

expected

toimprove

deviceproperties.

We

the

arXiv:2303.05085 (2023).

Fig. 1: Supercomputer System B at SCC-ISSP.

66

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Density functional theory study of adsorption and reactionof molecules on metal surfaces
Ikutaro Hamada
Department of Engineering, Graduate School of Engineering,Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871
mechanism of ORR on SAC is not yet fully
resolved. In this study [4], we focus on theexchange-correlation functional to be used to
study ORR on SAC, in particular Fe and Co
SAC embedded in a nitrogen-doped graphene(Fe/Co-N4-C). By choosing the results obtainedusing the Bayesian error estimate functionalwith van der Waals correlation (BEEF-vdW)[5] as references, we perform systematical
calculations of the ORR intermediates on FeN4-C and Co-N4-C using commonly usedsemilocal exchange-correlation functionals
with and without dispersion correction and findthat revised Perdew-Burke-Ernzerhof (RPBE)[6,7] functional with Grimme’s dispersion
correction [8] (RPBE-D3) gives the results
consistent with those obtained using BEEFvdW. The conclusion drawn in this work as
well as the strategy taken there will be useful tochoose an appropriate (low-cost) exchangecorrelation function to study electrochemicaland heterogeneous reactions.

Graphene doped with foreign elements has
attracted enormous attention because of
emergent electronic properties, besides its own
unique structural, electronic, and mechanicalproperties, as well as its stack(s) with the same
and/or different two-dimensional materials.
Graphene doped with nitrogen has beenshown to exhibit catalytic activity toward
electrochemical oxygen reduction reaction(ORR). To understand the mechanism of ORR
on nitrogen-doped graphene, it is important tounderstand the interaction between grapheneandwater,
acommonsolvent
inelectrochemistry. However, density functional
theory with the conventional semilocal
approximation fails to describe the weak watergraphene interaction accurately. In this work [1],we use rev-vdW-DF2 [2], one of the van der
Waals density functionals, which has beenshown to be able to describe the watergraphene interaction accurately [3], to study theinteraction between water molecule andnitrogen-doped graphene. We consider different
water orientations and different nitrogenconfigurations and obtain the preferredorientations of the water molecule, dependingon the nitrogen configuration. We reveal thatgraphitic and pyridinic nitrogen atoms arecharged positively and negatively respectively,
which lead to different water orientations. Theinteraction energy curves obtained in this work
may serve as references for future studies andbe useful for modeling of graphene/waterinterfaces
withhybridquantummechanics/molecular mechanics-type methods.
Nitrogen-doped graphene with a single
transition metal atom (single atom catalyst,
SAC) has also been attracted much attention as
it shows ORR activity comparable to platinum,and there have been numerous studies bothexperimentally and theoretically. However, theReferences[1] A. F. Z. Abidin and I. Hamada, Phys. Rev.
B 105, 075416 (2022).
[2] I. Hamada, Phys. Rev. B 89, 121103 (R)(2014).
[3] J. G. Brandenburg, A. Zen, D. Alfé, and A.
Michaelides, J. Chem. Phys. 151, 164702(2019).
[4] A. F. Z. Abidin and I. Hamada, Surf. Sci.
724, 122144 (2022).
[5] J. Wellendorff, et al., Phys. Rev. B 85,
235149 (2012).
[6] J. P. Perdew, K. Burke, and M. Ernzerhof,
Phys. Rev. Lett. 77, 3865 (1996).
[7] B. Hammer, L. B. Hansen, and J. K.
Norskøv, Phys. Rev. B 59, 7413 (1999).
[8] S. Grimme, J. Antony, S. Ehrlich, and H.
Krieg, J. Chem. Phys. 132, 154104 (2010).

67

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical determination of charge injection levels
in organic semiconductor films
Ryo Uza and Susumu Yanagisawa
Department of Physics and Earth Sciences, University of the Ryukyus
Senbaru 1, Nishihara Okinawa 903-0213

Zinc phthalocyanine (ZnPc) can be used as ap-type semiconductor with hole carriers. Fluorinated zinc phthalocyanine (F16 ZnPc) can
also be used as an n-type semiconductor.
ZnPc and F16 ZnPc are attracting attention
as organic solar cell materials. Fundamental understanding on the formation mechanism of charge injection levels is urgent for
their practical application. In the present
work, Vienna Ab-initio Simulation Package(VASP) was used to determine from firstprinciples the lattice parameters of the crystals and the atomistic structure of molecular films by the van der Waals (vdW) density functional[1]. Subsequently, the band energy calculations were performed with the GW
approximation, which included the eﬀects ofelectronic polarization. The ionization potential (I) or electron aﬃnity (A) of any molecule
depends on the electronic polarization of thesurrounding molecules and the electrostaticinteractions upon the ionized molecule fromits surroundings[2]. The eﬀect induced by
the molecules surrounding an ionized molecule,which stabilizes the charge injected into themolecule by the polarization clouds with an opposite charge, is called electronic polarization.
In this work, both the eﬀects of the electrostatic interaction and the electronic polarization were included in the calculations to quantitatively predict the level of charge injection.
The result indicates that in case of ZnPc thinfilm the energy levels are relatively shifted up
in the standing configuration and shifted downin the lying configuration. This comes fromthe electric quadrupole moment of the neutral
molecule. Electric quadrupoles generate electrostatic potentials in crystals and films. The
generated electrostatic potential is governedby the electric quadrupole tensor and depends
on the distance between molecules and theorientation angle of the constituent molecule.
Therefore, the shift is opposite for the standing and lying configurations, as the orientation
angle of the molecules relative to the nearest
neighbor molecules changes and the sign of theelectrostatic potential is diﬀerent. Similarly,
given the opposite signs of the zz component of
the electric quadrupole tensor, the signs of theelectrostatic potential for ZnPc and F16 ZnPc
are opposite.
The eﬀect of electronic polarization was determined using the GW approximation to calculate I and A, and the density of states was
obtained by matching the corresponding energy levels to the peak of the density of states.
It was found that the positions of the densityof states peaks are in good agreement with theexperimental photoelectron/inverse photoelectron spectra[3] (Fig. 1). The calculated energy
gap is slightly shallower than the experimental
results, which can be corrected by improving
the accuracy of the GW approximation.
Overall, it is concluded that the present theoretical method is of practical use in predicting the frontier energy levels of organic semiconductor thin film. Prediction of the charge
injection levels in mixed films of ZnPc and68

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

F16 ZnPc is in progress.

This work

This work

This work

This work

Figure 1: Theoretical density of states (DOS)of ZnPc and F16 ZnPc thin films with standing and lying configurations. The experimental DOS measured with direct/inverse
photoemission[3] are also displayed.

References[1] I. Hamada: Phys. Rev. B 89, 121103(2014).
[2] K. Yamada, S. Yanagisawa, T. Koganezwa, K. Mase, N. Sato, and H.
Yoshida: Phys. Rev. B 97, 245206 (2018).
[3] Y. Uemura, S. A. Abd-Rahman, S. Yanagisawa, and H. Yoshida: Phys. Rev. B 102,
125302 (2020).

69

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Reduction of Rare Metals in Fuel Celland Formic Acid Decomposition Catalysts
Norihito Sakaguchi
Center for Advanced Research of Energy and Materials, Faculty of Engineering,
Hokkaido University, Sapporo, Hokkaido 060-8628

We investigated the adsorption and diffusion

substrates. We revealed that the ferromagnetic

properties of single-atom catalysts on light-

electronic structures of metal substrates are notelement doped graphene supported on the metal

required to enhance the chemical bonding

substrates, with the aid of the first-principles

betweencalculation based on the density functional

element doped graphene light-element doped

theory (DFT). We also investigated the catalytic

graphene. In most cases of steric light-element

activities of the considered systems in oxygen

doped graphene, the non-magnetic substrates

reduction and formic acid decomposition

also weaken the Pt and Cu adsorption andreactions.

enhance the catalyst diffusion on the light-

At first, we investigated the stabilities ofsingle-atom

catalysts

andlight-

element doped graphene in the same way as the

single Pt and Cu atoms on light-element doped

magnetic substrates.

graphene supported on the metal substrates. We

Based on the previously reported volcano

considered Fe, Ni, and Cu as metal substrates.

plots, we also investigated the catalytic

We performed the total energy and electronic

activities of the considered systems in oxygen

structure calculations using The Vienna Ab

reduction and formic acid decomposition

initio Simulation Package (VASP). We installed

reactions from the adsorption energies of thea parallelized VASP with Intel® MPI Librarycomponents of the reactants. Although theand Intel® Math Kernel Library. We havestrong chemical bonds between catalysts andreported that the adsorption of Pt and Cu atoms

supports are expected to lead to higher catalyticon light-element doped graphene with flat

activities,

structures became stronger through supporting

reactions have been found only in a few

the magnetic substrates, i.e., Fe and Ni

systems.

theenhancementsofcatalytic

substrates, last year. We reinvestigated theadsorption properties of Pt and Cu atoms on

References

light-element[1] Y. Kunisada, N. Sakaguchi, Nano

dopedgraphene

with

flat

Express 3 (2022) 042001.

structures on non-magnetic substrates, i.e., Cu

70

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of Efficient Oxygen Storage Materials
and Hydrogen Permeation Barrier Materials
Yuji KunisadaCenter for Advanced Research of Energy and Materials, Faculty of Engineering,
Hokkaido University, Sapporo, Hokkaido 060-8628

We investigated the doping effects on the

We also investigated the hydrogen isotope

oxygen absorption/desorption properties ofsolubility and diffusion properties in thebrownmillerite-type oxides,[1] with the aid of

amorphous ceramic materials. We considered

the first-principles calculation based on the

Al2O3 as the hydrogen permeation membrane.

density functional theory (DFT). We also

We performed melt-quenching technique toperformed O K-edge electron energy loss

obtain the amorphous structure last year.

spectroscopy (EELS) simulations to build the

However, the obtained structures are not fully

EELS

the

in the amorphous phase due to insufficientexperimental EELS spectra obtained withmelting. Therefore, we obtained the atomic

transmission electron microscopy. Besides, thestructures of the amorphous Al2O3 using higher

solubility and diffusion properties of hydrogenmelting temperatures and longer time steps forisotopes in amorphous ceramic materials weremolecular dynamics simulations. Next, we

also investigated to validate its application as

performed 2000 DFT calculations with varioushydrogen permeation barrier materials.

hydrogen positions in amorphous Al2O3 todatabaseforcharacterizing

We investigated the oxygen absorption

determinetherelationshipbetweentheenergies with various heteroatom substitutions

dissolution energies and the local structures.

in Ca2AlMnO5 using The Vienna Ab initio

Using the Voronoi analysis, we evaluate theSimulation Package (VASP). We installed avolume occupied by the hydrogen atoms.

parallelized VASP with Intel® MPI Library and

Finally, we revealed the dependence of theIntel® Math Kernel Library. We revealed thedissolution energies and diffusion barriers on

effects of local atomic distortions induced by

the volume occupied by the hydrogen atoms.

dopants on the oxygen absorption energies. We

References

also

performed

simulationsof[1] K. Tanahashi, Y. Omura, H. Naya, Y.

using

Z+1

Kunisada, N. Sakaguchi, A. Kurniawan, T.

approximation to construct the database of the

Nomura, ISIJ International 62 (2022)

O K-edge EELS spectra.

2578-2586.

nonequivalent

EELS
O

atoms

71

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Densest binary/ternary sphere packings andprediction of quaternary hydrides
Ryotaro Koshoji, Masahiro Fukuda, Mutsuaki Kawamura, Taisuke Ozaki
Institute for Solid State Physics, University of Tokyo
Kashiwa-no-ha, Kashiwa, Chiba 277-8581

It was widely accepted in the 2000s that the Barlow packings such as FCC structure are the densest
unary sphere packings. Despite the simpleness ofthe problem, it is also too diﬃcult to identificate
the densest binary sphere packings (DBSPs), however, the development of computers has been enabling us to explore the DBSPs by computer simulations. If we only explore the periodic dense packings of spheres of n diﬀerent sizes by computer, thepacking fraction at given sphere-composition ratio
is maximized by filling the space with not morethan n kinds of periodic packings. In 2012, Hopkins et al. explored the DBSPs under the restriction that the number of spheres in the unit cellwith periodic boundary condition is not more than
12 and constructed the phase diagram for the firsttime. They also showed that in some radius andcomposition ratios a considerable number of thestructures have competitive packing fractions, so it
is necessary to optimize the packing structure precisely with small distortions.
We developed the structural optimization algorithm based on the steepest-decent method that iseasy to implement. The computational cost is small
and we showed that it is as precise as the TorquatoJiao algorithm. Our algorithm, which produces initial structures as layer-by-layer stacking structures,completely revisit the previous studies with small
corrections, and we successfully found the 12 putative DBSPs since the maximum number of spheresin unit cell is set to be double. As a result, a total of 28 putative DBSPs are known at the presenttime.
In ternary systems, the DBSPs are the candidates for the phase separations as well as the FCC
packings of small, medium, and large spheres. Following our studies, we constructed the phase diagrams for the first time since previous studies on
the dense ternary sphere packings (DTSPs) do not

(a)

(b)

Figure 1: (a) The (13-2-1) structure. (b) The (121-2-1) structure.
(a)

(b)

Figure 2: (a) The (13-3-1) structure. (b) The (121-3-1) structure.
construct the phase diagrams. As a result, we totally discovered the 59 putative DTSPs [1]. Oneof the well-ordered DTSPs is the (13-2-1) structure shown in Fig. 1(a). The structure is the
DTSP at several radius ratios such as 0.44 : 0.64
: 1.00, at which small and medium spheres are toolarge to be placed in the tetrahedral and octahedral sites if large spheres comprising the fcc structure contact with each other. The clathrate network of small spheres correspond to that of boron
in UB12 , and the (13-2-1) structure has one additional small sphere placed in the cuboctahedron ofsmall spheres. A medium sphere is placed in thetetrahedral site as CaF2 .
The clathrate network has structural similarity
with LaH10 and YH6 . The crystal structures of72

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Table 1: The list of substitution atoms for spheres, where the symbol E corresponds to empty.
sphere size
elements
smallH
semi-small E, H, Li, Be, Na, Mg, Al, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn
mediumFrom Li to Hg (except for B to Ne, Si to Ar, Br, Kr, Xe, Ce to Lu, Pt)
large
From K to Hg (except for Br, Kr, Xe, Ce to Lu, Pt)

the binary hydrides correspond to the DBSPs of the
XY10 and (6-1) structures, respectively. Therefore,
we can expect that the (13-2-1) structure also correspond the hydrides under high pressure. However,crystal structures tend to prefer the coordination
polyhedron [72]. Therefore, we replace the small
sphere at the center of the cuboctahedron withmetallic atoms so that the metallic atoms should
be coordinated by 12 small spheres comprising a
cuboctahedron. We call the quaternary structure
shown in Fig. 1(b) as the (12-1-2-1) structure. This
structure also has the F m3̄m symmetry. We also
focus on the (13-3-1) structure shown in Fig. 2(a).
It is the DTSP at several radius ratios such as
0.30 : 0.40 : 1.00 and can be derived by substituting an atom at the vertex of the unit cell of
the perovskite structure with a cuboctahedron of
13 small spheres. To produce the structural prototype of hydrides, we replace the small sphere at thecenter of the cuboctahedron with metallic atoms asshown in Fig. 2(b), and we call it as the (12-1-3-1)
structure.
Table 1 shows the list of substitution atoms forspheres in the (12-1-2-1) and (12-1-3-1) structures.
Small spheres are substituted with only hydrogenatoms. The number of chemical compositions foreach structural prototype is 36652. To screen out
unstable candidates, we execute the structural optimizations and molecular dynamic simulations withstatic/dynamic crystal lattices. We use the standard enthalpies of formations (SEFs) to estimate
the structural stabilities. We calculate the phonon
dispersions for some of hydrides which have lower
SEFs and no spin polarization.
As a result, we confirm that at least 23 hydrides
are dynamically stable [2]. We found that many
hydrides prefer the (12-1-2-1)V structure shown in
Fig. 3 to the (12-1-2-1) structure. It it worth mentioning that the (12-1-2-1)V structure is isotypic to
the P m3̄ structure of ScYH6 (cP8). Importantly,
the previous study indicated that cP8-ScYH6 may
possess the lowest enthalpy in the pressure rangeof 50150 GPa. Since several quaternary hydrides

(a)

(b)

Figure 3: The (12-1-2-1)V structure.
of which we confirm the dynamic stabilities are
the superstructures of cP8-ScYH6 , we can expectthat they may also have the lowest enthalpies under higher pressures. In fact, the SEFs under 10
GPa of the four kinds of the decomposition paths
from H12 ScY2 Ca:
ScH2 + 2YH2 + CaH2 + 2H2 ,(1)

ScH2 + 2YH3 + CaH2 + H2 ,(2)

ScH3 + 2YH2 + CaH2 + 1.5H2 ,(3)

ScH3 + 2YH3 + CaH2 + 0.5H2 ,(4)are calculated, and we found that H12 ScY2 Ca areconsiderably stable since it has almost the sameenthalpy as the decomposition of Eqs. (1) and(3) while it is less stable than the decompositionsof Eqs. (2) and (4) by about 1.2 eV/f.u., corresponding to the thermodynamic instability of 78.6
meV/atom compared to the case of Eq. (4).
Finally, we calculate the superconducting transition temperatures Tc by density functional theory
for superconductors, are found to be 5.7 and 6.7
K for the selected two hydrides H12 ScY2 Ca andH12 ScY2 Sr, respectively [2].

References[1] R. Koshoji and T. Ozaki: J. Phys. Commun.
6, 075002 (2022).
[2] R. Koshoji, M. Fukuda, M. Kawamura, T.
Ozaki: Phys. Rev. Materials. 6, 114802(2022).

73

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Control of magnetic anisotropy by strain andelectric polarization at interfaces
Yoshihiro GOHDA
Department of Materials Science and Engineering, Tokyo Institute of Technology
J1-3, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8502, Japaning to the ↑↓ spin-ﬂip term, i.e., couplings
between up-spin unperturbed states anddown-spin virtual states, in Fig. 1(b). In
contrast, the MCA energy modulation in
Fe3 Si was found to be attributed to neither
Bruno nor quadruple terms.
In addition, phase equilibria in permanent magnets were discussed through ﬁrstprinciples thermodynamics [3, 4].

E MCA (meV/atom)

In this project, we performed ﬁrstprinciples calculations of ferromagnetic
Heusler compounds to clarify the microscopic origin behind the strain-mediatedmodulation of the MCA energy EMCA . In
Co2 FeSi, site-projected EMCA of both Co
and Fe decrease with an isotropic expansion of the in-plane lattice as shown in
Fig. 1(a). This can be compared witha formulation connectable to X-ray magnetic circular dichroism observations via thequadrupole moment of the spin-density distribution (quadrupole term) and changes inorbital magnetic moments (Bruno term) [1].
As is clear from the ﬁgure, the quadrupoleterm is dominant for Co2 FeSi correspond-

0.10
0.08
0.06
0.04
0.02
0
−0.02
Bruno term
−0.04
−0.06 quadrupole term
EMCA
−0.08
−0.10
0.10
0.08
0.06
0.04
0.02
0
−0.02
Bruno term
−0.04
−0.06 quadrupole term
EMCA
−0.08
−0.10
−3 −2 −1
0

(b)

Co

E MCA (meV/atom)

E MCA (meV/atom)

(a)

Fe

1

Δa||/a0 (%)

2

E MCA (meV/atom)

Magnetocrystalline-anisotropy (MCA)
energy is of importance in controllingthe direction of magnetic moments. The
dependence of the magnetic anisotropy
on lattice constants can be utilized formagnetoelectric couplings via domain modulations of ferroelectric materials under
ferromagnetic ones. Such interface multiferroicity is promising for the reduction ofenergy consumptions in magnetic devices
avoiding the Joule heating by the electric
current.
The magnetoelectric eﬀect of
Co2 FeSi was found to be much larger thanthat of Fe3 Si [2], albeit its origin is yet to
be clariﬁed.

3

0.12

Co

0.08
0.04
0
−0.04
−0.08

E MCA

↑↑

E ↑↓
MCA

↓↓

E MCA

↓↑

E MCA

−0.12

0.12

Fe

0.08
0.04
0
−0.04
−0.08
−0.12
−3

E MCA

↑↑

E ↑↓
MCA

↓↓
E MCA

E MCA

−2

−1

↓↑

0

1

2

3

Δa||/a0 (%)

Figure 1: Site-resolved EMCA of Co2 FeSi as afunction of the distortion ratio ∆a|| /a0 : (a) total EMCA and contributions from the Bruno and↑↑↓↓↑↓quadrupole terms; (b) EMCA
, EMCA, EMCA,↓↑and EMCA[1] J. Stöhr, J. Magn. Magn. Mater. 200, 470(1999).
[2] S. Fujii, Y. Gohda, et al., NPG Asia Mater.
14, 43 (2022).
[3] S. Tsuna and Y. Gohda, J. Appl. Phys. 133,
115103 (2023).
[4] S. Nishino and Y. Gohda, Jpn. J. Appl.
Phys. 62, 030902 (2023).

74

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Discovery of Super-Composite Electrical Insulating Materials
Based on Multiscale Physics and Deep Learning of Polymers
Hajime SHIMAKAWA, Haruto SUZUKI, Chihiro TATEYAME, Yuki MORI,
Akiko KUMADA, and Masahiro SATO
Department of Electrical Engineering & Information Systems
The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656
electrical

Materials Informatics (MI), a data-driven

conductivity

of

the

compositematerial design method, is considered effective

materials in PoLyInfo [2] were used. The

for designing polymer materials that require athermal and electrical conductivities were

vast amount of manufacturing information.

learned by adding polymer information, filler

However,

information

information, volume fraction, measurement

including fillers and measurement conditions

temperature, sample thickness, and process

have a great influence on material properties,

conditions,the methods for extracting them as features

improved with each additional feature. The

have not been sufficiently investigated, and theprediction accuracy increased significantly

use of MI is currently limited [1]. In this study,

when filler information was added for thermal

we investigated electrical and thermal feature

conductivity, and when process information

extraction for polymers using multi-scale

was added for electrical conductivity. Whilephysics based on first-principles and molecularfiller volume fraction had a significant effect on

dynamics calculations. We also used machine

prediction of thermal conductivity, it was notlearning to predict the electrical and thermal

sufficient

properties of composite polymer materials.

conductivity, indicating that input of process

Furthermore, the importance of each material

conditions is necessary in predicting electricalinformation was examined based on feature

conductivity. Our results show a new potential

engineering.

of materials informatics for the prediction of

althoughsamplesuccessfully

developed

for

the

prediction

predictionofaccuracyelectricalcomplex polymer properties.

In multiscale electrical feature computation,weandcomputational

methods of ionic charge mobility in polymer

References

matrix and hole trapping barrier between[1] L. Chen, et al.: Mater. Sci. Eng. R Rep.,

polymer matrix and nano-filler. In machine

144, 100595 (2021)

learning, experimental results of thermal and[2] https://polymer.nims.go.jp/en/

75

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study of photoresponsive functional materials
Shinji TSUNEYUKI
Department of Physics, The University of Tokyo
Hongo, Bunkyo-ku, Tokyo 113-0033
The technology to connect and control

We also find that the four-phonon scattering

semiconductor or magnetic devices with light isprocess contributes as much to the phonon

attracting attention as an essential technology inlinewidths of some phonon modes as the third-

the era of 5G and beyond 5G. The development

order anharmonic term. This method is versatileof materials and devices necessary for thisand relatively computationally inexpensive, andpurpose is required. This research aims towill be useful for future development ofdevelop and demonstrate a first-principles

dielectric materials.

simulation method for the optical responsivityof materials, which will serve as a basis forsuch research and development.
This academic year, we developed a firstprinciples method to calculate the dielectric
properties

ofcrystalswithsignificant

anharmonic effect in phonon in the sub-THz to
THz range and applied the technique to rutile
TiO2 [1].
The method is based on Cowley’s latticeFig.1 The imaginary part of the dielectric

dynamics theory on dielectric properties [2].

function exx. The results of the present method

We calculate the Born effective charges of ionsand a perturbative approach are show in a solidfrom the Berry phase and employ the modified

line and a dashed line, respectively (from Ref.

self-consistent phonon approach to calculate[1]).

phonon frequencies and linewidths, including

References

third and fourth-order anharmonicity.
We find that the optical phonon frequencies[1] T. Amano, T. Yamazaki, R. Akashi, T.

and line widths at the gamma point better agree

Tadano and S. Tsuneyuki, Phys. Rev. B, 107,with experimental measurements than those

094305 (2023).

obtained by the perturbative approach (Fig.1).

[2] R. Cowley, Adv. Phy. 12, 421 (1963).

76

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analyses on electronic and magnetic structure and parallelization development in quasi-particle self-consistent GW code
Tatsuki ODA1,2, Kazuki MURANAKA2, Chandro PARDEDE2, Jakub LUTSINEC2,
Ko HYODO2, Masao OBATA1,2
1

Institute of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa 920-1192
2

Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa,
Ishikawa, 920-1192
We have studied electronic structure infunctional approach of generalized gradient

several systems of magnetic material. In one ofapproximation (GGA). From the analysis of

the investigations, we found new foundations ofgeneralized susceptibility in the cubic phase, themagnetic shape memory alloy on the electronic

instabilities responsible for the modulated

instability to modulated phases using the quasi-

structures of 10M, 14M, and 6M were found toparticles self-consistent GW method (QSGW) in

be an intrinsic property in the electronic states

which the electron-correlation of random phase[2]. These states may stabilize the modulated

approximation is explicitly included in the self-

one, accompanied by tetragonal local JT

energy part of one particle energy level. Thisdistortions. Their property of Fermi surface

method was used in the software ecalj [1] which

nesting sensitively depends on a subtle change

has been developed by the researcher T. Kotani.

in the magnetic moment, corresponding to the

Our group has developed its highly parallelized

experimental fact that the modulated structure

code, achieving a one-order faster using theappears depending on temperature and thecomputer facilitated in ISSP.

We have also

composition of the magnetic element. We also

developed the density functional theory (DFT)found that there is another secondary peak in thecode optimized for GPU architecture.

generalized susceptibility.

(A) Application to Ni2MnGa by QSGW method

The results of QSGW show a lot of improved

According to the QSGW approach, the Ni eg

features in the electronic structure. The Ni 3d eg

orbitals in the cubic (austenite) phase, which

component, appearing just at the Fermi level,lead to martensite phase transition by band Jahn-

can be definitive theoretical evidence for the

Teller effect, were found to locate just on theexistence

Fermi level. This implies a clear definitive origin

temperatures. Compared with the GGA +U orof band Jahn-Teller (JT) effect in comparison

GGA results, the eigenvalue levels of thewith the results obtained by the density

minority spin state shift to higher energies,

77

of

phase

instability

at

low

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

indicating an increase in exchange splitting and,thus, an increasing total magnetic moment. Theenergy level shift in the minority spin state issmall but makes a drastic change in thegeneralized

susceptibility. Thechangeisquantitative, but the meaning of its result
provides a qualitative conclusion in themartensite phase of 10M or 14M appearing at
low temperatures. Such an instability indicatedfrom the investigation of susceptibility is foundFig. 1: Time ratio of GPU vs. CPU.

to be much more sensitive to the magnetic

We combined the use of OpenACC program-

moment, implying a close relationship with theming and CUDA library that provides thecomposition of the magnetic element and theroutines of FFT and MMM. The OpenACC canexternal magnetic field.

manage data transfer from host to device and(B) Optimization of DFT code for GPU

vice versa easily and parallelize some kinds of

The use of GPU parallelization has shown acalculations

great promise in accelerating DFT calculations

withsimpledirective.

We

performed DFT calculations on the different

and reducing the computational cost. The results

system size; modulated magnetic shape memoryobtained from our GPU-accelerated DFT codealloy Ni2MnGa (NMG); (NMG)10(40 atoms),

demonstrate its potential to accelerate electronic(NMG)20(80structure calculations, making it a promisingatoms),(NMG)14(56atoms),(NMG)28(112 atoms). Our code gained speed-up

tool for studying large-scale systems in materials

65-195-fold depending on its system size.

science, physics, and chemistry.

However, we faced memory limitation due to

Several of the subprogram in the DFT code

memory capacity on the GPU. As the larger

need a lot of memory data for accomplishingsystem we calculate, the large memory capacity

their operations. In a plane-wave-basis code, thewe need to perform the calculation.

routines of fast Fourier transformation (FFT)

References

and matrix-matrix multiplication (MMM) are[1] T. Kotani, J. Phys. Soc. Jpn. 83, 094711

essential in the total computational cost. The(2014); ecalj: https://github.com/tkotani/ecalj/.

problem has been a large amount of data transfer[2] M. Obata, T. Kotani, and T. Oda, Phys. Rev.

between GPU and CPU. Such problem may be

Mater. 7, 024413 (2023).

resolved in our plane wave code with a currently
available GPU equipped at ISSP computer.

78

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Systematic elucidation of structure and electronic state of πelectron-proton coupled molecular conductors under pressure
Shun DEKURA†
Institute for Solid State Physics, The University of Tokyo,
Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8581
κ-H3(Cat-EDT-TTF)2 (= H-TTF) and its

below 2.0 GPa. The results are consistent withanalogues, which have been recently developed

the experimentally observed behavior, andin our group, show unique π-electron–proton

suggests that isotropy of the applied pressure, in

coupled physical properties owing to theaddition to the band width increase, is key tostrongly correlated electrons and dynamics of

cause metallization in H-ST. However, structural

protons in the H-bonds: such as quantum spin

optimization of H-TTF under hydrostatic

liquid / quantum paraelectric states or chargepressure did not result in proton localization

ordering transition coupled to the dynamics ofunlike the experimental observation, which

1–4)

protons.

Although H-TTF shows charge

indicates the importance of quantum nature ofordering

withprotons to fully understand the behavior of H-

protonlocalizationunderhydrostatic pressure, it was very recently foundTTF analogues under pressure.

that S/Se substituted H-TTF analogue, H-ST,

Referencesshows1) H. Mori, S. Yokomori, S. Dekura, and A.

metallization

andsuperconducting

transition under hydrostatic pressure, and shows
metal–insulator

uniaxial

2) A. Ueda, S. Yamada, T. Isono, H. Kamo, A.

pressure. To understand the π-electron–proton

Nakao, R. Kumai, H. Nakao, Y. Murakami,

coupled physical properties of H-ST underK. Yamamoto, Y. Nishio, and H. Mori, J. Am.

physical pressure, in this study, the author

Chem. Soc. 136, 12184 (2014).

performed

transition

under

Ueda, Chem. Commun. 58, 5668 (2022).

first-principles

structural

3) A. Ueda, K. Kishimoto, T. Isono, S. Yamada,

optimization of H-ST under hydrostatic and

H. Kamo, K. Kobayashi, R. Kumai, Y.

uniaxial pressure, using OpenMX software (Ver.

Murakami, J. Gouchi, Y. Uwatoko, Y. Nishio,

3.9) on the ISSP Supercomputer System B

and H. Mori, RSC Adv. 9, 18353 (2019).

(ohtaka), using GGA-PBE exchange-correlation4) M. Shimozawa, K. Hashimoto, A. Ueda, Y.

functional.

Suzuki, K. Sugii, S. Yamada, Y. Imai, R.

Structural optimizations were performed by

Kobayashi, K. Itoh, S. Iguchi, M. Naka, S.

minimizing the enthalpy under hydrostatic or

Ishihara, H. Mori, T. Sasaki, and M.

uniaxial pressures up to 2.0 GPa. The optimized

Yamashita, Nat. Commun. 8, 1821 (2017).

structures under hydrostatic pressures did not†show proton localization up to 2.0 GPa. On thefor Advanced Materials (IMRAM), Tohoku University,

other hand, the optimized structures under

2-1-1 Katahira, Aoba-ku, Sendai 980-8577

Current address: Institute of Multidisciplinary Research

uniaxial pressures showed proton localization

79

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Elucidation of the mechanism of fast proton conduction
based on proton tautomerism in molecular crystals
by using first-principles calculations
Shun DEKURA†
Institute for Solid State Physics, The University of Tokyo,
Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8581
The author has been developing anhydrous

formation with transient proton transfer tosuperprotonic conductors based on single-

phosphatecrystalline molecular solids, and elucidatingcorresponding Ea was ca. 1.2 eV, consistent with

their peculiar conduction mechanism involving

the experimentally observed one. The result

1–4)

molecular internal degrees of freedom.

In thisintheadjacent

layer.

The

strongly supports the low-barrier anhydrous

study, we elucidated the mechanism of

protonconduction

realizedbyproton−3anhydrous superprotonic conduction (σ > 10

tautomerism. However, only one step of wholeS/cm) with the low activation energy (Ea) of ca.

proton conduction process has been elucidated

1.0 eV based on proton tautomerism in 1,2,3-

in this research; the other processes are now

triazolium phosphate. To evaluate the activation

under consideration.

energies

References

accompanied

with

the

protonconduction in the crystal structure, first-

1) Y. Sunairi, S. Dekura, A. Ueda, T. Ida, M.

principles NEB calculations were performed

Mizuno, and H. Mori, J. Phys. Soc. Jpn. 89,

using OpenMX software (Ver. 3.9) on the ISSP

051008 (2020).

Supercomputer System B (ohtaka), using a2) S. Dekura, Y. Sunairi, K. Okamoto, F. Takeiri,

generalized gradient approximation (GGA)

G. Kobayashi, Y. Hori, Y. Shigeta, and H. Mori,

proposed by Perdew, Burke, and Ernzerhof toSolid State Ionics 372, 115775 (2021).

the exchange-correlation functional.

3) Y. Hori, S. Dekura, Y. Sunairi, T. Ida, M.

At first, the experimentally obtained X-ray

Mizuno, H. Mori, and Y. Shigeta, J. Phys. Chem.

structure was optimized fixing the unit-cell

Lett. 12, 5390 (2021).

geometry for the initial state, where all the four4) S. Dekura, M. Mizuno, and H. Mori, Angew.

1,2,3-triazolium in the unit cell are 1H,3H-

Chem. Int. Ed. 61, e202212872 (2022).

tautomer. Then, the structure with one 2H,3H-†

tautomer out of four 1,2,3-triazolium in the unit

for Advanced Materials (IMRAM), Tohoku University,

cell was optimized as final state. The NEB

2-1-1 Katahira, Aoba-ku, Sendai 980-8577

Current address: Institute of Multidisciplinary Researchcalculation for this step suggested that thistautomerization occurs via hydrogen-bond80Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles calculations of electron correlation parameters to
elucidate π-electron–proton coupled physical properties of theunconventional molecular conductors Cat-TTF analogues
Shun DEKURA†
Institute for Solid State Physics, The University of Tokyo,
Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8581
κ-H3(Cat-EDT-TTF)2 (= H-TTF) and its

from the band crossing the Fermi level using

analogues, which have been recently developed

RESPACK software. Then, U and V for eachin our group, show unique π-electron–proton

analogue were evaluated by the screened direct

coupled physical properties owing to theintegrals between two MLWFs in the crystals.

strongly correlated electrons and dynamics ofBased on the comparison of the obtained1)

protons in the H-bonds. In particular, a charge-

electronicordering (CO) phase transition coupled to thetemperature (TCO), W and V were found to belocalization of D in H-bonds occurs in H/Dcorrelated with TCO. Considering that the CO

2)

and

CO

transitionCOtransition occurs between CO and Mott

transition temperature varies upon the S/Se

insulating states, the author concluded that V

substitution in the π-electron framework and theplays important role to determine TCO althoughisotopesubstituted

analogue.

3,4)

application of physical pressure;The

parameters

however, thepreviously H(D) in the H-bonds governs andmechanism had not been revealed. In this study,

triggers the CO transition.

to investigate the impact of electron correlation

Referenceson the π-electron–proton coupled CO transition,

1) H. Mori, S. Yokomori, S. Dekura, and A.

the author evaluated the bandwidth W, on-site

Ueda, Chem. Commun. 58, 5668 (2022).

Coulomb repulsion U, and inter-site Coulomb

2) A. Ueda, S. Yamada, T. Isono, H. Kamo, A.

repulsion V of the H-TTF analogues by first-

Nakao, R. Kumai, H. Nakao, Y. Murakami,

principles DFT calculations based on the

K. Yamamoto, Y. Nishio, and H. Mori, J. Am.

experimental X-ray structures.

Chem. Soc. 136, 12184 (2014).

All the calculations were performed on the3) A. Ueda, A. Hatakeyama, M. Enomoto, R.

ISSP Supercomputer System B (ohtaka). The

Kumai, Y. Murakami, and H. Mori, Chem.

electronic band structures were calculated by

Eur. J. 21, 15020 (2015).

using Quantum Espresso (version 6.8), where

4) A. Ueda, K. Kishimoto, T. Isono, S. Yamada,the half-filled HOMO–HOMO antibonding

H. Kamo, K. Kobayashi, R. Kumai, Y.

band crosses the Fermi level. The maximally

Murakami, J. Gouchi, Y. Uwatoko, Y. Nishio,

localized Wannier functions (MLWFs) with theshapesconsistent

withand H. Mori, RSC Adv. 9, 18353 (2019).

HOMO–HOMO†

Current address: Institute of Multidisciplinary Research

antibonding orbitals were successfully obtainedfor Advanced Materials (IMRAM), Tohoku University,
2-1-1 Katahira, Aoba-ku, Sendai 980-8577

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Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Structural analysis on twist grain-boundaries
Kazutoshi INOUE1 , Mitsuhiro SAITO2 , and Yuichi IKUHARA1,2,∗
1Advanced Institute for Materials Research, Tohoku University, Sendai, Miyagi, 980-8577
2
Institute of Engineering Innovation, The University of Tokyo, Yayoi, Tokyo, 113-8656

Revealing the relationship between atomic
structure and macroscopic properties is one of
the most important issues in materials science.
Grain boundaries (GBs) are especially important for their complex atomic structures andcontribution to the properties. Historically,
atomic structures of tilt GBs have been discussed by structural unit model. However, it
is essential to consider the 3D atomic structure for twist GBs. The polyhedral unit model,
which is an updated version of the structural unit model, rigorously describes the 3D
GB atomic structure using a combination of
atomic polyhedra. In this study, atomic models for [001] twist GBs in metals with Σ ≤ 53
were built with a 3D periodic boundary condition. The translation models are systematically constructed by the 0.1 Å steps within the
Displacement-Complete-Shift lattice to screen
the stable atomic structures. Each model was
ﬁrstly calculated to obtain GB energy without relaxation to screen the translation states.
We applied the ﬁrst-principles DFT calculations with the plane-wave basis projectoraugmented wave method included in VASP
to screen and determine the stable atomic
structure by using cpu nodes in System B.
The generalized gradient approximation wasused for the exchange-correlation potentials in
the Perdew-Burke-Ernzerhof form, employing
an ultrasoft pseudopotential. The cutoﬀ energy was set 400 eV for all plane-wave basis
sets. The Brillouin-zone integrations were performed over a 4 × 4 × 1 k-point mesh generated
by the Monkhorst-Pack scheme. The GB energy is the interfacial excess free energy calcu-

lated by∆E =1
(Etotal − N σi ) ,2A

where Etotal is the total energy of the system
including GBs, σi is the energy of the unit cellof the bulk crystal, N is the number of unit
cells contained in the supercell, and A is thearea of the GB. The GB energies for a ﬁxed
intergrain separation are within 0.1 J/m2 , indicating the energy landscape is almost ﬂat.
Then, atomic positions as well as the supercell
volume of the most stable structure were relaxed such that all forces were < 1.0 × 10−5eV/Å, and the residual force on each relaxed
atom was 0.05 eV/Åunder the constant pressure of 0 Pa and constant temperature of 0 K.
Then, interstitial voids in each model are calculated by Voronoi analysis, placing the sphereof maximal radius at the Voronoi vertex. The
maximum diameter for each void center can becalculated within the hard sphere model andtheir maximum values vary from 0.30 to 0.50
in the unit of the lattice constant a0 . We showthat the GB energies and the maximum void
volumes have relatively high correlation, suggesting that the maximum void volume can beused to screen low energy translation states for
twist GBs [1].

References[1] K. Inoue, K. Kawahara, M. Saito, M.
Kotani, Y. Ikuhara: preprint (2022).

82

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-Principles Lattice-Dynamics Calculations andThermal Expansion Behavior for NASICONs
Yasuhide MOCHIZUKI1, Takayuki NAGAI2, Suguru YOSHIDA3, Tsuyoshi KIMURA2
1

Department of Materials Science and Engineering,Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo
2

Department of Advanced Materials Science,

University of Tokyo, Kashiwa 277-8561 Chiba, Japan
3

Materials Research Institute, Pennsylvania State University, University Park,
Pennsylvania 16802, United States

Negative-thermal-expansion materials haveattracted considerable attention because they
contribute to sustain the lifespan of largely
expanding materials and also because of theirfascinating

andcounter-intuitive

thermalproperties. The well-known and representative
NTE materials are Si [1], ReO3 [2], ScF3 [3]ZrW2O8 [4] and KZr2P3O12 (NASICON) [5].
Since the reports of NTE in various materials in
the past few decades, it has been widely known
that the mechanism for NTE is the transverse
acoustic phonon modes, which have negative

Fig. 1: Calculated phonon bands for the R 3̅ c

Grüneisen parameters. However, the detailed

phases of (a) KZr2(PO4)3, (b) KGe2(PO4)3, andmechanisms for the NTE properties are

the R 3̅ phase of (c) KGe2(PO4)3. Calculated

uncovered ever since now. Here, we report ourthermal expansion coefficients of KZr2(PO4)3 andprogress for elucidating the microscopic origin

KGe2(PO4)3 are also shown.

of NTE in KZr2P3O12 and the relevant[7] as implemented in VASP [8]. The phononcompounds.

band

structures

werederived

from

the

were

calculated force constants using PHONOPY [9].

performed by using the projector augmented-

We present the calculation results of phonon

wave method [6], and the PBEsol functional̅ c phases of KZr2(PO4)3 (KZP)
bands for the R3

within the generalized gradient approximation

and KGe2(PO4)3 (KGP) as shown in Fig. 1(a, b).

Ourfirst-principles

calculations

83

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

We can see that KZP is dynamically stable,

representation Γ2+ triggers second-order Jahn-

whereas KGP is dynamically unstable. We

Teller effect which lowers the electrons energy.

found that the imaginary phonon mode in the

Further, because the Γ2+ phonon mode is crucial

̅ c phase of KGP is Γ2+ (A2g) phonon mode
R3

for realizing negative thermal expansion, the̅ phase, whichleading to dynamically stable R3

̅ phase)lowered symmetry structure of KGP (R3is shown in Fig. 1(c). In our previous report, we

was transformed into a positive thermalfound that the Γ2+ phonon mode (the rotational

expansion material.

modes of ZrO6 octahedra and PO4 tetrahedra) is

References

the most important for realizing negative[1] S. Biernacki and M. Scheffler, Phys. Rev.

thermal expansion in KZP [10] since the Γ2+

Lett. 63, 290 (1989).

phonon mode has the largest negative value of[2] T. Chatterji et al., Phys. Rev. B 78, 134105

Grüneisen parameter. By substituting d-block(2008).

element Zr with p-block element Ge, the Γ2+[3] B. K. Greve et al., J. Am. Chem. Soc. 132,

phonon mode became unstable because the15496 (2010).

rotational Γ2+ mode of GeO6 octahedra and PO4[4] C. Martinek and F. Hummel, J. Am. Ceram.

tetrahedra trigger second-order Jahn-Teller

Soc. 51, 227 (1968); T. A. Mary et al., Science

effect, which lowers the electrons energy [11].

272, 90 (1996).

Here, as shown in Fig. 1(d), we have calculated[5] W. Miller et al., J. Mater. Sci. 44, 5441

the thermal expansion coefficients for KZP(2009).

̅ c phase) and KGP (R 3
̅ phase) by using(R 3[6] P. E. Blöchl, Phys. Rev. B 50, 17953 (1994).

quasi-harmonic approximation. We found that[7] J. P. Perdew et al., Phys. Rev. Lett. 100,

̅ phase of KGP has positive thermal
the R 3136406 (2008).

expansion coefficients above room temperature[8] G. Kresse and J. Furthmüller, Phys. Rev. B

because the Γ2+ phonon mode was transformed

54, 11169 (1996); G. Kresse and D. Joubert,

̅ , the negative
into Γ1+ (Ag) phonon in R 3

ibid 59, 1758 (1999).

Grüneisen parameter value of which was[9] A. Togo and I. Tanaka, Scr. Mater. 108, 1

weakened.

(2015).

In

conclusion,

we

have

shown

that

[10] Y. Mochizuki, S. Bae, and H. Raebiger,

substituting Zr site with p-block element Ge

Activity Report of Supercomputer Center̅ c phase (NASICON structure)makes the R 3

Institute for Solid State Physics 2021.

dynamically unstable because the rotational[11] T. Nagai, Y. Mochizuki, S. Yoshida, and T.

phonon mode transforming as irreducible

Kimura, J. Am. Chem. Soc. 145, 8090 (2023).

84

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Prediction of CO Adsorption Energy on Single AtomCatalysts Embedded in TiO2 by Machine Learning
Kyoichi SAWABE
Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603

on r-TiO2 . Applying the learning model obtained with the CO/r-TiO2 data to the caseof CO/a-TiO2 (anatase type TiO2 ), we obtained Figure 1b, in which the deviation ofdata points from the straight line of the prediction model appears as CO adsorption becomesstronger. Thus, the features of π back donation and structural relaxation for the CO adsorption can be extracted from the additional
data for a-TiO2 .
By eliminating the parameters that arehighly correlated with each other using a
Lasso regression, etc., a multiple linear regression (MR) model shown in Figure 1c
was obtained.
We used six parameters:
Eads (CH3 CN), Charge, melting point, the heatof melting, crystalline system, and RMO,
which is the distance between the embedded
metal and the horizontally neighboring oxygen. Although the melting point and the heatof melting do not appear to have any chemicalsigniﬁcance for CO adsorption, the above analysis indicated that they relate to the π backdonation and/or the structural relaxation.
(a)

(b)

(c)

Eads(CO) /eV

This year, we conducted a feature analysis for machine learning (ML) prediction of
CO adsorption energy on single-atom catalysts(SAC) using TiO2 substrates.
We used the VASP program for spin polarization DFT calculations. Slab units withn (n = 2 − 6) layers were used as models of
TiO2 surfaces. The electronic states of the
SAC were modulated by changing both the
thickness of the slab unit and the single metals
embedded in TiO2 .
Good features for ML would require parameters of a chemically meaningful nature suﬃcient to describe the adsorption. In the caseof CO adsorption on the SAC, σ donation, πback donation, and structural relaxation due
to the adsorption are involved in the adsorption strength. Therefore, ML should use features that can describe these properties. Furthermore, data with a suﬃcient variation ofthese features must be used for ML. The σ donation is related to the Lewis acidity of the adsorption site. The strength of CH3 CN adsorption is often used experimentally and theoretically in order to measure the strength of Lewis
acidity. Therefore, we calculated the strengthof CH3 CN adsorption on SACs. A linear regression of CO adsorption energy, Eads (CO),on r-TiO2 (rutile type TiO2 ) with respect toEads (CH3 CN) was obtained with good accuracy, as shown in Fig. 1a. This means that
σ donation is dominant for the CO adsorption on r-TiO2 . In other words, informationon π back donation and structural relaxation
was not available in the CO adsorption data

R2=0.93
RMSE=0.14

Eads(CH3CN) /eV

Eads(CH3CN) /eV

MR prediction /eV

Figure 1:
Linear regression model for
Eads (CO) on (a) r-TiO2 and (b) both r-TiO2
and a-TiO2 using Eads (CH3 CN). (c) Multiple
linear regression model.

85

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Quantum transport theory based on large-scale
first-principles electron transport calculations
NOBUHIKO KOBAYASHI
Department of Applied Physics, University of Tsukuba
1-1-1 Tennodai Tsukuba Ibaraki 305-8573

ture at the atomistic levels, and also to analyze
the transport properties of materials weakly
bonded by van der Waals interactions. The
electron and hole mobilities of the pentacenethin-film are calculated taking the eﬀect of intramolecular vibrations on both the partially
dressed polaron and the dynamic disorder into
consideration by using TD-WPD method. It
is demonstrate that electron mobility in highmobility organic semiconductors is indeed limited by polaron formation. [4]Analysis of transport properties from theatomistic level is an important issue from theviewpoint of materials science and technology. The purpose of this project is to analyze
and predict the transport properties of materials from first-principles. We have developed
the nonequilibrium Green’s function (NEGF)
method and the O(N) time dependent wavepacket diﬀusion (TD-WPD) method on thebasis of the density functional theory (DFT).
By using these methods, we have investigatedcharge, head and spin transport properties ofmaterials. [1]We have developed a Simulation code for
Atomistic Kohn-sham Equation (SAKE) for
the ab-initio electron transport calculation
based on the DFT and NEGF formalism. [2]We have applied the method to analysis ofthermoelectricity of Heusler compounds, chalcopyrite, and skutterudites. High performancesystems are designed based on analysis of electronic structures and thermoelectric properties.

Figure 1:
CuFeS2.

Organic semiconductors have attracted
much attention for their applications to flexible, printable, lightweight, and low-cost electronic devices. They are crystals that areassemblies of π-conjugated molecules weakly
bonded by van der Waals interactions, andelectron transport properties are significantly
influenced by electron-phonon interactions.
We developed the O(N) TD-WPD method forthe quantum transport calculation of huge systems of up to 100 million atoms a decadeago, and have been applied organic semiconductors. [3] It is possible to calculate theconductivity and the mobility of the systemwith micron-order lengths at room tempera-

Wavefunctions of chalcopyrite

References[1] N. Kobayashi, H. Ishii, K. Hirose, in 3D Local Structure and Functionality Design of Materials eds H. Daimon, Y. C. Sasaki (World
Scientific, 2018) p133.
[2] H.Takaki, N.Kobayashi, K.Hirose, J. Phys.:
Condens. Matter. 32 325901(2020)[3] H. Ishii, S. Obata, N. Niitsu, S. Watanabe, H.
Goto, K. Hirose, N. Kobayashi, T. Okamoto,and J. Takeya, Sci. Rep. 10, 2524 (2020)[4] H. Sato, S. A. Abd. Rahman, Y. Yamada,
H. Ishii and H. Yoshida Nat. Mater. 21, 910(2022).
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Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles simulation of interfacial reactions
using density functional theory and classical liquid
theoryMinoru OTANICenter for Computational Sciences, University of Tsukuba
1-1-1, Tenno-dai, Tsukuba, Ibaraki 305-8577, JapanThe electrochemical properties at the interface between electrode and electrolyte havemuch attention to improving the electrochemical performances of rechargeable batteries, fuelcells, and electrochemical catalysts. Because
the electrochemical properties depend on thematerial properties constructing the electrochemical interface and environmental parameters such as the bias voltage, an exhaustive
study is indispensable to understand the details of physical phenomena at the electrochemical interfaces.

derestimates the dielectric constant of a solution with dipolar solvent molecules. The dielectrically consistent RISM (DRISM) is oneof the solutions to overcome the drawback of
the RISM theory. This year, we have combined DRISM with the ESM-RISM framework to increase the accuracy of electrochemical interface simulations and applied it to thePt(111)/aqueous water interface as a benchmark calculation [4].

To simulate the physical phenomena at theelectrochemical interface, we have continuously developed the ESM-RISM method [1]that combines density functional theory using the eﬀective screening medium technique(ESM) [2] and reference interaction site model(RISM) [3]. In this method, we treat the electrode surface and the reactants using the quantum mechanical theory and the solvation system using the classical solution theory. The
electrostatic and van der Waals-type potentials
describe the interaction between the quantum mechanical particles and classical solution. Because ESM-RISM is formulated under the grand-canonical ensemble, we can naturally address the formation of an electric double layer at the electrochemical interface using
the half-cell system.

First, to check the results of DRISM, we calculated the salt-concentration dependence of
the activity coeﬃcients for the bulk NaCl aqueous solution. The results of the conventional
RISM underestimate the activity coeﬃcientscompared to the experiment, but DRISM well
reproduces the experiment. Thus, DRISM improves the dielectric properties of the bulk solution. The results of electrochemical properties at the interface, such as the potentialof zero charges, standard hydrogen electrodepotential, double-layer capacitance, and thickness of the contact layer, are improved by
DRISM and in reasonable agreement with theprevious experiments and theories.

Although the modeling of the ESM-RISM
method is physically reasonable, there is a wellknown drawback of the RISM theory that un-

Further application results such as the theoretical analysis of oxide electrode degradations
and the electrochemical catalysts will be reported elsewhere.

87Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

References[1] S. Nishihara and M. Otani: Phys. Rev. B
96, 115429 (2017).
[2] M. Otani and O. Sugino: Phys. Rev. B
72, 115407 (2006).
[3] A. Kovalenko and F. Hirata: Chem. Phys.
Lett. 290, 237 (1998).
[4] S Hagiwara, S Nishihara, F Kuroda, andM Otani: Phys. Rev. Mater. 6, 093802(2022).

88

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theory of tunneling currents at semiconductor pn junctions
in electric fields based on first-principles calculation
Takashi NAKAYAMA
Department of Physics, Chiba University
1-33 Yayoi, Inage, Chiba 263-8522
The tunnel field-effect transistor (TFET) is oneof promising candidates for future energy-saving
devices, due to its much steeper on-off switching
features compared to conventional MOS FETs.
Recently, we showed by the first-principles andone-dimensional wave-packet model calculations
that the cooping of Al and N atoms around theSi-pn junctions produces impurity states in Siband gap and such states make the resonance with
conduction-band states under the electric field of
pn-junction, which shortens the tunneling length
between p- and n-Si layers and markedly increases
tunneling currents, in agreement with experiments.
The purposes of this work are to study (i) thetunneling current at Al-N co-doped Si-pn junctions
by the three-dimensional more realistic calculationsand (ii) how such tunneling current changes by the
N-atom doping into the pn junctions made of direct
band-gap semiconductors such as InP.
We consider the (100)-directed 2x2 pn junctions
with 104 atom-layers of 5 typical semiconductors
like Si and InP, as shown in Fig.1. The N-atom
impurity is inserted in this junction. To simulate
electronic structures of pn junctions, we adopt theconventional sp3d5s* tight-binding model, whoseparameters are determined so as to reproduce
electronic structures by the first- principles
hybrid-DFT calculation. The calculation of thetunneling currents are performed using thenon-equilibrium Green’s function (NEGF)
method, where the semi-infinite electrodes areattached to the left and right sides of the present
junction in Fig.1.
Figures 2(a)-(b) show calculated tunnelingcurrents as a function of the electric field, for Si, Ge,
and GaP, and for InP and GaAs, respectively.

Fig.1. Schematic view of Al-N doped (100) Si-pnjunction employed in this work.

Fig.2. Calculated tunneling current as a functionof electric field in pn junctions made of (a)Al-N-doped Si and Ge and N-doped GaP, and (b)N-doped GaAs and InP. The results for nondoped cases are also shown by dashed lines.

Here, both the currents in the cases with andwithout Al-N/N impurity atoms are shown. It isclearly seen that the Al-N/N-atom doping
markedly increases the current by about 102-107
times for the former indirect band-gap systems,
while induces a slight current change for the latter

89

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Fig.3. Calculated transmission spectra acrosspn junctions with and without Al-N/N impurity
atoms by red and black lines, respectively, as afunction of the energy in the tunneling energy
window, for (a) Si and (b) InP.

Fig.4. Schematic pictures to explain the effectsof Al-N/N-atom doping on tunneling currents
at pn junctions made of (a) indirect band-gap
semiconductors like Si, Ge, and GaP, and (b)direct band-gap ones like InP and GaP.

direct band-gap systems.
To clarify the origin of current enhancement,
we show in Fig.3(a) the transmission spectra ofelectrons for Si. It is seen that the transmission
becomes much larger when impurity atoms arepresent, and its spectra have an extremely large
peak around E=-0.66. By analyzing the local
density of states around the pn junction, as shownin Fig.4(a), we found that the electric field in pnjunctions produces the resonance between isolated
Al-N/N states in the band gap and conductionband states. These resonance states shorten thetunneling length and markedly enhances thetunneling current, which is in good agreement withexperiments.
With respect to direct band-gap systems, weshow in Fig.3(b) the transmission spectra for InP.
It is seen that the transmission spectra have flat
shape not depending on the energy without
impurities, while they show small modulation

around E=-0.4eV for the N-doped junctions. We
found that, since the N-impurity states are locatedin the conduction bands for the direct band-gap
systems as shown in Fig.4(b), the impurity doping
only modulates the bands of host semiconductors,
resulting in the slight change of tunneling currents.
All these calculations were performed using thexTAPP, VASP, and our original pspwf and NEGF
codes. In order to realize the calculations for thepresent pn-junction systems, because the system ismade of a large number of atoms (1000-2000
atoms), the advanced computing facility having
multi-task and higher-speed CPU (more than 1280
cores × 2.0G Hz), larger-size memory (around
256GB), and larger-size strange (more than 2 TB)
is indispensable. These conditions are realized onlyby the present ISSP supercomputing systems.

90

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Data-driven materials development using anharmonic phonon database
Masato OHNISHI
Department of Mechanical Engineering, The University of Tokyo, Japan
In recent years, Materials Informatics (MI)the previous fiscal year (April 2022 to Marchtechnology, which integrates informatics and2023), we focused on establishing an automatedmaterials science, has been rapidly developing.

workflow

However, there is still a lack of databases for

conductivity of the stable materials, thoseanharmonic phonon properties, which arewithout

crucialthermalfrequencies, in Phonondb1. We also generatedfunctional materials, such as thermal insulators,

thermal conductivity data for many materials

thermoelectric materials, and thermal interface

using the developed automation code.

for

the

development

of

for

calculating

negativethe(imaginary)

thermalphononmaterials. In addition, because mechanicalThe developed automation code, written inproperties are closely linked to phonon

Python, efficiently handles crystal structures andproperties, atomic vibrations, the availability ofcalls first-principles software (VASP2) andan anharmonic phonon property database would

phonon analysis software (ALAMODE3). The

be valuable also for the design and development

established workflow is illustrated in Figure 1.

of various structural materials.

Although multiple processes are involved in the

In this project, we have been developing anentire calculation, the most computationallyanharmonic phonon property database (APDB)

expensive one is calculating forces using thefor data-driven materials development. During

first-principles approach. As we aim to analyze

Fig. 1 Workflow for the automation calculation of anharmonic phonon properties

91

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

many materials, parallelizing the calculation formaterials in Phonondb in the fiscal year of 2023,

each material is unnecessary. Instead, the "bulk"

we will release the developed database withjob, which allows the submission of numerous

computational details. The released databasesimilar jobs as a single job, is optimal for ourshould allow easy accessibility to anharmonic

simulation. Using the "bulk" job, we can analyze

phonon properties, enabling accurate prediction

up to 144 materials simultaneously in ISSP

of material properties as well as material design

supercomputer. As a result, we have calculated

for target properties.

thermal conductivities for approximately 2,000

Referencesmaterials using the ISSP supercomputer as well

[1] Togo, http://phonondb.mtl.kyoto-u.ac.jp.

as HPCI supercomputers. Moreover, we have[2] G. Kresse and J. Hafner, Phys. Rev. B 47 ,shared the developed automation code with558 (1993); ibid. 49 , 14 251 (1994).

collaborators worldwide so that they can also

[3] T. Tadano, Y. Gohda, and S. Tsuneyuki, J.

work on data generation.

Phys.: Condens. Matter 26, 225402 (2014)

After finishing the calculation for the stable

92Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Impurity effects on TiO2 and X-ray emission spectra ofmolecules by all-electron GW calculations using TOMBO
Kaoru OHNO
Graduate School of Engineering, Yokohama National University79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501
We found a new stable phase of anatase

RIXS spectra of a CH3OH molecule calculated

TiO2 codoped with C and N having a relatively

by our method together with the experimental

small band gap in our GW calculations [1]data [5]. The agreement is excellent without

using the all-electron mixed basis program,

introducing any empirical fitting parameter.

TOMBO, which uses both plane waves andnumerical atomic orbitals as basis functions [2].
Under intermediate oxygen pressure, the band
gap of TiO2 codoped with C and N was foundto be 2.28 eV. Therefore, this phase can be used
as a visible-light-response photocatalyst.
The initial state of X-ray emission spectroscopy (XES) and resonant inelastic X-raya deep core hole after the X-ray photoelectron

Fig. 1: Calculated [4] (above) and experimental[5] (below) RIXS spectra of a CH3OH molecule.

spectroscopy (XPS) and X-ray photoabsorption

References

spectroscopy (XAS), so that their calculations[1] T. Ishikawa, R. Sahara, K. Ohno, K. Ueda, & T.

offer a good example of extended quasiparticle

Narushima: Comp. Mat. Sci. 220 (2023) 112059.

theory (EQPT) [3] in many-body perturbation[2] S. Ono, Y. Noguchi, R. Sahara, Y. Kawazoe,

theory (MBPT). Moreover, to overcome the& K. Ohno, Comp. Phys. Comm. 189 (2015) 20.

basis set incompleteness problem, we adopt the[3] K. Ohno, S. Ono, & T. Isobe: J. Chem. Phys.

all-electron mixed basis program, TOMBO.

146 (2017) 084108.

Here we applied the one-shot GW + Bethe--[4] K. Ohno & T. Aoki: PCCP 24 (2022) 16586.

Salpeter equation (BSE) approach in MBPT to[5] A. Benkert, F. Meyer, D. Hauschild, M.

this problem on the basis of EQPT and analyzeBlum, W. Yang, R. G. Wilks, M. Bär, F. Reinert,

XES and RIXS energies for CH4, NH3, H2O,

C. Heske & L. Weinhardt,: J. Phys. Chem. A

and CH3OH molecules [4]. Figure 1 shows the120 (2016) 2260.

scattering (RIXS) is an excited eigenstate with93

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of a first-principles calculation software
for a many-body wave function theory
Masayuki OCHI
Forefront Research Center, Osaka University
1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043

We have developed a first-principles electronic structure calculation software using thetranscorrelated (TC) method [1, 2]. The TC
method is a many-body wave function theory,
where Hamiltonian is similarity-transformed
with the Jastrow correlation factor. By thistransformation, electron correlation eﬀects are
eﬃciently considered.
In particular, oneelectron orbitals in the Jastrow-Slater-typewave function can be optimized in the samemanner as the Hartree–Fock (HF) method, tosay, by solving a one-body self-consistent-field(SCF) equation. It is advantageous that thecomputational cost for this process is the sameorder as that for the HF method [3].
In this year, we have published our computational code TC++ on github [4] together
with its technical details [5], including efficient treatment of the three-body interactions included in the similarity-transformed
Hamiltonian and accurate correction terms
for the divergence of the eﬀective potentials in the reciprocal space. One can perform the TC calculation using TC++ by reading some output files dumped by DFT calculation using the Quantum-Espresso package [6]. TC++ supports the following functionalities: HF, TC, and biorthogonal TC(BITC) calculations, SCF and band calculations, solids and homogeneous electron gas,a plane-wave-basis set, and norm-conserving
pseudopotentials. At present, the Jastrow factor has a simple random-phase-approximationtype form, but TC++ will support more general

types of the Jastrow factor soon. Calculation is
MPI-parallelized for the k-point and band indices. Using supercomputers of ISSP, we have
performed several test calculations on several
kinds of solids, to check the applicability of
our code and verify the accuracy of calculated
quantities, e.g., a band structure and a totalenergy. As reported in our previous studies(e.g., [3]), calculated band gaps are more accurate than LDA and GGA, but the total energy
is at present less accurate. Now we have tested
the accuracy using a polynomial-type Jastrowfactor including a larger number of optimizable
parameters.

References[1] S. F. Boys and N. C. Handy, Proc. R. Soc.
London Ser. A 309, 209 (1969); ibid. 310,
43 (1969); ibid. 310, 63 (1969); ibid. 311,
309 (1969).
[2] N. C. Handy, Mol. Phys. 21, 817 (1971).
[3] M. Ochi, K. Sodeyama, R. Sakuma, and S.
Tsuneyuki, J. Chem. Phys. 136, 094108(2012).
[4] https://github.com/masaochi/TC[5] M. Ochi, Comput. Phys. Commun. 287,
108687 (2023).
[6] https://www.quantum-espresso.org/

94

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of Polymer Electret Materials for Energy Harvesting
Using Machine Learning
Yucheng ZHANG, Zeitan MAO, Kuniko SUZUKI, and Yuji SUZUKI
Department of Mechanical Engineering
The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656
Electret is a dielectric material withgroup enrichment analysis, we successfully

quasi-permanent charges and can trap

proposed the electret CTX-A/APDEA withcharges stably for decades. Vibrational

high bipolar charging performance via

electret energy harvester (VEEH) can

combining CTX-A with N-(3-aminopropyl)

generate electricity efficiently from kinetic

diethanolamine [2].

energy via the electrostatic induction. The

This result encouraged us to move

VEEH with bipolar (both positively andfurther to search new amines in the open-

negatively charged) electret leads to four

source database PubChem, aimed attimes output power theoretically, thus

designing better bipolar polymer electret

specifying the importance of designing

based on CYTOP CTX-A after thehigh-performance bipolar polymer electrets.

dehydration reaction. It is also shown thatCYTOP (Cyclic Transparent Opticalthe ionization potentials (IPs) computed byPolymer, AGC Chemicals) is one of thethe density functional theory (DFT) withbest polymer electret materials as shown inpolarizable

Fig. 1. Recently, we utilized quantum

correction agree well with the trends of thechemical analysis for evaluating the charge

surface charge density and charge stability

trap of CYTOP electrets [1]. It is found thatmeasured by the wet experiments [3,4].

continuum

model

(PCM)

although the repeat-unit-number of CTX-A
is above 1000, the trapped charge islocalized at the amide bond, which isformed by dehydration reaction between
the carboxyl end group and the amine
introduced.
Recently, by employing the de novo

Fig. 1. Chemical structure of CYTOP series.

molecule generation and the functional

95

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

-3000
-2500
-2000
-1500
-1000

(-) CTX-A/APAEPPA(-) CTX-A/ABPE(-) CTX-A/BAPP(-) CTX-A/APDEA

-500
0
0

500

1000
1500
Elapsed Time [Hours]-2000time for negatively-charged with elapsed

3.5 kV, stored under room temperature.
-1500

To-1000
prepare the labeled data, 5522 amines(-) CTX-A/APAEPPA_115°C
were -500
initially sampled fromthe PubChem.
(-) CTX-A/ABPE_115°C(-) CTX-A/BAPP_115°C(-) CTX-A/APDEA_115°C

Thereafter, the virtual dehydration reaction
0

3500

thermal curing temperature of the CYTOP

3000

polymer.

2500
2000

Candidates are re-examined with PCM-DFT to get accurate solid-state IP. Three

1500

amines APAEPPA, ABPE,
and BAPP have(+) CTX-A/APAEPPA

1000(+) CTX-A/ABPE

CTX-A/BAPP
finally been selected.(+)
2 shows the
500(+)Figure
CTX-A/APDEA

0
surfacepotential
for thosefilms(15 µm in
0
500
1000
1500
2000

2000

c
Figure2. Surface potential decay versus
Negative Surface Potential at 115°C [V]Positive Surface Potential [V]

b

-3500

Elapsed Time [Hours]dPositive Surface Potential at 115°C [V]Negative Surface Potential [V]

a

0
500
1000
1500
2000
was conducted
and PCM-DFT
computation

thickness) after charging to -3.5 kV. It isfound that the materials obtained in this2000

study are superior to our previous CTXA/APDEA in terms of charge stability [4].

1500

All the quantum chemical calculations
1000

are made with the software GAUSSIAN [5](+) CTX-A/APAEPPA_115°C(+) CTX-A/ABPE_115°C
at the DFT levelwith the CAM-B3LYP

500(+) CTX-A/BAPP_115°C(+) CTX-A/APDEA_115°C

functional and 6-31+G(d,p) basis set, while
0
0

500

1000

1500

2000

PCM is combinedforsolid-state analysis
Elapsed Time
[Hours]Elapsed Time [Hours]

was automatically made. Subsequently, 80%

due to the solvation effect correction.

of the data for solid-state IPs and theThis work was partially supported byinformation on molecules and bonds was

JST CREST Grant Number JPMJCR15Q3

employed to teach the deep learning modeland JPMJCR19Q1. The calculations are

named MEGNet [5]. Two sets of the data

performed with SGI ICE XA ISSP system(10 % each) were used as the validation/test

B with 1 node (24 CPUs).

sets. As a result, the mean absolute error(MAE) of solid-state IP is found to be as

References

small as 0.326 eV. The computational cost

[1] Kim S., et al., J. Phys. Chem. B, Vol.

with this approach is significantly lower

124, No. 46, pp. 10507-10513 (2020).

than PCM-DFT, enabling rapid screening[2] Zhang, Y., et al., Appl. Phy. Lett., 118,of huge databases to find candidates for

223904 (2021).

new high-performance bipolar polymer[3] Mao, Z., et al., IEEE Conf. Electr. Insul.

electrets.

Dielectr. Phenom., pp. 667-670 (2021).

We also made another MEGNet to[4] Mao, Z., et al., Adv. Mater., submitted.

predict the boiling point, because the[5] M. Frisch et al., “Gaussian 09, Rev. A.

amines should not be evaporated at the

1,” Gaussian, Inc. Wellingford, CT, (2009).

96

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Design and Understanding of Catalysts Realized by Theory
and Machine Learning
Hao LiAdvanced Institute for Materials Research (WPI-AIMR),
Tohoku University, Sendai 980-8577, Japan

1. Introduction

adsorbate, the surface state of an electrocatalyst

Catalyst design is essential for realizing a

is usually different from its pristine form atsustainable society. However, it is sometimes

operatingchallenging due to the complicated reaction

electrochemical surface state of a catalyst is

networks and surface phases under reaction

essential in determining the catalyst activity. In

conditions. To address this challenge, ab initio

this project, we analyzed the surface states ofcalculations,molecularandtypical transition metal X-ides (TMXs) andmicrokinetic

modeling

betteremerging M-N-C catalysts, and found that theirdynamics,
can

help

conditions.

Meanwhile,theunderstand the reaction and make predictions.

catalytic surfaces generally differ from their

2. Computational Methods

stoichiometric forms [1-2]. A typical example is

In

this

project,

DFT

calculations

were

shown in Fig. 1, where the surfaces of dual-

performed using VASP with the exchange–

atom M-N-C are usually pre-covered [1]. These

correlation energetics described by the Perdew,

show that we should probe the surface state

Burke, and Ernzerhof (PBE) or the revised PBE

before analyzing the electrocatalytic activity.

(RPBE) functional. The generalized gradientapproximation was employed. Ion–electroninteractions were described by the frameworkof projector-augmented plane-wave method.
The energy cutoff was set to at least 400 eV.
Spin-polarization was included when necessary.
Brillouin zone was sampled by the MonkhorstPack method. Transition states were located by
the climbing-image nudged elastic band.

Fig. 1: Examples of the calculated surface

3. Results and Discussion

Pourbaix

3.1. Surface state analysis

catalysts. (a-b) Optimized structures. (c-d)

Due to the equilibrium between water andSurface Pourbaix diagrams. Reprinted with97

diagramsofdual-atom

M-N-C

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

permission from Ref. [1].

ORR in alkaline media [6]. Based on ~7800

3.2. Catalysis theory development

experimental data, we derived the key role of
La and found that those materials with La could
possess good ORR performance. These showthat ML can not only provide prediction, butalso unravel the structure-performance relationof electrocatalysts.
4. Conclusion
Through this ISSP project, we performed
comprehensive analyses to understand somepromising electrocatalytic materials. We foundFig. 2: (a) The Er-NiFe-LDH considered forthat surface state is an essential factor insimulations. (b) Microkinetic modeling toelectrocatalysis that should not be dismissed

analyze OER activities of various sites at Er-

before the activity analyses of many catalysts.

NiFe-LDH. (c) Charge density differences. (d)Also, explainable ML can help identify the

Projected density of states. (e) Calculated spin-

critical factor of a material in electrocatalysis.

polarized d-band centers of different systems.

References

Reprinted with permission from Ref. [3].

[1] W. Yang, J. He, B. Zhou, L. Wei, Z. Gao*,

We also analyzed various catalysts and their

H. Li, Commun. Chem. 6, 6 (2023).

performances based on catalysis modeling. The[2] H. Liu, X. Jia, A. Cao, L. Wei, C.

analyzed catalyst systems include TMXs andD'agostino, H. Li, J. Chem. Phys. 158 (2023).

single-atom catalysts. The analyzed reactions[3] Y. Zhu, X. Wang, X. Zhu, Z. Wu, D. Zhao, F.

include oxygen evolution (OER) [3], oxygen

Wang, D. Sun, Y. Tang, H. Li, G. Fu, Small, 19,

reduction [4], and nitrogen reduction [5]. An

5 (2023).

example is shown in Fig. 2 [3], in which we[4] C. Liu, Z. Yu, F. She, J. Chen, F. Liu, J. Qu,

analyzed the OER activities of Er-doped NiFe

J. M. Cairney, C. Wu, K. Liu, W. Yang, H.

layered double-hydroxide (LDH). Besides, we

Zheng, Y. Chen, H. Li, L. Wei, Energy Environ.

also studied thermal catalysis, such as Hg 0

Sci. 16, 446 (2023).

oxidation.

[5] Y. Zhang, Z. Yu, F. She, L. Wei, Z. Zeng, H.

3.3. Machine learning (ML) analysis

Li, J. Colloid Inter. Sci. 640, 15 (2023).

In addition to DFT-based analysis, this project[6] R. Zhao, Z. Chen, Q. Li, X. Wang; Y. Tang,

performed explainable ML modeling to identify

G. Fu, H. Li, J-M. Lee, S. Huang, Chem. Catal.

the role of element La as the active center of

2, 3590 (2022).

98

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First principles study of the adsorption structure of heliceneon the Ag(111) surface
Yuji HAMAMOTO
Department of Precision Engineering, Graduate School of Engineering
Osaka University, Yamada-oka, Suita, Osaka 565-0871
Molecular chiral recognition has drawn

adsorption height and relax the whole system togrowing attention due to its importance indetermine the adsorption structure of 7TH on

biochemistry and pharmacology, and has beenAg(111). The adsorption structure shown in Fig.

studied using a model system composed of

1 indicates that 7TH physisorbs on Ag(111), i.e.,chiral molecules adsorbed on a solid surface.

the S atoms play a minor role in the molecular

The molecular adsorption structure provides aadsorption. This allows us to use classicalkey to the origin of chiral recognition, whereas

molecular

its detail is beyond the reach of experimental

computationally much cheaper than DFT, totechniques

investigate the formation of a 7TH chain on

such

as

scanning

tunneling

dynamics

(MD),

which

is

Ag(111). The results for the MD simulations

microscopy.

will be discussed in more detail elsewhere [3].

Here we resort to density functional theory(DFT) calculations to investigate the adsorption
structure of 7-thiaheterohelicene (7TH) on theAg(111) surface. Although 7TH forms a onedimensional chain on Ag(111), we focus on
single molecule adsorption to clarify theinteraction of the S atoms of 7TH with the Ag

Fig. 1: Adsorption structure of 7TH on Ag(111).

surface. The van der Waals interaction between

Top (a) and side (b) views are shown.

7TH and Ag(111) is considered by using thevan der Waals density functional (vdW-DF)

References

method [1] and the rev-vdW-DF2 functional [2].

[1] M. Dion, H. Rydberg, E. Schröder, D. C.

We first estimate the adsorption site andLangreth, and B. I. Lundqvist, Phys. Rev.

orientation of a 3TH molecule on Ag(111). The

Lett. 92, 246401 (2004).

optimal site and orientation for 3TH are used to[2] I. Hamada, Phys. Rev. B 89, 121103(R)make an initial guess on the local structure of(2014).

7TH near Ag(111). We then optimize the[3] C. Ye et al., in preparation.

99

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Global search for metastable structures of siliceneon the Ag(111) surface by Gaussian process regression
Yuji HAMAMOTO
Department of Precision Engineering, Graduate School of Engineering
Osaka University, Yamada-oka, Suita, Osaka 565-0871
Silicene, a silicon analog of graphene, hasresults predict at least seven phases for the

been intensively studied in the last decade,√13 × √13𝑅19.1° unit cell relative to Ag(111),

because of its peculiar phenomena, as well as

which are classified into type-II [Figs. 1(a)-its better compatibility with the silicon-based

1(c)] and type-I [Figs. 1(d)-(g)] phases based

electronics than graphene. Density functionalon the angle between the Ag[110] and Si[110]theorythat

directions. The type-I phases are characterized

freestanding silicene is characterized by theby one, two, or three protruded Si atoms, andalternately buckled honeycomb lattice, whereas

are energetically comparable with each other.

silicene grown on the Ag(111) surface exhibits

These behaviors are analogous to the so-calleda variety of nontrivial buckling patterns, which

T phase, whose structures is hard to identify

makes it difficult to theoretically predict stable

experimentally and still under discussion.

(DFT)

calculations

revealstructures of silicene on Ag(111). To overcome
the difficulty, we here adopt a structure searchmethod based on an evolutionary algorithm(EA) and the Gaussian process (GP) regression[2]. This method accelerates the structure
search by relaxing the structures generated with

Fig. 1: √13 × √13𝑅19.1° phases obtained with

EA, using the energy landscape predicted withthe structure search method. The bright (dark)

GP instead of that obtained by computationallycyan balls denote higher (lower) Si atoms.

expensive DFT calculations.
Our results demonstrate that the method not

References

only reproduces the well-known buckled[1] K. Takeda and K. Shiraishi, Phys. Rev. B

structures of silicene on Ag(111), but also

50, 14916 (1994).

predict new structures that have never been

[2] M. K. Bisbo and B. Hammer, Phys. Rev.

reported as far as we know. For example, ourLett. 124, 086102 (2020).

100

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

High-accuracy machine-learning interatomic potential and massively
large-scale molecular simulation for microscopic mechanisms of grainboundary-dislocation interactions
Tatsuya YOKOI
Department of Materials Physics
Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601
In polycrystalline metals and alloys, grainthese lattice defects. In addition, classicalboundaries (GBs) exist and generally interact

empirical potentials are typically based onwith dislocations, thereby having great impacts

simple analytic functions and thus show limitedontransferability to various atomic environments

mechanicalproperties

thoughGBstrengthening. It is thus essential to understandfor lattice defects.

the relationship between GB structures, their

To tackle the above issue, this work constructedinteraction with dislocations and mechanicalan artificial-neural-network (ANN) interatomic

properties at various length scales, with the goal

potential and combined it with molecularofsimulations.

optimaldesignofpolycrystallineForapreliminary

analysis,

microstructure in metals and alloys.

aluminum was chosen as a model system [1,2].

For this purpose, previous theoretical studies

The ANN potential was used to predict favorable

performed large-scale molecular simulations

atomic structures and energetics for symmetric

basedinteratomic

tilt GBs. The predicted results were thenpotentials, in order to determine atomic structure

validated by performing density-functional-

and energetics at GBs. However, their adjustable

theory (DFT) calculations.

parameters are fitted only to bulk properties

As illustrated by Fig. 1, the ANN potential was

without consideration of atomic environments ofconstructed by following the architecture

GBs. This often leads to critical errors inreported by Behler and Parinello [3] and Behler

predicting atomic structures and energetics of[4], with two hidden layers each having 48 nodes.

onclassical

empirical

Fig. 1 Schematic illustration of an ANN potential.

101Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Two- and three-body symmetry functions wereenergies for symmetric tilt GBs with the [001]employed to encode the atomic environment ofand [1̅10] rotational axes. The predictedeach atom and to provide the input value for theatomic structures were used to perform DFT

ANN potential. In order to generate training

calculations and to calculate their GB energies

datasets, DFT calculations were performedin the DFT level. As a result, the ANN potential

using the projector augmented wave (PAW)

is found to accurately predict GB energies frommethod in the VASP [5,6]. The exchange-

low to high energy states for all the GBs

correlation energy was calculated using a

examined. In addition, the lowest-energy

revised version of the generalized gradientstructures predicted by the ANN potential wereapproximation parameterized by Perdew, Burke

the same as those for DFT calculations. Theseand Ernzerhof (GGA-PBEsol) [7].

results suggest that the ANN potential can be

In order to cover a wide range of atomic

used to predict the lowest-energy structures andenvironments, not only single crystals but also

their GB energies prior to DFT validation, which

lattice defects including point defects, surfaces

will greatly reduce computational cost for

and GBs were used as references for generating

searching for energetically favorable atomic

the training datasets. With those reference

structures for GBs.

structures, structural relaxation and molecular

In future research, the ANN potential will be

dynamic simulations were performed, andapplied to dislocations, in order to evaluate its

snapshots were extracted from the calculated

ability to predict core structures and formation

results. The total potential energy and atomic

energies for dislocations.

force were used as the training datasets. The
ANN potential was trained using an extended

References

Kalman filter and then combined with structural[1] T. Yokoi et al., submitted.

relaxation and molecular dynamics.

[2] T. Yokoi et al., prepared.

It was found that all training datasets exhibit[3] J. Behler, M. Parrinello, Phys. Rev. Lett.
98, 146401 (2007).

sufficient small errors, including the GBs in the[4] J. Behler, Int. J. Quantum Chem. 115,

training datasets. The mean absolute errors

1032-1050 (2015).

(MAEs) were evaluated to be 1.46 meV/atom[5] G. Kresse, D. Joubert, Phys. Rev. B 59,

and 17.1 meV/Å for the total energies andatomicforces,respectively,

which

1758-1775 (1999).

are[6] G. Kresse, J. Furthmüller, Comput. Mater.

comparable to previous studies. It is thus

Sci. 6, 15-50 (1996).

expected that the present ANN potential exhibits[7] J. P. Perdew et al., Phys. Rev. Lett. 100,an excellent accuracy to predict GBs.

136406 (2008).

Then structural relaxation calculations with the
ANN potential were performed to predict therelationship between atomic structures and GB

102

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of crystal structure prediction method
and material search
Tomoki YAMASHITATop Runner Incubation Center for Academia-Industry Fusion, Nagaoka University of Technology
1603-1 Kamitomioka-machi, Nagaoka, Niigata, 940-218
We have studied the structural stability of
SrO on MgO substrates since SrO with unknown crystal structure synthesized on MgOsubstrate has been reported [1]. There isan approximately 20 percent mismatch between the lattice parameters of SrO (5.16
Å) and MgO (4.22 Å), which could affectthe structural stability of SrO We performed
crystal structure prediction (CSP) simulationsfor Sr4 O4 using CrySPY [2]. Four hundred
structures of tetragonal Sr4 O4 were randomly
generated with the lattice constant of the
MgO(100) substrate. Only the lattice constant c was relaxed during structural optimization using Quantum ESPRESSO. Here,GGA is used for the exchange-correlation functional. The results of the search showed thatthe rocksalt-type structure was not the moststable under the constraint on the lattice constant a. The four-coordinated structures weremore stable than others. Alhough the predicted structure differs from that obtained experimentally, we found that the lattice constraints make the rocksalt structure unstable.
We have also searched for solid electrolytematerials that can be synthesized in the systems of Li-Mg-P2 O7 using CSP with CrySPY[2].
We perfromed randam search simulations for LiMg1.5 P2 O7 , Li2 MgP2 O7 , andLi3 Mg0.5 P2 O7 . In each composition, 1000 random structures were locally optimized using
the VASP code. The CSP simulations wereconducted using GGA-PBE, and PBEsol was
also used for the structures with low energy.

We obtained a structure with a hull distanceof 2 meV/atom for Li2 MgP2 O7 , and structureswith a hull distance of about 20 meV/atom for
LiMg1.5 P2 O7 and Li3 Mg0.5 P2 O7 . In addition
to the randam search simulations, DFT calculations were also performed to evaluate the energy of Li2 MgP2 O7 with the P2 O7 frameworkin the Li2.2 Zn0.8 P2 O7 (LZ) structure [3]. Froma vast number of combinations of cation sites
in the LZ structure, the top 10 structures withthe lowest Mardelung energy were adopted for
DFT calculations. The lowest energy of the LZ
structure was only a few meV higher than theenergy of the structure found in RS simulations(RS structure). The RS structure become unstable when the cationic site changes, which
increases the energy. On the other hand, theLZ structure have almost no change in energy
when the cation site was exchanged.

References[1] K. Komatsu, T. Shirai, A. Nakamura, A.
Kato, S. Ohshio, N. Nambu, I. Toda, H.
Muramatsu, H. Saitoh, Ceramics International 39, 7115 (2013).
[2] T. Yamashita, S. Kanehira, N. Sato, H.
Kino, H. Sawahata, T. Sato, F. Utsuno,
K. Tsuda, T. Miyake, and T. Oguchi, Sci.
Technol. Adv. Mater. Meth. 1 (2021) 87.
[3] A. E. Lapshin and M. A. Petrova, Glass
Physics and Chemistry, 36,75 (2010).

103

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Study of the Principle of Photothermal Conversion by Ab
Initio Calculations
Mizuho ONO1, Hiroki GONOME2
1

Graduate School of Engineering,Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845
2

Graduate School of Science and Engineering,

Yamagata University, Jonan, Yonezawa, Yamagata 992-8510
In light-matter interactions, the electrons

W/cm2 and the central frequency is 3.10 eV.

and nuclei that composes matter interact with

Figure 2 shows the total energy excluding theeach other, but the physical processes are

kinetic energy of the lattice and the kinetic

extremely complex and fast. In simulations ofenergy of the lattice in the TDDFT-MD

matter that reproduce this situation, the Born-

simulation results for the silicon crystal. During

Oppenheimer

typically

the application of an electric field, the energy ofapplied and the motion of the electrons is

the system increases rapidly, while the kinetic

decoupled from that of the nucleus. On theenergy of the lattice remains almost unchanged.

other hand, it has been reported that non-In other words, the energy increase of thenegligible non-adiabatic effects between thesystem is dominated by the interaction between

electrons and the nucleus can act on molecules

the electromagnetic waves and the electrons.

moving under a strong external field [1]. The

The kinetic energy of the lattice then begins to

objective of this work is to evaluate the effectfluctuate after 300 fs due to electron-latticeof the external field on the energy of the systeminteractions. The numerical analysis therefore

by performing coupled calculations of theshows that the lattice system is hardly displaced

approximationiselectron and lattice (nuclear) systems without
applying the Born-Oppenheimer approximation.
The coupled calculations treat non-adiabatic
motion by applying Ehrenfest dynamics with
time-dependent density functional theory andclassical molecular dynamics (TDDFT-MD) forthe electron and lattice. The time waveform of
the incident electric field in the simulation isFig. 1: Incident electric field

shown in Figure 1. The light intensity is 1013

104

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Fig. 2: Total energy and kinetic energy of lattice.

directly by the applied electric field but
receives energy through the interaction with theelectron system.

References[1] C. Lian, S.B. Zhang and S. Meng, Phys.
Rev. B. 94, 184310 (2016).

105

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of a full GW electron-hole interaction kernel for
the Bethe-Salpeter equation
Yoshifumi NOGUCHI
Department of Applied Chemistry and Biochemical Engineering, Graduate School ofEngineering, Shizuoka University, Johoku 3-5-1, Hamamatsu, Shizuoka 432-8561, JapanIn 1995, Onida, et al., initiated the first-

gap of 28 typical organic molecules in Thiel’s

principles GW+Bethe-Salpeter simulations for aset [4] and revealed the contributions of the two

Na4 cluster [1]. Since then, the method has been

second-order exchange terms. The effects of theapplied to a wide-range of materials in which itmethod with a full GW electron-hole interaction

has demonstrated its accuracy and reliability.

kernel are 0.2 eV maximum for the n à π*

However, the conventional simulations need toexcitations and negligibly small for the πàπ*employ an additional approximation to a GW

Ξelectron-hole interaction kernel (Ξ!" ) without
exception solving the equation. Specifically, theFigureemployed approximation neglects the two

Full

+

GW

electron-hole

the those of the conventional method. The

unconfirmed assumption that the second-orderresults of our exciton analysis method suggest

terms have a negligibly small contribution.

that the contribution of the second-order

Therefore, it is evident that the conventional

exchange terms tends to be larger for higher

GW+Bethe-Salpeter method does not satisfy

exciton binding energies.

the Baym-Kadanoff conservation low [2].

References

Considering not only the first-order direct[1] G. Onida, et al., Phys. Rev. Lett. 75, 818

and exchange terms but also the two second-(1995).

order exchange terms, we have developed a[2] G. Baym and P. Kadanoff, Phys. Rev. 124,

GW+Bethe-Salpeter method with a full GW
kernel1.

+

and π àRydberg excitations compared withelectron-hole interaction kernel based on aninteraction= +interaction kernel.

second-order exchange terms in the GW

electron-hole

GW

287 (1961).

and[3] S. Yamada, et al., Phys. Rev. B. 105, 045113

implemented it into our original all-electron(2022).

mixed basis program [3]. Figure 1 shows the[4] M. R. Silva-Junior and W. Thiel, J. Chem.

Feynman diagrams of the full GW electron-hole

Theoryinteraction kernel. We simulated the S1 optical

106

Comput.

6,1546(2010).

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab-initio research on nano structures of magnetic nanoparticles
Yasutomi TATETSU
Meio University, Biimata, Nago, Okinawa 905-8585
The search for advanced materials that possess both thermodynamic stability and instability for
different applications has become a hot topic in recent years. With the advancements in technology,
chemical synthesis techniques are being developed to control nanoparticles with precision, allowing
the discovery of new functional materials with unique properties. Teranishi’s team at Kyoto
University has recently made an important breakthrough by discovering a new behavior of crystal
structure transformation in an ionic nanocrystal [1]. Moreover, the team was able to synthesize a new
Z3-type Fe(Pd, In)3 crystal structure by introducing indium as a third element into L12-FePd3, which
could have significant implications for the development of new technologies [2]. The discovery ofthese new materials is critical for advancements in various fields such as medicine, energy,
electronics, etc.
In this report, we have conducted first-principles calculations to explore the stability ofcompounds with Z3-type structures. Our research aimed to estimate the formation energies forvarious Z3-Fe(Pd, M)3 structures, where M represents different transition metals. To perform thesecalculations, we utilized the ab-initio code, OpenMX [3], to compute the ground states of L12-(Fe,M)Pd3 and L12-(Fe, M)Pd3 structures. We compared the energies obtained to analyze the stability ofthese structures. Our results indicated that some Z3-type structures exhibit lower energies comparedto the L12-type structures, indicating that they could be synthesized experimentally. Further
theoretical investigations are required to explain the coercivity mechanism in the Z3-Fe(Pd, M)3
structures.

References[1] Z. Li, M. Saruyama, T. Asaka, Y. Tatetsu, and T. Teranishi, Science, 373, 332 (2021).
[2] K. Matsumoto et al., Nat. Commun., 13, 1047 (2022).
[3] http://www.openmx-square.org

107

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Machine Learning Based Optimized Polymer for Thermal
Function Materials
Bin XU
Department of Mechanical Engineering,
The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656
Polymer informatic is an emerging filed

simulation.

where the AI and machine learning are beingThe

temperaturedependent

thermalused in the efficient discovery and design ofconductivity of cellulose polymer with thepolymer with target properties and has large

temperature up to 300 K is shown in Fig. 2. The

impact on several aspect of human life, science,

thermal conductivity of filaments with lower

and technology. Cellulose is an organic

crystallinity index (CI) also increases with acompound with the formula (C6H10O5)n, a

similar slope until 240 K, but then saturates to apolysaccharide consisting of a linear chain of

constant value until 300 K. Temperature-

several hundred to many thousands of β linked

dependence thermal conductivity reveal that the

D-glucose units. Cellulose is an importantfilaments exhibit phonon transport at effective

structural component of the primary cell wall ofdimension between 2D and 3D.

green plants, many forms of algae and theoomycetes. In this work, we applied themolecular dynamics simulation in combination
with the machine learning to explore the effectof strain, hydrogen bonds, and structure orderingon thermal transport in cellulose. The structure
for the simulation is shown in Fig. 1.

Figure 2 temperature dependent thermal
conductivity of cellulose nanofiber.

References[1] Mu, Fengwen, Bin Xu, Xinhua Wang, Runhua Gao,Sen Huang, Ke Wei, Kai Takeuchi et al. Journal of
Alloys and Compounds 905 164076 (2022).
[2] Wang, G., Kudo, M., Daicho, K., Harish, S., Xu, B.,
Shao, C., Lee, Y., Liao, Y., Matsushima, N., Kodama, T.
and Lundell, F., Nano Letters, 22, 8406-8412 (2021).

Figure 1 Schematic illustration of structure usedfornon-equilibrium

molecular

dynamics

108

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical study of quantum eﬀects innanographene devices
Koichi KUSAKABE
Graduate School of Science, University of Hyogo
Kouto, Kamigori, Hyogo 5-8581

1

Introduction

New quantum devices for quantum information and quantum electronics are being developed by exploring various quantum effects. We are studying graphene-based quantum computation resources,[1] and graphenebased spin-electronic devices.[2, 3] We havedeveloped theoretical approaches to study
stubility of adsorbed molecules on graphene
in solvents,[4] acceleration methods utilizing
evolutionary algorithms,[5] and light-induced
structural transformation of nanomaterials.[6]2Quantum computation resources by poly-PTM

The design of a hydrogenated poly-PTM
measurement-based quantum computation resources was promoted by evaluating decice behavior based on proton NMR simulations on
adsorbed hydrogen on the poly-PTM. The design of a two-dimensional S = 3/2 antiferromagnetic Heisenberg system was promoted
based on the design of a two-dimensional
honeycomb poly-PTM network.
We concluded that possible computational resource
states in a two-dimensional hydrogenatednanographene requires control of the eﬀective many-body interaction between localized
spins.

3

Stability and functions of
nanographene devices

The structural stability of hydrogenatednanograpehe structures was evaluated, as wellas the activation energy barrier heights on thehydrogen diﬀusion path. To evaluate decoherence, which is the central concern of quantum information operation, we developed atheory of spin-current-rotation coupling andthe eﬀect of inserting insulating hBN between
metallic Ni substrate and graphene. We concluded that control of the decoherence process
requires the control of the interaction between
electron spins and current rotation.

Acknowledgement
The author acknowledges the big contributionsof Dr. N. Morishita, Mr. K. Komatsu, andProf. M. Kitatani on nanographene quantum computation resorces. He also thanks
Dr. Y. Wicaksono, Ms. H. Harfah, Dr. G.
K. Sunnardianto, and Prof. M. A. Majidi forcollaboration on graphene quantum spintronics devices, and all collaborators for theoretical
approaches to nanomaterial device structures.

References[1] N. Morishita, Y. Oishi, T. Yamaguchi,
K. Kusakabe, Appl. Phys. Express 14,
121005 (2021).
[2] Y. Wicaksono, H. Harfah, G. K. Sunnardianto, M. A. Majidi, and K. Kusakabe,
RSC Adv., 12, 13985 (2022).
[3] Y. Wicaksono, H. Harfah, G. K. Sunnardianto, M. A. Majidi, and K. Kusakabe,
Magnetochem. 9, 113 (2023).
[4] Y. Oishi, H. Ogi, S. Hagiwara, M. Otani,
and K. Kusakabe, ACS Omega, 7, 35,31120 (2022).
[5] T. Ishikawa, K. Kusakabe, Y. Makino, S.
Sakamoto, N. Okuyama, J. Phys. Chem.
A, 126, 8082 (2022).
[6] M. Nagai, Y. Higashitani, M. Ashida,
K. Kusakabe, H. Niioka, A. Hattori, H.
Tanaka, G. Isoyama, N. Ozaki, Commun.
Phys., in press (2023).

109

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo!"#$%&'$(#)*$+",&#+$%*'-,+-+"./*/,0/*-1,2#-/*%.,30-$%*'-+",$+"$0"+%*'-,4,*)5"*$*%,/'"6+%*'-,)'2#" 7!"#$%&'()&*&!"#$%$&$'()*+(,*-%.(,$/$'(012#%3#4
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6OQQS8#77ITQJ9#:$"# 0"%V' %(# %00/.A+2%("34# OQQQRFIQQB# 7SQQB#

LOM [9# ,%/)4%2%B# :9# X);+2.(.B# %1*# -9# X);+1.B#%1*# SQQR7OQQ ?2$% %/" ?.20.'"*# .<# ($"# -,#"#$%&''()*\ $((0'W==+''01'C;+(3%@9+''09)C(.V4.9%?9'(/"(?$+1;B# ,!-# @"1*+1;B# %1*# ,!-# 3+@/%(+.1#]0=]C$%/)4%2%=5(777^,O-C2.1.3%4"/

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110

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Discovery of Fast Anhydrous Proton Conduction in α-MoO3
Atsuo YAMADA
Department of Chemical System Engineering,
The University of Tokyo, Bunkyo-ku, Hongo, Tokyo 113-8656
Aqueous proton batteries show potential as

calculate proton diffusion pathways.

high-power energy storage devices because of

The energy profiles of H+ diffusion in

the small size of the protons and their high

MoO3 are shown in Fig. 1. At the early stages ofmobility in aqueous solutions. Among various

protonation and deprotonation, the activationtransition metal oxides, orthorhombic MoO3 (α-barriers for proton diffusion between the oxygenMoO3) is one of the most promising proton hosts

arrays of MoO3 were below 0.4 eV, which iswith fast kinetics and large capacities. Herein,comparable to that of Grotthuss mechanism in

we investigated the mechanism of proton

water. Therefore, further exploration of otherintercalation and transportation in α-MoO3

host materials with dense and continuous

based on theoretical calculations [1].

oxygen arrays capable of fast anhydrous proton

The spin-polarized DFT calculation was

conduction is an important challenge for the

adopted to trace the H+ dynamics in α-MoO3practical application of high-power aqueous

with VASP program. Based on a 2 × 1 × 2

proton batteries.

supercell (Mo16O48), a series of H-intercalated

References

structuresof

HxMoO3 (0 ≤ x ≤ 3.0)

was[1] Z. Ma, X. M. Shi, S. Nishimura, S. Ko, M. Okubo, A.

calculated. The CI-NEB method was used to

Yamada, Adv. Mater., 34, 2203335 (2022).

Figure 1 Anhydrous proton transport via hydrogen bond network and corresponding energy barriers at the earlystages of protonation (a) and deprotonation (b). The three most stable H+ absorption sites in MoO3 are labeled as
A, B, and C, respectively.

111

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles prediction of anomalous Hall effectin antiferromagnetic perovskites
Kunihiko Yamauchi
Department of Precision Engineering, Graduate School of Engineering,Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871
Recently, large anomalous Hall conductivity
innoncollinear

antiferromagnetic(AFM)

systems has been recently observed and attracted
much attention while the anomalous Hall effecttakes place typically in ferromagnetic (FM)materials with the finite magnetization.
In this study, by using DFT calculation, we
predict the anomalous Hall effect (AHE) in
perovskite CaCrO3 as a representative ofcollinear antiferromagnetic materials [1]. We
showed that the C-type AFM ordering (Fig. (a))
generatesthesizableanomalousHallconductivity and revealed two essential roles of
the non-symmorphic Pbnm symmetry. (i) The
screw and glide symmetry operations bind the

Figure: (a) C-type AFM ordering in Pbnm

AFM and FM order parameters in the same

crystal structure of CaCrO3. (b) Berry curvatures

irreducible representation so that AHE is activein the orthorhombic Brillouin zone.

in the AFM order. (ii) The band-sticking effectat the Brillouin-zone surface makes Cr-t2g state

References

form the narrow bands near the Fermi energy; a[1] Thi Phuong Thao Nguyen and Kunihikocouple of those bands cause anticrossing andYamauchi, Phys. Rev. B. 107, 155126 (2023).

enhancement of the Berry curvature (Fig. (b)).

[2] A. D. Vita, T. T. P. Nguyen, .., K. Yamauchi,

In this year, we also studied 2D magnetism

et al., Nano Letter 22, 7034 (2022).

as reported in Ref. [2] and [3] in collaboration[3] K. Riedl, .., T. T. P. Nguyen, K. Yamauchi, etwith theoretical and experimental groups in Italyal., Phys. Rev. B 106, 035156 (2022).

and Germany.

112

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab-initio electron dynamics simulation for nonlinear opticalphenomena in solids
Shunsuke SATO
Center for Computational Sciences
University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan

We have studied light-induced electron

both delocalized and bound electrons in solids.

dynamics in solids based on the time-dependent

We further plan to apply the developed method

density functional theory. This year, we focusedfor the investigation of nonlinear opticalon the development of a novel analysis

phenomena in solids in order to develop thetechnique for light-induced linear and nonlinear

microscopic interpretation of perturbative andoptical phenomena in solids based on the time-nonperturbative nonlinear phenomena.

dependent current density [1]. Here, we first

In addition to the development of the above

compute the time-dependent current density as

theoretical scheme, we have studied transient𝒋(𝒓, 𝑡) = −optical properties of solids under the presence𝑒∫ 𝑑𝒌 ∑ 𝑓𝑏𝒌
Ωme 𝐹𝐵𝑍𝑏∗(𝒓,× 𝜓𝑏𝒌(𝒓,𝑡)(𝒑 + 𝑨(𝑡)) 𝜓𝑏𝒌 𝑡),

of intense femtosecond laser fields. For the(1)

investigation of nickel, we analyzed the light-

where 𝜓𝑏𝒌(𝒓, 𝑡) are time-dependent Kohn-

induced spin-dynamics and transient absorption

Sham orbitals, and 𝑨(𝑡) is the vector potential

based on the pump-probe technique, and wethat is related to the applied external electric

found that the local spin-density dynamics𝑡field as 𝑨(𝑡) = − ∫ 𝑑𝑡 ′ 𝑬(𝑡 ′ ) . By applying

causes the change of the photoabsorption

Fourier transform to the computed current

around the absorption edge. Based on thisdensity in Eq. (1), we obtain the frequency-

finding, we further proposed the attosecond

resolved microscopic current density as

spin-dynamics spectroscopy to investigate the𝒋̃(𝒓, 𝜔) = ∫ 𝑑𝑡 𝑒 𝑖𝜔𝑡 𝒋(𝒓, 𝑡).

(2)element-specific light-induced spin-dynamics

The frequency-resolved microscopic current

in the attosecond time-scale.

density contains the atomic scale real-space

References

information of light-induced linear and optical[1] Shunsuke A. Sato, “"Frequency-resolved

phenomena. In Ref. [1], we demonstrated thatmicroscopic current density analysis of linear

the developed current-density analysis capturesand nonlinear optical phenomena in solids",

microscopic insight into optical phenomena inarXiv:2302.05859

113[cond-mat.mtrl-sci].

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study on the structure of water/grapheneinterfaces depending on the number of graphene layers
Tatsuhiko OHTO
Graduate School of Engineering Science,
Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531
Ab initio molecular dynamics (AIMD)

The simulations were performed using thesimulation is a powerful tool to describe

CP2K code [3]. After obtaining the sufficientheterogeneous systems such as the water/solid

length of trajectories, we are going tointerface. Although AIMD is computationallyconstruct machine learning force field toexpensive, it describes electronic states beyond

simulate larger scale interfaces between

classical force fields,[1] which is important for

carbon/water.

interfacial structures.
We have simulated sum-frequency generation(SFG) spectra of isotopically diluted water at thewater-graphene sheet interfaces using ab initio
molecular dynamics simulations, with changing
the number of the graphene layers from one tothree. The simulation of water-single grapheneinterface has already been performed using

Fig. 1: Structures of the graphene-water

ISSP.[2] A sharp ‘dangling’ O-D peak aroundinterface.

~2640 cm-1 appearing in simulated SFG spectra
evidencesthatgrapheneisReferenceshydrophobic.

Although the results obtained so far are still[1] T. Ohto et al. Phys. Chem. Chem. Phys. 19,

preliminary, the dangling O-D peak is blue-

6909 (2017).

shifted by increasing the number of the graphene[2] T. Ohto et al. Phys. Chem. Chem. Phys. 20,

layer. This frequency difference manifests a

12979 (2018)

weaker O-D…C intermolecular interaction[3]

between water and thicker graphene, indicating

http://cp2k.berlios.de/that graphite is more hydrophobic than graphene.

114

The

CP2K

developersgroup,

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Multiscale simulations for magnetic materials
Hung Ba TRAN
Laboratory for Materials and Structures, Institute of Innovative Research,
Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan

In our recent works, we consider the spin reorientation effect in Nd2 Fe14 B material basedon first–principles calculations[7]. Nd2 Fe14 B isfamous material for permanent magnets thatare widely used in power generation, motors,
and so on due to the high magnetic anisotropy
energy, saturation magnetization, and Curie
temperature. However, the material has aproblem at low temperatures. It is spin reorientation from the easy axis (z–direction) tocone magnetization (where the magnetization
is tilted). In previous theoretical works, thespin reorientation in Nd2 Fe14 B is usually considered using empirical parameters as crystal–electric field term. In contrast, in this work,
we calculate the Dzyaloshinskii–Moriya interactions (DMI) by first–principles calculations
for the first time. We found that the DMI is
the origin of spin reorientation in Nd2 Fe14 B.
The spin reorientation in Nd2 Fe14 B can be re-

(b)

25

Mtotal
Mz
Mxy

20
15

𝑧

10

𝜃

15

𝑀

10
5

5

0

0

0.8
0.6
0.4
0.2

50 100 150
T (Κ)

0

0
0

200

(c)

400

T (Κ)

4

600

800

1000

0.2

0.4

0.6
T/TC

4

1
0

0.8

1

1.2

H = 1TH = 2TH = 3TH = 4TH = 5T

3∆SR (J/kg.K)

2

0

(d)
H = 1TH = 2TH = 3TH = 4TH = 5T

3−1

Monte Carlo
DFT
EXP(raw)
EXP(fit)1

w DMI
w/o DMI20θ (degree)

M (µB/f.u)25

MAE(T)/MAE(max)(a)∆SR (J/kg.K)

Our previous works have studied the magnetocaloric effect by multiscale simulations. The
magnetic parameters, such as magnetic exchange coupling constants Jij and magnetic
anisotropy energy, are calculated from first–
principles calculations. Then, the Monte-Carlosimulations are performed to estimate themagnetic properties at thermal equilibrium,
such as magnetization curves and isothermal
magnetic entropy change. Several types ofthe magnetocaloric effect, such as conventional(direct) magnetocaloric effect, giant magnetocaloric effect, anisotropic magnetocaloric effect, and inverse magnetocaloric effect, can beconsidered using our in–house program[1, 2, 3,
4, 5, 6].

2
1
0

0

50

100
T (K)

150

200

−1
650

700

750
T (K)

800

850

Figure 1: (a) Total (red) and projected spontaneous magnetization in the out–of–plane(green) and in–plane (blue) directions as afunction of the temperature of Nd2 Fe14 B (inset figure: Temperature dependence of thetilt angle between the magnetization direction and z–direction in the case of switching on (red) and switching off (black) the
Dzyaloshinskii–Moriya interaction). (b) The
magnetic anisotropy energy obtained is basedon DFT (green) and Monte Carlo method byintegrating the M –H curves (black) and experimental raw data (red dots) and that derived from anisotropy constants (continuous
red curves). (c) Rotating magnetic entropychange as a function of temperature and themagnetic field around the spin reorientation
temperature and (d) Curie temperature.

produced in Figure. 1 (a) by introducing the
DMI. In addition, the peak like in magnetic
anisotropy energy of experimental work can be115

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

dition, two types of helicity can be realized
in CrCl3 and VCl3 due to the nearly opposite direction in Dzyaloshinskii–Moriya vector.
Not only skyrmions but also antiferromagnetic
skyrmions and meron are observed in MX3 .

References

Figure 2:
In–plane components of
Dzyaloshinskii–Moriya vector for the second nearest neighbor of intra–layer of CrCl3
and VCl3 , where the red and green arrows
indicate pairs with different sub–lattices, andthe yellow arrow indicates the direction of
Dzyaloshinskii–Moriya vector. Snapshot ofMonte Carlo simulation of CrCl3 at 10 K withexternal magnetic field equal to 4 T along
the positive z–direction. Snapshot of theMonte Carlo simulation of VCl3 at 10 K withexternal magnetic field equal to 6 T along thepositive z–direction.

reproduced quantitatively, as shown in Figure.
1 (b). The spin reorientation in the material
is usually not desirable for the application ofa permanent magnet. However, we found thatthe rotating entropy change around spin reorientation is almost four times higher than at
the Curie temperature, as shown in Figure. 1(c, d) due to the peculiar properties of spin
reorientation.
On the other hand, we also consider theskyrmions in van der Waals centrosymmetric MX3 (M: V, Cr, Mn, Fe, Co; X: Cl, Br,I) [8]. Skyrmions usually appear in non–centrosymmetric material due to the DMI lacking inversion symmetry. Although MX3 has
space group R3̄ being centrosymmetric withhoneycomb lattice, the broken local inversion
symmetric of the second nearest neighbor of
intra–layer stabilizes the finite DMI. It leads
to ultra-small skyrmions with a diameter being 2.0 nm, as shown in Figure. 2. In ad-[1] H. B. Tran, T. Fukushima, K. Sato, Y.
Makino, and T. Oguchi, J. Alloys Compd.
854, 157063 (2021).
[2] H. B. Tran, T. Fukushima, Y. Makino,
and T. Oguchi, Solid State Commun. 323,
114077 (2021).
[3] H. B. Tran, T. Fukushima, H. Momida, K.
Sato, Y. Makino, and T. Oguchi, Comput.
Mater. Sci. 188, 110227 (2021).
[4] H. B. Tran, T. Fukushima, H. Momida,
K. Sato, Y. Makino, and T. Oguchi, J.
Alloys Compd. 926, 166718 (2022).
[5] H. B. Tran, H. Momida, Y. Matsushita,
K. Sato, Y. Makino, K. Shirai, and T.
Oguchi, Phys. Rev. B 105, 134402 (2022).
[6] H. B. Tran, H. Momida, Y. Matsushita,
K. Shirai, and T. Oguchi, Acta Mater.
231, 117851 (2022).
[7] H. B. Tran, Y. Matsushita, Appl. Mater.
Today 32, 101825 (2023).
[8] H. B. Tran, Y. Matsushita, Skyrmions in
van der Waals centrosymmetric materials
with Dzyaloshinskii-Moriya interactions,
arXiv:2209.02333 (2022) (under review).

116

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical design of novel functional materials
based on abundant elements for energy conversion
and storage.
Tetsuya TAKETSUGU
Faculty of Science, Hokkaido University
N10W8, Sapporo, Hokkaido 060-0810

DFT computations using QuantumEspresso
and VASP packages are used to gain physicalchemical insights and to design novel functional materials with abundant elements forenergy conversion and storage processes. This
helps to reduce costs and dependences on precious metals in energy-related industrial applications.
We have demonstrated that oxygenfunctionalized hexagonal boron nitride (h-BN)
can be an efficient catalyst for oxidative
dehydrogenation (ODH) of light alkanes,
specifically ethane (C2 H6 ), propane (C3 H8 ),butane (C4 H10 ), and isobutane (HC(CH3 )3 )[1]. This is particularly interesting because
it is commonly accepted that hexagonalboron nitride is an inert material. However,
we have demonstrated that h-BN can befunctionalized and serve as an active catalyst.
It has been found that the reaction pathway
involves two H atom transfer steps with small
activation energies. We demonstrate thatthe synergy of two active sites, B-O-O-B and
B-O-B (Figure 1), is crucial for the first andsecond H-transfer, respectively. With theincrease in molecular mass of the consideredlight alkanes, the ODH reaction temperature
decreases. The charge redistribution during
H-transfers and localized oxygen atomic
states in the conduction band are explored tosuggest possible descriptors for the rational
design of new catalysts. The universal actionof the B-O-O-B and B-O-B active sites for

ODH of the light alkanes paves the way formetal-free BN-based materials for future catalytic applications.

Figure 1: Catalyticaly active (a) B-O-O-B and(b) B-O-B sites [1].
The multielectron transfer is a key process being indispensable for a wide spectrumof modern electrochemical energy technology.
Finding promising multielectron-transfer materials with abundant elements is especially
important to advance the present rechargeable battery technology mainly relies on single electron transfer type electrodes. To date,117

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

a few oxide-based materials can reach an
electron-transfer number per metal-cation (e)larger than 2 upon a (de)intercalation mechanism. However, these oxide-based electrodes
face challenges in improving electrochemical
properties as they still suffer from considerable degradation during charge/discharge reactions due to irreversible rearrangements ofbonds between metallic cation and anionic
oxygen. Furthermore, these high-performance
multielectron-transfer oxides are mainly constituted of precious metals. As it is wellknown, these elements are limited, and therefore, electrode materials based on precious
metals are inappropriate candidates to replace
the present cathode materials.

work provides new insights into the affordable
multielectron-transfer electrodes and uncovers
an alternative strategy to advance the electrochemical energy storage reactions.

References[1] S. Kumar, A. Lyalin, Z. Huang, and T.
Taketsugu, Catalytic Oxidative Dehydrogenation ofLight Alkanes over Oxygen Functionalized Hexagonal Boron Nitride, ChemistrySelect 7, e202103795(2022).
[2] D. Xia, K. Sakaushi, A. Lyalin, K. Wada, S. Kumar, M. Amores, H. Maeda, S. Sasaki, T. Taketsugu and H. Nishihara, Superior MultielectronTransferring Energy Storage by π-d Conjugated
Frameworks, Small 18, 2202861 (2022).



A significantly reversible
Figure 2:
multielectron-transfer is demonstrated byusing only abundant elements [2].
We have demonstrated that the non-oxide
electrode based on the bis(diimino)copper
framework can show e = 3.5 with cation/anion
co-redox mechanism together with a dual-ion
mechanism (Figure 2). In this study, the roleof the cation-anion interactions has been unveiled by using an experiment/theory collaboration applied to a series of the model nonoxide abundant electrode systems based on different metal-nitrogen bonds. These models
provide a route for the design of the multielectron transfer materials based on the tunable πd conjugated electronic structures. It is foundthat the Cu-nitrogen bonds show a unique reversible rearrangement upon Li-intercalation,and this process responds to acquire a significant reversible multielectron-transfer. This118

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Microscopic structure of water/CeO2 interface
Akira NAKAYAMA
Department of Chemical System Engineering,
The University of Tokyo, Tokyo 113-8656, JAPANThe structural properties and dynamical

calculations. For each interface, a slab model

behaviors of the interface between water andwas created with a surface size of p(4×4) and acerium oxide (CeO2) are investigated bywater thickness of 30 Å. The conventional andreactive molecular dynamics (MD) simulations

enhanced sampling DFT-MD methods were

employing

performed for 20 ps, yielding a total of 8000

theneuralnetwork

potentials(NNP)[1][2] that are trained to reproduce

configurations as training data.

density functional theory (DFT) results. In the

We mainly discuss the results for theconstruction of the neural network potentials,

water/CeO2(110)DFT-based MD (DFT-MD) simulations withprojection of the density distribution of O andenhanced sampling schemes[3] are employed to

H atoms on the CeO2 surface and in the firstefficiently acquire training data that include

hydration layer obtained from the NNP-MD

diverseconfigurations

simulations is shown in Figure 1. Note that thecaused by proton hopping events. The water

average position of the topmost Ce atoms is set

interfaces with three low-index surfaces of

to z = 0 Å.

(111), (110), and (100) are explored with thesesimulations provide sufficient statistics toneural network potentials, and structure andanalyze the interface structure in more detaillong-range proton and hydroxide ion transfer

compared to previous studies.

hydrogen-bonding

dynamics are examined with unprecedented

interface.

Thez-axisThe large-scale and long-time

The mechanism of proton transfer occurring

system sizes and long simulation times.

at the water/CeO2(110) interface is then

The time step for DFT-MD simulations wasanalyzed. Proton transfer can be roughly

set to 1 fs and the temperature was controlled at

divided into surface proton transfer (SPT), in

360 K. RPBE was used for the DFT functional.

which proton transfer occurs between a water

The DFT-D3[4] and DFT+U methods was usedmolecule coordinated on a Ce atom and a

to

and

surface OS atom, and adlayer proton transfer

electron correlations for Ce 4f electrons,(APT), in which proton transfer occurs between

respectively. k-point sampling was performedaat Γ points only. CP2K was used for DFT-MD

coordinated on a Ce atom. The proton transfer

incorporate

dispersion

interaction

119

water

moleculeandhydroxideion

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

between surface species is further classifiedhydrogen bonds with neighboring surface O

into direct and indirect transfer that involves

atoms, thus making SPT less likely to occur. In

neighboring water molecules.

addition, more migration was observed in the y-

At the water/CeO2(110) interface, a total of

direction since the distance between surface Ce

863 proton transfers were observed during 4 ns

is closer.

of trajectory, when thermal equilibrium isconsidered to have been reached.

In summary, we have generated training

Table 1

data using DFT-MD calculations with enhanced

shows the observed ratio of each proton transfer.

sampling scheme and constructed NNPs for the

Since the structure of the CeO2(110) surface iswater/CeO2 interface.

not symmetric with respect to the x-axis and y-

NNPs, we performed large-scale and long-timeaxis directions, the APT were also classified

simulations

according to whether the proton transfer

information on the structure and proton transfer

occurred in the x- or y-axis direction.

mechanisms near the interface, which wereandUsing the constructedobtainedthedetaileddifficult to obtain using the conventional DFTMD simulations.
Table 1: Proton hopping machanims

References[1] J. Behler and M. Parrinello, Phys. Rev. Lett.
98, 146401 (2007).
Fig. 1: Density profiles of oxygen andhydrogen at the water/CeO2(110) interface.

[2] J. Behler, J. Chem. Phys. 145, 170901(2016).

As seen, APT occurred more frequently than[3] L. Maragliano and E. Vanden-Eijnden,

SPT, possibly because the distance between

Chem. Phys. Lett. 426, 168 (2006).

surface O atoms is closer. H atoms bonded to[4] S. Grimme, J. Antony, S. Ehrlich, and H.

surface O atoms are stabilized by forming

Krieg, J. Chem. Phys. 132, 154104 (2010).

120

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Prediction of properties of organic ferroelectrics andpiezoelectrics by ﬁrst-principles calculation
Shoji ISHIBASHI
National Institute of Advanced Industrial Science and Technology (AIST)
Tsukuba, Ibaraki 305-8568

Many azole compounds such as imidazoles
and tetrazoles contain polar and bistablehydrogen-bonded molecular sequences suitable for ferroelectricity or antiferroelectricity.
In this study, we have computationallyinvestigated relative stabilities of possible ferroelectric (FE) and antiferroelectric(AFE) phases in eight azole compounds:
5-(4-aminophenyl)-1H-tetrazole(APHTZ),
5-(4-ﬂuorophenyl)-1H-tetrazole(FPHTZ),
5-(4-chlorophenyl)-1H-tetrazole(CPHTZ),
5-(4-methylphenyl)-1H-tetrazole (MPHTZ),
5-phenyl-1H-tetrazole (PHTZ), 2-phenyl1H-imidazole (PHIM), 2,4,5-tribromo-1Himidazole (TBIM), and 2-bromo-4,5-dimethyl1H-imidazole (DM-BIM) [1].
The Perdew-Burke-Ernzerhof (PBE) version of the generalized gradient approximation (GGA) [2] was used to describe the electronic exchange-correlation energy. Startingfrom the experimental structures, the atomic
positions were optimized. The convergence criterion was set to 5 × 10−5 Ha/bohr for the
maximum force. All the calculations were performed using the QMAS code based on the
projector augmented-wave method [3] and theplane-wave basis set.
The obtained results are shown in Fig. 1 together with schematic illustrations of various
states in a zero ﬁeld based on the polarization
hysteresis experiments as well as the structural
analyses. It is conﬁrmed that the computational and experimetal results are consistent
with each other.

Figure 1: Ferroelectric (FE), antiferroelectric (AFE), and phase-coexisting (F/A hybrid and A/A hybrid) states in the PHTZs
crystals. (a) Schematic illustrations of various states in a zero ﬁeld. (b) Energy histogram of the candidate H-ordered states relative to each FE (or FE-I) form. Filled andopen circles point to the non-degenerate andnearly degenerate ground states, respectively(S. Horiuchi, H. Minemawari, and S. Ishibashi,
Mater. Horizons, Advance Article (2023),
DOI: 10.1039/d2mh01530g).

References[1] S. Horiuchi, H. Minemawari, and S.
Ishibashi, Mater. Horizons, Advance Article (2023).
[2] J.P. Perdew, K. Burke, and M. Ernzerhof,
Phys. Rev. Lett. 77, 3865 (1996).
[3] P. E. Blöchl, Phys. Rev. B 50, 17953(1994).

121

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab initio calculation for transition-metal-oxideinterface
Kazuma NAKAMURA
Quantum Physics Section, Kyushu Institute of Technology
1-1 Sensui-cho, Tobata, Kitakyushu, Fukuoka, 804-8550

In the present study, we investigate electronic structures of interfaces and surfaces oftransition-metal oxides using first-principles
calculations based on density functional theory. In material science, important physicalproperties often occur at the surfaces and interfaces of materials. Currently, it is possible
to predict physical and chemical properties ofthe surfaces and interfaces by using ab initio
electronic structure calculations. On the other
hand, since the size of systems including thesurface and interface becomes large, and complicated problems such as the generation of an
artificial electric field in the surface system are
known to occur, so it is necessary to accumulate detailed know-how to perform stable abinitio calculations.
Here, we focus on a representative oxide interface system of SrTiO3 /SrVO3 (STO/SVO)
hetero structure, and study its microscopic
electronic structure and optical properties indetails. The STO/SVO system is a fascinating
system realizing a metal-insulator transition at
the interface [1, 2], especially small thicknessof SVO block. In this study, we analyzed thissystem with ab initio calculations, particularly
focusing on optical spectra.
We performed ab initio self-consistent pseudopotential calculations in which wavefunctions were expanded in a plane-wave basis [3].
We employed norm-conserving pseudopotentials, and the generalized-gradient approximation for exchange-correlation energy. The cutoff energies for the wavefunction and charge

density are 100 Ry and 400 Ry, respectively.
The atomic geometry was fully optimized withkept at inplane lattice constant a = 3.9451
Å, where the force on each ion were relaxed
to less than 0.001 a.u. and a MonkhorstPack k-grid of 10×10×2 was employed. Optical calculations were performed with using
RESPACK [4]: The energy cutoff for the polarization function was set to 3 Ry. The total
number of bands considered in the polarization
calculation was determined to cover unoccupied states up to 10-15 eV above the Fermi
level. The integral over the Brillouin zone
was calculated with the generalized tetrahedron technique with a smearing of 0.01 eV.
Figure 1 shows our structure models tobe analyzed, where we consider a multilayer
model consisting of SVO and STO blocks[panel (a)] and a symmetric slab model [(b)].
The slab model includes a vacuum region with
20 Å, and has a mirror symmetry with respect
to the central TiO2 plane. Then, artificial electric fields due to asymmetry in the both ends ofthe slab do not occur. The structural models
include several SVO blocks, where we specify
the number of the blocks as n. In the present
study, we consider the structural models until
n = 4. The number of the STO blocks was
fixed to 5 for the multilayer and 8.5 for theslab (0.5 indicates an additional central TiO2
layer).
Figure 2 shows our calculated band structures of the multilayer (a) and slab (b), where
the band diagrams for the n = 2 model are

122

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo(a) Multilayer

SrVO

SrTiO

unitcell(b) Symmetric slab
vacuumvacuumFigure 1: Two structural model: (a) Multilayer consisting of SrTiO3 and SrVO3 blocks. (b)Symmetric slab having a mirror symmetry with respect to the center TiO2 plane.

[1] D. H. Kim, et al., Solid State Commun.
114, 473 (2000).
[2] K. Yoshimatsu, et al., Phys. Rev. Lett.
104, 147601 (2010).
[3] P. Giannozzi, et al., J. Phys. Condens.
Matter 29, 465901 (2017).
[4] K. Nakamura, et al., Comput.
Commun. 261, 107781 (2021).

Phys.

Energy (eV)2(a) Multilayer

1
0
-1
-2

Energy (eV)3

Reflectivity

Figures 2(c) and (d) show our calculated reflectance spectra for the multilayer and slab
models, respectively. We see that the both
spectra exhibit a lowering of the plasma edge
compared to the bulk SVO one. We also see
the appreciable n dependence of the plasmaedge. The difference between the multilayerand slab results seems to be small.
In summary, we have calculated electronic
structures and reflectance spectra of the
STO/SVO system from first principles. In theexperiments, the system is insulator at small
thickness of the SVO blocks, and this origin
should be further investigated from view ofstrongly correlation physics. To this end, weneed to perform ab initio derivations of thelow-energy model of SVO-t2g bands near theinterface, which leaves as a next step.

32(b) Symmetric slab

1
0
-1
-2
-3
R
G
1
(c) Multilayer

X

0
1

M

GZ

1

10

n=1
n=2
n=3
n=4
Bulk SVO

0.5

Reflectivity

displayed. From the band structures, we seethat both two systems are metal; the SVO t2gbands cross the Fermi level, and the STO t2gband is about 1 eV above from the Fermi level.

(d) Symmetric slab

0.5

0
0.01

0.1

Enegy (eV)Figure 2: Our calculated band structures of(a) multilayer and (b) slab model where weshow n = 2 case. Panels (c) and (d) show ourcalculated reflectance spectra of multilayer andslab models, respectively.

123

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Two-color mixing enhancement of nonlinear opticalabsorption for a semiconductor
Yasushi SHINOHARA1,2, and Mizuki TANI3
1

Photon Science Center,

The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656.
2

NTT Basic Research Laboratories,

NTT Corporation, 3-1 Morinosato Wakamiya, Atsugi, Kanagawa 243-0198.
3

Department of Nuclear Engineering and Management

The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656.

We have theoretically studied dielectrics

energy absorption of Si crystals exposed to

exposed to strong laser fields using a first-

strong laser field that has two color components,

principles theoretical framework based on time-

1.6 eV, and 3.2 eV [2]:dependent density-functional theory (TDDFT)
𝐸(𝑡) = 𝑓(𝑡) [𝐸1.6 eV cos (within SALMON-TDDFT [1]. The real-time

1.6 eV𝑡)ℏ

solution of the time-dependent quantum system+ 𝐸3.2 eV cos (is one of the most accurate schemes to evaluate

3.2 eV𝑡)],ℏnonlinear optical responses that perturbative

where 𝑓(𝑡) is an envelope function that has 14.4

expansions cannot describe.

fs full-width-half-maximum. The second color,

One of the most prominent features of the

3.2 eV, is slightly above the direct gap of thenonpertubative response of the material is the

crystal. To model an experimental setup ofcomplex mixing of multiple frequencies of an

frequency conversion for 3.2 eV from 1.6 eV via

applied field. We do not have a simple formulasecond harmonic generation, we change theto model the response written as a combination

relative power ratio such that the sum of twoof amplitudes depending on the frequency of thecomponents is kept constant:field, i.e., the Fourier component of the field, in𝐼tot = 𝐼1.6 eV + 𝐼3.2 eV ,contrast to simple power expansion within the1
𝐼𝑖 = 𝜖0 𝑐|𝐸𝑖 |2 , 𝑖 = 1.6 eV, 3.2 eV,
2perturbation theory. We need a theoreticaldescription

capableofnonperturbative

where 𝜖0 and 𝑐 are the vacuum permittivity andresponses to evaluate the response.

the

We have performed TDDFT simulations for

speed

of

light.

The

criteria

ofnonperturbative response based on the Keldysh

124

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

parameter [3] is 6.91 TW/cm2 and 27.2 TW/cm2

resonant excitation due to the 3.2 eV component.

for 1.6 eV and 3.2 eV. The absorbed energy is

When the lower frequency component does notevaluated by the total work from the field to theexist, 3.2 eV component cause Rabi oscillation

systembecause of the strong field. Rabi oscillation leads
to saturation of absorption in a pulse. By the∞𝐸abs = ∫ d𝑡 𝑱(𝑡) ⋅ 𝑬(𝑡)lower frequency driving for intraband motion, a0where 𝑱(𝑡) is the induced charge current

resonant point undergoes off-resonant condition

evaluated by TDDFT.

by the detuning. Then another off-resonant state

Our simulation shows maximal energy
absorption

isrealizedbyabecomesresonant. Thissequence

avoidscondition

saturation, and the number of excited electrons

𝐼1.6 eV ⁄𝐼3.2 eV ∼ 1.0 , when we have 𝐼tot =increases with the two-color mixture for the

1 TW⁄cm2 . This fact is hardly explained bydriving field.

perturbative expansion because the lower-ordernonlinear response is expected to dominate theReferences

dynamics for such weak intensity compared to[1] https://salmon-tddft.jp/, M. Noda, S.A. Sato,the atomic unit value of 35 PW/cm2. The

et al., Computer Physics Communications. 235,

perturbative expansion predicts 𝐼1.6 eV ⁄𝐼3.2 eV ∼356 (2019).

0.0 for the maximal absorption condition.

[2] Mizuki Tani, Kakeru Sasaki, Yasushi

This nontrivial maximal energy absorption

Shinohara, and Kenichi L. Ishikawa, Phys. Rev.

mixing ratio appears for other combinations (0.2

B 106, 195141 (2022).

eV, 3.2 eV), (0.8 eV, 3.2 eV). This generic[3] L. V. Keldysh, Sov. Phys. JETP 20, 1307

behavior is explained by energy detuning due to(1965).

the lower frequency components with the strong

125

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles calculations of complex metallic alloy
surfaces
Kazuki NOZAWA
Department of Physics and Astronomy, Kagoshima University
1-21-35, Korimoto, Kagoshima 890-0065

High-resolution transmission electron microscopy experiments observed the formationof small ZnO patches on the PdZn(111) surface during the methanol steam reforming reaction, indicating the ZnO patches plays animportant role in the CO2 selectivity of thiscatalyst [1]. Last year we obtained an oxidized
PdZn(111) surface having a distorted hexagonal Zn-O structure at the top layer [2]. In thisfiscal year, we studied the dehydrogenation ofwater on this oxidized PdZn(111) surface. Calculations are performed with VASP program
package as flat MPI jobs on system B and C.
Because the obtained Zn-O layer on theoxidized PdZn(111) surface is corrugated asshown in the figure, first we calculated the potential energy surface (PES) of water with fixing atomic positions to find out promising candidates for the starting structure of the structural relaxation. We investigated the PES forwater with its molecular plane parallel and perpendicular to the surface, keeping the distanceto the nearest surface atom at 2.0 and 2.5 Å.
Many of these calculations were done as bulk
jobs on system B. Next, we performed structural relaxation from 20 stable starting structures obtained. We performed similar calculations for the hydroxyl and hydrogen on thesame surface to determine the stable coadsorption structure. The stable adsorption site ofwater was found on a Zn atom forming thehexagonal Zn-O ring. The obtained adsorptionenergy of water was larger than that on the
non-oxidized PdZn(111) surface but smaller

than that on ZnO(0001) surface [3]. However,the coadsorption energy of hydroxyl and hydrogen obtained in this calculation was larger
than that on the non-oxydized PdZn(111) surface [3]. It means this surface is not active forthe hydrogenation of water.

Figure 1: Side view of the oxidized PdZn(111)
surface.
In addition to the above work, we studied
pentacene adsorption on the twofold surface of
the icosahedral Ag-In-Yb quasicrystal [4] andthe electronic structure of trace (Pt, Ni, Pd)doped Al13 Fe4 intermetallic compounds.

References[1] M. Friedrich et al., Angew. Chem. 52,
4389 (2013).
[2] K. Iwamura, Master Thesis (Kagoshima
University, 2023).
[3] G. K. Smith et al., Surf. Sci. 605, 750(2011).
[4] M. Sato et al., J. Phys.:Conf. Ser., 2461,
012016(2023).

126

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Adsorption States of Oxygen on Pt Nanoparticles
Takehiko SASAKI and Yasumasa IMAI
Department of Complexity Science and Engineering, Graduate School of Frontier Sciences,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8561
and contains 215 Pt atoms and oxygen atoms.

The surface state of the catalyst platinum
nanoparticles determines the performance ofAfterpolymer

cuboctahadral nanoparticle is obtained byelectrolyte

fuel

cells

(PEFC).

optimizationofoperation.

this
The

unit

cell,

Characterization of the electrochemical cycle

symmetry

structureand oxygen adsorption state on the surface of

optimization calculation was performed byplatinum nanoparticles, as well as the high-allowing the relaxation of the first and second

coverage

oxygenadsorption

state

with

neighbors of oxygen atoms. The energy cutoff

subsurface

oxygengeneration,

has

been

is 400 eV and the k-point mesh is 3x2x2. The

investigatedusingsynchrotron

representative models are shown in Fig. 1.

radiationtransient response XAFS and resonant inelastic
X-ray

scattering(RIXS).

Althoughcomputational studies on oxygen species on Pt
surfaces have been published [1,2], it isnecessary to determine the oxygen adsorption
structure on the Pt nanoparticles in order toFig. 1

conduct spectral analysis.

Pt586O64.

Obtained models Pt586O32 and

The Pt nanoparticles to be calculated are Pt
Nownanoparticles composed of 586 atoms of thecalculations

todetermine

cuboctahedron type corresponding to the actual

chemical potential for each species undercatalyst particle size range of 2.5 nm in order toelectrochemical processes are in progress.

study the high-coverage oxygen adsorption

References

state where subsurface oxygen atoms also exist.

[1] J.K. Norskov et al. , J. Phys. Chem. B 108,

The primary purpose is to obtain the adsorption

17886 (2004).

structure by VASP calculation and provide the[2] R. Jinnouchi et al., Catal. Today 262, 100

coordinates for FDMNES simulation. The unit

(2016).

cell has a volume of 22.13×44.26×33.19 (Å3)

127

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Modeling of the Ammonia Decomposition Reaction
on Iron-based Material Surfaces
Peijie FENG, Minhyeok LEE, and Yuji SUZUKI
Department of Mechanical Engineering, School of Engineering,
The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656
Ammonia is expected as a next-generation

barrier would significantly facilitate ammonia

green energy carrier due to its high hydrogen

decomposition. To estimate the reactivity ofdensity and ease of liquifying for storage andammonia on iron nitride and compare it with thattransportation. However, the direct application

on iron, DFT calculations are performed thatof ammonia as a fuel suffers from its low

illustrate the activation barrier of the rate-

flammability and potential NOx emission [1]. A

determining step on iron and iron nitride. Firstly,

fundamental understanding of ammonia reaction

the surface energy is calculated to identify the mostkinetics is necessary to overcome these issues.

common lattice surface where the reaction happens.

On the other hand, since ammonia-related

Secondly, the adsorption conformation of N2 andreaction kinetics has been developed andatomic N is calculated to obtain the system's total

validated

DeNOxenergy. Finally, the calculated conformation for theapplications, the kinetics model often loses its

reactant and product is used to estimate the totalrobustness in absence of oxygen, where thermalenergy of transition states. Based on a series ofdecomposition mainly occurs [2].

calculations, the activation energy can be estimatedmainlyfocusing

on

Therefore, we conducted density functionalfrom the energy difference between the transition

theory (DFT) calculations using the Vienna Ab

state and the initial reactant state.

initio Simulation Package (VASP) with the aid

The surface energy calculation on iron nitrideof the supercomputer system at ISSP to evaluate(FeN) is performed on lattice surfaces 100, 110

the rate-determining step of ammonia surface(with Fe or N at the top layer), and 111 (with Fe or

decomposition on iron-based materials.

N at the top layer). The result shows the lattice

It has been demonstrated that the nitrogensurface 110 has the lowest surface energy at aroundlargest0.086eV/Å2 as shown in Table 1. The lower theactivation energy on metal surfaces such as Fe,

surface energy, the more stable the surface is andCo, and Ni [3], and accordingly, it can be

the more common it is on the catalyst surface asrecombination

reaction

shows

the

assumed as the rate-determining step. Any surface
offering a lower N-N recombination activation

128

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

experimentally prepared. On the other hand, aclosed-packed surface (110) can be found on ironsurfaces, which usually possess the lowest surface
energy. Thus, FeN with lattice surface 110 and Fe
with lattice surface 110 are used to estimate andcompare the heterogeneous reaction of ammonia.
Table 1: Surface energy of iron nitride FeN.
Lattice
Surface

110

Top
Element

-

100

Fe

N

Fe

111

Fig. 2: Initial and transition states of N-N
recombination for (a) Fe-110 and (b) FeN-110
surfaces.

Nnudged elastic band (CI-NEB) method [4]calculation can be performed first-principally,

Surface
Energy[eV/Å2]0.086

which yields the transition states and the total

0.186 0.361 0.361 0.093

energies of the reaction between the given

Since N-N recombination is the key rate-

reactants and the products. As shown in Fig. 2, thedetermining step of ammonia decomposition, theFeN surface provides a lower activation energy

most stable adsorption site for N is found by(0.278 eV) than the Fe surface (2.41 eV),placing N atoms at all possible adsorption sites (asindicating a promising catalyst for ammonia

shown in Fig. 1) on the surface both for FeN-110

decomposition reaction.

and Fe-110. Among all possible adsorption sites,

Further improvements in finding the reaction

the Fe-top site on FeN-110 and the Hollow site on

kinetics shall be made through the harmonic

Fe-110 showed the lowest adsorption energy,transition state method.

indicating they are the most preferable active site

References

to adsorb free N atoms.

[1] M.V. Manna, P. Sabia, R. Ragucci, and M. de

By defining the product conformation for N2

Joannon, Fuel 264, 116768 (2020).

molecules on the surface, the climbing image[2] P. Glarborg, H. Hashemi, and P. Marshall,
Fuel Commun. 10, 100049 (2022).
[3] X. Duan et al., J. Mol. Catal. A Chem. 357, 81(2012) .
[4] G. Henkelman and H. Jónsson, J. Chem. Phys.
111, 7010 (1999).

Fig. 1: Adsorption site of (a) Fe-110 and (b) FeN110 surfaces.

129

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Study on the Catalytic Mechanism of RuTi Alloyin Catalyst-Referred Etching Method
Pho Van BUI, Daisetsu TOH, Kouji INAGAKI, Yoshitada MORIKAWA
Grad. School of Engineering,Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871

Polishing is an extremely important techniqueformed and bonded to the catalyst surface.

used in the finishing processes for optical and

To improve the removal rate (RR) andsemiconductor surfaces and determines thestability, many catalyst metals have tested theirperformance of the final products. To produce

capability as a catalyst metal in CARE. Oursmoothany

recent studies found that Ni and Ru alloy are

crystallographically damaged surface, only

the best catalysts in terms of RR [4]. However,pure chemical etching method is desired.

the RR is decayed in time due to poisoning by

Recently, catalyst-referred etching (CARE)

removal products. Our recent experimental

method using Pt catalyst and water (as an

results have shown that alloying Ru with Ti

etchant) has been proposed [1]. CARE can

could effectively improve its stability forplanarize

crystalline

several hours of polishing compared to Ni or

semiconductor materials to atomically smooth

Ru itself [5]. The long-term stability of asurfaces [2,3]. The main role of the catalyst iscatalyst could reduce the cost and increase theto dissociate water molecules and to stabilize

reliability

the five-fold coordinated states. After a Si was

ultraprecision polishing method for next-

removed from the material, silicic acid isgeneration optical devices. Therefore, purpose

surface

SiC

withoutandintroducing

various

of

CARE

to

be

a

practical

Fig. 1: Top and side views of the Ru2M slab model with silicic acid. Adsorption energy of silicic acid.

130

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyoof the proposed research is to elucidate theshown in Fig. 1. The adsorption energy ofcatalytic mechanism of RuTi alloy and generalsilicic acid on RuTi alloy is the lowest among

understanding of the catalytic decay using first

the investigated catalysts. DFT calculations

principles calculations.

showed that Ti doping to Ru reduces the

The DFT calculations were performed using

adsorption energy of silicic acid on the Ru site

the Simulation Tool for Atom Technology

from 0.61 to 0.32 eV and efficiently restorespackage, which has clarified the adsorption andthe active Ru sites.

dissociative reaction on metal surfaces [6-8].

References

The electron–ion charge interactions were

[1] H. Hara, Y. Sano, H. Mimura, K. Arima, K.

described by an ultra-soft pseudopotential. The

Kubota, K. Yagi, J. Murata, and K. Yamauchi, J.

wavefunction

Electron Mater. 35, L11 (2006).

andchargedensitywere

expanded by a plane-wave basis set with 25 and[2] D. Toh, P.V. Bui, N. Kidani, S. Matsuyama,225

Y. Sano, Y. Morikawa, and K. Yamauchi, K.

Ry

cut-off

energies,

respectively.

Optimization was iteratively performed until

Rev. Sci. Instrum. 90, 045115 (2019).

the residual forces acting on all atoms at the[3] A. Isohashi, P.V. Bui, D. Toh, S. Matsuyama,saddle point were reduced to below 10−3 Eh/a0,

Y. Sano, K. Inagaki, Y. Morikawa, and K.

where Eh = 27.211 eV and a0 = 0.529 Å.

Yamauchi, Appl. Phys. Lett. 110, 201601

In this study, we used the 3×4×4 supercell(2017).

model of Ru with (0001) surface as the host[4] D. Toh, P.V. Bui, A. Isohashi, S. Matsuyama,

metal catalyst model, as shown in Fig. 1. A few

K. Yamauchi, and Y. Sano, Rev. Sci. Instrum.

Ru atoms are substituted by a transition metal

91, 045108 (2020).

atom, such as Zr, V, and Ti, creating a Ru-based[5] D. Toh, K. Kayao, P.V. Bui, K. Inagaki, Y.

alloy catalyst model. The adsorption energy,

Morikawa, K. Yamauchi, and Y. Sano, Pre. Eng.

Eadsorb, of silicic acid on Ru, Ru-V, Ru-Ti, andsubmitted.

Ru-Zr alloy catalyst surfaces was calculated by,[6] T. Hayashi, Y. Morikawa, and H. Nozoya, J.

𝐸𝑎𝑑𝑠𝑜𝑟𝑏 = |𝐸𝑅𝑢+𝑠𝑖𝑙𝑖𝑐𝑖𝑐 𝑎𝑐𝑖𝑑 − (𝐸𝑅𝑢 +Chem. Phys. 114, 7615 (2001).

𝐸𝑠𝑖𝑙𝑖𝑐𝑖𝑐 𝑎𝑐𝑖𝑑 )|,[7] Y. Hamamoto, I. Hamada, K. Inagaki, and Y.

where ERu+silicic acid, ERu, and Esicilic acid are theMorikawa, Phys. Rev. B 93, 245440 (2016).

total energies of the Ru-based catalyst with

[8] J. Quan, F. Muttaqien, T. Kondo, T.

adsorbed silicic acid, the Ru-based catalyst, andKozaeashi,

T.

Mogi,

silicic acid, respectively.

Hamamoto,

K.

Inagaki,

The adsorption energies of silicic acid on the

Morikawa, and J. Nakamura, Nature Chem. 11,

Ru catalyst and Ru-based alloy catalyst are

722 (2019).

131

T.

Imabayashi,

Y.

I.

Y.

Hamada,Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Proton Storage in Ruddlesden–Popper-type Sr3Fe2O7
Kosuke Kawai, Masashi Okubo
Department of Electrical Engineering and Bioscience, School of Advanced Science andEngineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555

We investigated proton storage properties of

performed in the same way. Graphics of crystal

Ruddlesden–Popper-type

structures were drawn by VESTA software.4

Sr3Fe2O7

using

density functional theory (DFT) calculations.

Three thermodynamically stable H+

This year, we focused on thermodynamicallysites were identified around interlayer

stable sites of proton in the lattice of Sr3Fe2O7.

space after structure optimization. Site A

DFT calculations were performed with theis bridged to the nearest O atom in the

Vienna ab initio simulation package (VASP).

same FeO6 octahedron, and the mostThe projected augmented wave method and athermodynamically stable. Site B in theplane basis set implemented in the VASP code

interlayer space is directed to an O atom

were utilized with a cutoff energy of 520 eV

in neighboring Fe2O7 layer. Site C is alsoThein the interlayer space but directed to a

generalized gradient approximation of theSr atom, resulting in high electrostatic

Perdew–Burke–Ernzerhof exchange-correlationenergy.

functional was used with Hubbard U = 4.0 eV

References

and k-point sampling on a 6×6×2

grid.1for Fe to correct the self-interaction error of[1] G. Kresse and J. Furthmüller, Phys. Rev. B

correlated d electrons.2,3 An initial structure

54, 11169−11186 (1996).

model of Sr3Fe2O7 was obtained from theMaterials

Project

expanded

to a

(ID:

mp-18820),

superstructureof[2] J. P. Perdew, et al., Phys. Rev. Lett. 77,

and3865−3868 (1996).

2×2×1[3] F. Zhou, et al., Phys. Rev. B - Condens.

(Sr24Fe16O56, Fig.1a). Structure optimization

Matter Mater. Phys. 70, 1–8 (2004).

was performed with a convergence condition of[4] K. Momma and F. Izumi, J. Appl.

ΔF < 0.01 eV/Å. A H atom was located

Crystallogr. 41, 653−658 (2008).

manually near an O atom with a H–O distanceof < 1 Å, and then structure optimization was

Fig.1 (a) Crystal structure of Ruddlesden–Popper-type Sr3Fe2O7, (b) typical H+ sites, and (c) totalenergies of HSr24Fe16O56.

132

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ultrafast adsorption states of two-dimensional metal-organicframeworks and semiconductors
Kenichi SHUDO
Fac. of Eng/Sci, Yokohama Nat’l Univ.
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8581
We performed calculation for elucidation of

motion was thus clarified.

a nonlinear optical effect of a typical transition

Metastable-atomelectron

spectroscopy

metal dichalcogenides, MoSe2, using Vienna ab(MAES) reveals electric states of a surface,initio Simulation Package (VASP). Molecular

exclusively giving information of the electron

dynamics produces well the atomic trajectories

cloud protrude into the vacuum. We measured

from an initial kick due to potential deformation

the spectra of such electrons of a typicalcausedHyperlinear

topological insulator, Bi2Se3. Our preliminary

components gives a sum frequency andcalculation of one to a few layers of this crystal,harmonics of fundamental oscillation (Fig.1).

using VASP. The obtained results are analyzed

These Fourier components are contrary to thebased on the local density of state dependent onlinear normal modes reachable either via

the distance from the top-most surface atoms.

experimental cw-Raman spectroscopy and

The spectral features of the MAES applied to thetheoretical diagonalization of atomic potential

crystal are concluded to be originated fromalong with the displacement of each atom. The

concurrent processes of resonance ionization

nonlinear optical effect derived by atomic

and Auger neutralization.

byphoto-transition.

Similar local electron distribution curves are
obtained also for layler-by-layer structures ofmetal-organic framework (MOF) of 5,10,15,20Tetrakis(4-carboxyphenyl)-porphyrin.

References[1] S. Bae, K. Matsumoto, H. Raebiger, K.
Shudo, Y.-H. Kim, Ø.S. Handegård, T. Nagao, M.

Fig. 1: Example of nonlinear vibronic

Kitajima, Y. Sakai, X. Zhang, R. Vajtai, P.

modes of MoSe2 simulated by means of

Ajayan, J. Kono, J. Takeda, I. Katayama:

molecular dynamics at femtosecond scale.

Nature Communications 13, 4279 (2022)

See Ref [1] for detail.

133

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analyzing Reaction Mechanism of Charge Transfer inCatalysis by Electronic Structure Calculations
Tatsuya JOUTSUKA
Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki
University, Hitachi, 316-8511 Ibaraki, Japan.

Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1
Shirakata, Tokai, Ibaraki 319-1106, Japan.
Carbon Recycle Energy Research Center, Ibaraki University, Hitachi, 316-8511 Ibaraki,
Japan.

Focusing on the selectivity of zirconia-

suggesting that Zn species are unevenly

catalyzed methanol synthesis, we calculated

distributed on the surface and deposited nearadsorption and reaction energies to clarify thethe surface; by adding excess Zn to ZrO2, bothreaction mechanism. [1-2] In addition, polaronZn-containing clusters and ZnO nanoparticles

transfer rate constants in bulk titanium dioxide

were formed. We also analyzed the dynamics in(TiO2) and SrTiO3 were calculated by theadsorption and chemical reactions by molecularconstrained density functional theory (CDFT)

dynamics simulation and develop a method tomethod.

Then,

the

analyze charge transfer. In addition, we

calculation

was

used

electronic
tostructureelucidatetheelucidated the mechanism of Cu nanoparticle

photocatalytic reaction mechanism and crystal

formation with a size <10 nm using DFT

plane selectivity in photocatalysts.

calculations.[3]Furthermore,

weanalyzed

A zirconia-based solid solution catalyst

theoretical methods for proton transfer in liquid

ZnZrOx was prepared by substituting Zn withwater,[4] cross-coupling of arylboronic acidZr, which has high catalytic activity. The

and imidazole on t-ZrO2,[5] and Cu deposition

correlation between the binding strength of theby chemical vapor deposition using a CuI

substituted elements and adsorbates (reactants,

precursor[6] using VASP and cp2k program

products, and intermediates) and methanol

packages.

synthesis capacity was clarified. The DFT

In addition, the polaron transfer rate

calculations using cp2k program package

constants in bulk TiO2 and SrTiO3 (Fig. 1) was

showed that the Zn species in the clusters arecalculated by the CDFT method along themore likely to be exposed on the surface. This

several directions (such as [101] direction in

result is consistent with experimental results,

TiO2) using cp2k program package. We found134

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

that the CDFT method can evaluate the

Kinoshita,

Mitsuhiro

Yoshida,Natsumipotential energy profile more accurately than

Shimada,TatsuyaJoutsuka,

Masahikolinear interpolation of structures that has been

Nishijima, Tetsuo Honma, Noriko Yamauchi,frequently employed for bulk TiO2. We next

Yoshio Kobayashi, and Kenta Iyoki, ACS

moved on to the SrTiO3 (001) and (110)

Catal., 12, 7748–7759 (2022).

surfaces to understand the porlaron transfer at[2] Tatsuya Joutsuka and Shohei Tada,* J. Phys.

the surface. We are now studying the relation

Chem. C, 127, 6998–7008 (2023)

with the oxygen vacancy and electron polaron[3] Tatsuya Joutsuka, Ryu Hamamura, Kakeru

to discuss the photocatalytic mechanism further

Fujiwara, Tetsuo Honma, Masahiko Nishijima,using cp2k program package.

and Shohei Tada, Int. J. Hydrog. Energy, 47,
21369–21374 (2022).
[4] Tatsuya Joutsuka, J. Phys. Chem. B, 126, 24,4565–4571 (2022).
[5] Masaru Kondo, Tatsuya Joutsuka, Kakeru
Fujiwara, Tetsuo Honma, and Shohei Tada,
Catal. Sci. Technol., 13, 2247-2254 (2023).
[6] Gento Toyoda, Hikari Kikuchi, Satoshi
Yamauchi, Tatsuya Joutsuka, Takashi Fuse, andFig. 1: Bulk SrTiO3.

Yusuke Kubota, Jpn. J. Appl. Phys., 62,
SH1002 (2023).

References[1] Shohei Tada, Nagomu Ochiai, Hiroka

135

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles calculation of oxygen defects on the surfaceof titanium dioxide TiO2
Shoya Kawano
Department of Electrical and Electronic Engineering, Kyushu Institute of Technology,
Kitakyushu, Fukuoka, 804-8550

We have studied stability of oxygen defects
on

TiO2

surfacebyfunctionalthem from the PseudoDojo [3]. The exchange-

calculations in this project. Oxygen defects incorrelation function is used Perdew-Burke-

TiO2

catalytic

Ernzerhof type. For example, Γ-point-centeredperformance, carrier transport, hydrophilicity,

2×2×1 k-points sampling were used for 2×2×4

and other functions. Therefore, if we cansurface unit cell of TiO2 (110) included 238

successfully control these oxygen defects, it

atoms. We use the energy cutoff of 96 Ry forwill be possible to design the function of TiO2.

the wave function, a convergence criterion for

For this purpose, we have studied thethe electronic self-consistency loop of 10−10 Ry,

configuration of oxygen defects on TiO2

and the Gaussian smearing method with asurface using scanning probe microscopy

smearing width of 0.002 Ry. Lattice parameters(SPM) image with template matching method.

of TiO2 is referred to previous report [4].

significantly

density

Vanderbilt PSeudopotential), and are obtainedchanges

its

This SPM image analysis indicated typicalFigure 1 shows calculated structure of TiO2

configuration of oxygen defects. Therefore, we

surface model of 2×2×4 surface unit cell withinvestigated

two defects (238 atoms) and their defect energy

stabilityof

configurationofoxygen defects on TiO2 surface by density

Evac. Evac is defined as follows
𝐸𝑣𝑎𝑐 = 𝐸𝑇𝑖𝑛 𝑂2𝑛−1 + 𝐸𝑂2 − 𝐸𝑇𝑖𝑛 𝑂2𝑛 ,functional calculations.
functional

where 𝐸𝑇𝑖𝑛 𝑂2𝑛−1 , 𝐸𝑂2 and 𝐸𝑇𝑖𝑛 𝑂2𝑛 are total

calculations for slab models of rutile TiO2 (110)energy of slab with defects, total energy ofby using Quantum ESPRESSO code [1,2]. The

oxygen molecule and total energy of slab

slab models have two oxygen defects on

without

surface and 1 nm vacuum gaps. The unit cellconfigurations for two defects introduced atincluded 144, 240, 300 and 450 atoms arebridge oxygen on the surface. The bridge

considered for slab models without defects. In

oxygen is bonded with titanium along the

Quantum ESPRESSO, we use the norm-

parallel axis in Fig. 1. Configurations of defects

conserving pseudo potentials generated by thelike Fig. 1 (a)-(c) are more stable than defects

code ONCVPSP (Optimized Norm Conserving

along parallel axis in Fig.1 (d) and (e). ThisWe

performed

density136

defects.

We

consideredfiveActivity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

trend of results is consistent with our STM[2] P. Giannozzi et. al. J. Phys. Condens. Matter.

image analysis.

29, 465901 (2017)

We have used the L4cpu of system B with

[3] M. J. van Setten, M. Giantomassi, E.

512 parallel computing for 144 and 240 atoms

Bousquet, M. J. Verstraete, D. R. Hamann, X.

unit cell, the L16cpu of system B with 2048

Gonze, G.-M. Rignanese, Computer Physics

parallel computing for 300 and 450 atoms unit

Communications 226, 39-54 (2018)cell.

[4] X. W. Wang, B. H. Zhang, L. Y. Sun, W. N.
Qiao, Y. D. Hao, Y. C. Hu, and X. E. Wang,

References

Journal of Alloys and Compounds 745, 856[1] P. Giannozzi et. al. J. Phys. Condens. Matter.

(2018).

21, 395502 (2009).

Fig. 1 Calculated structure of TiO2 surface model and their defect energy.

137

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Thermal conductivity calculation for high thermal conductive
insulator
Shoya Kawano
Department of Electrical and Electronic Engineering, Kyushu Institute of Technology,
Kitakyushu, Fukuoka, 804-8550

We have computed the lattice thermal

Ernzerhof type exchange-correlation function.

conductivity of several materials to create aFor

finitedisplacement

andrandomdatabase for the design of high thermal

displacement

approaches,

we

used

conductive

displacement distances of 0.02 and 0.04 Å,

insulators.

High

thermalconductivity insulators are essential for therespectively.

substrate of power devices. To develop high-We

calculatedthelatticethermalperformance power devices, it is necessary to

conductivity of AlAs, CaO, SrO, YN, CeO2,

discover new substrate materials with high

AlN, CaF2, MgBe2N2, TaGaFe2, and BN. Thesethermal conductivity insulators. In this project,structures were collected from the Materials

we created a database of lattice thermal

Project [5]. For the random displacement

conductivity for materials informatics.

approach, we used 20-500 structures andWe performed density functional phononcompared their thermal conductivity accuracy.

calculations using the ALAMODE code [1]We found that a set of 20 structures satisfied thewith the Quantum ESPRESSO code [2,3] toaccuracy for the lattice thermal conductivity

compute the lattice thermal conductivity. We

database. We continue to calculate the latticecalculated the second- and third-order force

thermalconstants from density functional theory. The

parameters in this project to create a database.

conductivity

with

the

obtainedsecond-order force constants were calculated

We used the F16CPU of system B withusing the finite displacement method, while the2048 parallel computing by MPI for the density

third-order force constants were calculated

functional calculations for each displacement.

using

For

the

randomdisplacement

methodthermalconductivity

calculation,

implemented in ALAMODE. In the density

MPI/OpenMP hybrid parallelization was usedfunctionalwith the F16CPU of system B.

calculations,

we

used

norm-

conserving pseudo-potentials generated by the
Optimized

Norm

Pseudopotential

Conserving
code,

References

Vanderbilt

obtainedfrom[1] T. Tadano, Y. Gohda, and S. Tsuneyuki, J.

PseudoDojo [4]. We used the Perdew-Burke-

Phys.: Condens. Matter 26, 225402 (2014)138

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo[2] P. Giannozzi et. al. J. Phys. Condens. Matter.
21, 395502 (2009).
[3] P. Giannozzi et. al. J. Phys. Condens. Matter.
29, 465901 (2017)[4] M. J. van Setten, M. Giantomassi, E.
Bousquet, M. J. Verstraete, D. R. Hamann, X.
Gonze, G.-M. Rignanese, Computer Physics
Communications 226, 39-54 (2018)[5] https://materialsproject.org/

139

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Stable structures of low-dimensional systems fromﬁrst-principles
Shota ONO
Department of Electrical, Electronic and Computer Engineering, Gifu University
Gifu 501-1193

In this project, we have studied (i) stable structures of two-dimensional (2D) hexagonal materials [1], (ii) structural and electronic
properties of 2D ionic crystals [2], and (iii) surface rippling on non-close-packed metal surfaces [3] using density functional theory (DFT)and machine-learning approaches.
For the case (i), we have explored the stable
conﬁgurations of atomic species on a hexagonal plane in 2D binary systems. The conﬁguration search was accelerated by using theBayesian optimization (BO) approach. For the
2D copper-based systems of Cu-X, we haveshown that the structures having a hexagonal or elongated ring of Cu (or X) atoms containing a X (or Cu) cluster in the unit cellare relatively stable, in particular, for X =Be, Pd, and Au (see Fig. 1(a)). The binary
Lennard-Jones model was used to interpret the
optimized structures predicted by DFT calculations.
For the case (ii), we have shown that 4 and
12 IA-VII alkali halides in the 2D hexagonal and tetragonal structures (see Fig. 1(b))
are dynamically stable, respectively. The electronic band gaps range from 6.8 eV for LiF to
3.9 eV for RbI and CsI in the tetragonal structure within the generalized gradient approximation. A hard sphere model that considers
the Madelung energy and the core-core repulsion explains the nearest-neighbor bond lengthand the cohesive energy of 2D alkali halides.
For the case (iii), we have studied surface
rippling of X/A(100) (see Fig. 1(c)), assuming

X = H to Bi except for noble gases and A =Cu, Ag, and Au. We have shown that small
atoms (such as H, C, N, O and F) attract electrons from the substrate due to the large electronegativity, which prevent them from passing through voids in the (100) surface. We
have also discussed a breakdown of the hard
sphere model for predicting the surface rippling amplitude.

Figure 1: Stable structures (a), (b), and (c)studied in Refs [1], [2], and [3], respectively.
The structures in (a) were found by using BO.

References[1] S. Ono: AIP Advances 12, 085313 (2022).
[2] S. Ono: J. Phys. Soc. Jpn. 91, 094606(2022).
[3] S. Ono, H. Satomi, and J. Yuhara: Comp.
Mater. Sci. 218, 111959 (2023).

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Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Stable structure of vacancy cluster in tungsten and irontrapping multiple hydrogen atoms
Kazuhito Ohsawa
Institute for Applied Mechanics, Kyushu University,
Kasuga-koen, Kasuga, Fukuoka 816-8580

Introduction

Simulation method

Tungsten (W) and Iron (Fe) are important

Stablevacancyclusterstructuresandmaterials for plasma facing materials (PFMs)

positions of multiple H atoms trapped in theused in fusion reactors. In particular, W shows

vacancy clusters in W and Fe specimen werepromise as divertor armor tiles exposed to thecalculated

most

irradiation.

calculations based on density functional theory

Vacancy (V) and vacancy clusters nucleated in(DFT). We used the Vienna ab-initio simulation

the metals under the irradiation circumstancepackage (VASP) for the DFT simulations. A

are considered to be a large amount oflarge simulation cell, composed of 5x5x5 bcc

hydrogen (H) and hydrogen isotope trap sites.

lattice (250 atoms), were used in order to

In particular, tritium (T) retention in the PFMs

reduce the effects of periodic boundary

is a serious problem for safety operation of

condition imposed on the simulation cell. The

fusion reactor because T is radio isotope whose

cut-off energy of plane wave was 350eV.

intenseplasmaparticle

in

terms

of

first-principle

The binding energy Eb of di-vacancy V2 washalf-life is about 12 years. So, the investigation

defined asof the vacancy clusters in the metals and H

Eb(V2) = 2E[V]-E[V2]-Eref,trapping are important subjects in the field of(1)

PFMs. In the present work, stable structures ofwhere E is cohesive energy of the supercell andvacancy clusters and their interaction withEref indicates energy of perfect crystal. For

multiple H atoms in W and Fe lattice areexample, E[V] and E[V2] mean cohesive

investigated by computational methods. A

energies of supercells containing mono- and di-difference of vacancy clusters in W and Fe wasvacancy, respectively. Positive binding energy

clarified. Besides, positions of multiple H

Eb corresponds to attractive interaction of theatoms trapped in the vacancy type lattice

two vacancies. Similarly, the binding energy ofdefects are examined.

V-H complex V2H2 i.e., di-vacancy trapping

The effects of H were

two H atoms, is defined as

investigated on the stable structures of theEb(V2H2) = 2E[VH]-E[V2H2]-Eref,.

vacancy clusters.

141

(2)

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Results and discussion
Stable structures of di-vacancy in W and Fe
are different, as shown in Fig.1.

W is <111> arrangement in both cases. Figure 3

The most

shows two H atoms trapped in di-vacancy in W

stable arrangements of two vacancies are <111>

and Fe. H atoms trapped in the vacancy type

in W and <100> in Fe, respectively. Actually,lattice defects are allocated in the vicinity ofbinding energy between two vacancies arranged

octahedral interstitial (O-site). In addition to it,

in <100> direction is larger than that of <111>

H atoms preferentially occupy O-sites locatedin Fe estimated in Eq. (1), according to Fig. 2.

in the center of the di-vacancy where two

However, <111> arrangement of di-vacancy

vacancies are in contact with each other.

trapping two H are more stable than <100> one

In the present work, H trapping are supposed

estimated in Eq. (2). Therefore, stable structure

to play important roles for stabilization ofof di-vacancy in Fe is changed from <100> tovacancy clusters. The binding energy of<111> arrangement by the H trapping. By thevacancy clusters increase and structure of di-way, the most stable structure of di-vacancy invacancy are changed by the H trapping in Fe.

Fig. 1: Most stable structure of di-vacancy in bcc lattice. Arrangements oftwo vacancies are (a) <111> in W and (b) <100> in Fe, respectively.

Fig. 2: Binding energy of di-vacancy andFig. 3: Positions of two H atoms trapped in

di-vacancy trapping two H atoms in Fe.

di-vacancy in W and Fe.

142

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab initio molecular-dynamics study of structural and transport
properties of liquid mixtures containing hydrocarbon underultra-high pressure
Satoshi OHMURA
Department of Civil and Environmental Engineering,
Hiroshima Institute of Technology, Saeki-ku, Hiroshima 731-5193
Understanding the structures and physicalthe first peak are highly stable and strong. The

properties of the C-H system at higher pressuressimulation found that the interaction remains

is essential to constrain the interiors of the ice

even under ultrahigh pressure conditions of 1300

giant planets (extrasolar planet). Therefore, it isGPa. For hydrogen, molecular hydrogen isimportant for planetary science to understand theobserved after methane dissociation (at 150

behavior of this important material in extreme

GPa). When the pressure becomes higher,

conditions. For this reason, we have performedhydrogen molecule becomes unstable.

ab initio molecular-dynamics (MD) simulations
for liquid Methane (CH4) under high pressures.
We used a 500-atom system consisting of 400
hydrogen and 100 carbon atoms in a cubic
supercell with periodic boundary conditions.
Figure 1 shows the pressure dependence ofthe pair distribution functions gαβ(r) of liquid
CH4 obtained from the MD simulation. Since
methane molecules remain intact up to 100 GPa,
the shape of gCC(r), gCH(r) and, gHH(r) at 55 and100 GPa are almost the same. Above 150 GPa,in gCC(r), a new peak appears at approximately
1.4 Å and its position gradually shifts to asmaller r with increasing pressure. Moreover,Fig. 1: Pressure dependence of the pair distribution

the first peak of gCC(r) is clearly separated fromfunctions gαβ(r) of liquid CH4.

a second peak at pressures of 150 GPa,suggesting that the C-C bonds contributing to143

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Temperature dependence of structural and electronic
properties of organic molecular thin film surfaces
Kaori Niki
Graduate school of science
Chiba University, Yayoi-cho, Inage-ku, Chiba 263-8522
In recent years, it has been reported that

The Generalized Gradient Approximation

organic molecules' electronic and physical(GGA) within the Perdew-Burke-Ernzerhof

properties interact with the surface using Wave

(PBE) formalism described the exchange-

numberPhotoelectron

correlation effects. We used a unit cell with

Spectroscopy. We have investigated the copper

lattice constants a = b = 3.53 Å, c = 20.0 Å, α(Ⅱ) phthalocyanine (CuPc) - monolayer= β = 90° and γ = 120°, and plane-wave basis

substrate system. This year, we investigated

set with the projector augmented wave (PAW)

molecular motion depending on the terminal.

approach with an energy cutoff of 380 eV. The

Monolayer TiSe2 has two typical phases

Brillouin zone integration was performed on adepending on the temperature. A (1 × 1)

Monkhorst-Pack of 18×18×1 grid of k-points.

structure (normal phase) is shown at room

The energy convergence criterion chosen fortemperature, and a (2 × 2) superstructure

the self-consistency cycle was 1×10-7 eV. To(CDW phase) is realized under the 200 K.

account

Each phase has a band gap of 83 meV and 153

temperature parameter σ for Methfessel-

meV, respectively [1, 2]. We have adopted

Paxton smearing was applied [5]. So far, we

this interesting thin film as the substrate andhave found the parameter set (U = 3.9 eV andreported the structural changes depending on

σ = 0.01 eV), which reproduces thethe temperature in the previous year andexperimental result [6]. We used thesestructureparameters for the MD simulation of the CuPc

space-resolved

optimization,

resulting

in

an

for

Fermi

surfacebroadening,

adsorption distance of 3.16 Å.

/ TiSe2 structure. After relaxing the geometries

This time, we performed Molecular dynamics

at 0 K, the systems were brought up to 654 K(MD) simulation using these structures as theby repeated velocity rescaling using the spin-

ground state, and clarified the structures after

polarized PBE+U DFT-D3 functional at the Γ-

temperature change.

point. Then 5

MD calcuration of CuPc on TiSe2

trajectories were generated with a 1 fs time

We performed density functional theory

step.

(DFT) calculations using the Vienna Ab Initio

Molecural rotation of CuPc/TiSe2

Software Package (VASP) version 5.4.4 [3,4].

ps microcanonical MD

Figure 1 shows the geometry of CuPc on

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Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

at lower temperatures.

TiSe2 at 0 K. S1 and S2 indicate the axis of thesurface. “Center, " one of the molecular axes,

On the other hand, after MD calculation, thenumber of Se electrons in TiSe2 is slightly

is tilted 30 degrees from the axis s2.

larger than before calculation. On the other
hand, the number of electrons in Cu atom
decreases. A stable structure is due to the close
distance between Cu and Ti creates. Nitrogencloser to the center has additional electrons andapproaches Ti atoms. This also creates a stablestructure.
Figure 1. Geometry of CuPc/TiSe2

Conclusion
Figure 2 shows the geometry of CuPc/TiSe2

By performing MD calculations using VASP,

after MD. A temperature of 654 K is assumed.

we clarified changes in the charge distribution

We can see the motion of the molecule to theof molecules and substrates and molecular

lower left. The angle between the central andmotions with increasing temperature.

s2 is magnified to 60 degrees.

References

After MD

[1] J.-P. Peng et. al., Phys. Rev. B 91, 121113(2015).
[2] P. Chen et. al., Nat. Commun 6, 8943
(2015).
[3] G. Kresse and J. Furthmuller, Phys. Rev. B,
54, 11169 (1996).
[4] G. Kresse and J. Hafner, Phys. Rev. B, 49
14251 (1994).
[5] M. Methfessel and A. T. Paxton, Phys. Rev.
B 40, 3616 (1989).

Figure 2. Geometry of CuPc/TiSe2[6] R. Bianco et.al., Phys. Rev. B 92, 094107
Cu is adsorbed between Ti and Se atoms(2015).

before MD simulation. At this time, charge
repulsion occurs between Cu and surrounding
Se, and between carbon and Se near the center

145

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of First Principles methods for Light-Matter
Interaction
Hiroki KATOW
Photon Science Center, Graduate School of Engineering,
The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, JapanThe electronic dipole moment calculation isstates of monolayer (ML) and bulk hexagonala fundamental of the light-matter interaction. In

boron nitride (hBN) for further systematic study.

isolated systems, the dipole moment is defined

Massively parallelized calculations using 2048

by an expectation value of dipole operator and

cpu in F16cpu class were conducted. We show

no ambiguities in its definition. Contrarily inthe exciton energy spectrum of ML- and bulk-

periodic systems, ambiguity of the choice of

hBN in Figure 1. Due to the weak screening ofcell boundary leads to the indefiniteness of its

two-dimensional system ML-hBN possesses

definition. Modern understanding of this issue

larger GW gap (8.12 eV) than bulk-hBN (5.54

is that the ambiguity is rooted in the indefiniteeV). We also confirmed huge exciton binding

complex phase factor of one-particle orbitals,

energy of ML-hBN. As a future prospect, we

which is called gauge degrees of freedom. A

apply our gauge-free method to ML- and bulk-

solution is proposed for ground states by King-hBN by utilizing the excitonic wave functions

Smith and Vanderbilt where the dipole moment

computed in this project.

is reformulated to exclude explicit dependency
on the gauge [1].
A same obstacle is present in excitonic
systems. The author of this report andcolleagues have developed a gauge-free method
for excitonic systems [2] as an extension ofKing-Smith and Vanderbilt’s formula. We
demonstrated the validity of our gauge-freeFig. 1 Exciton energy spectrum of thedipole calculation of Graphane exciton by using

monolayer hBN (left) and bulk hBN (right)

System B. We employed Quantum ESPRESSO

calculated by using BerkeleyGW package [4][3] and BerkeleyGW [4] package to computewhich is based on GW+BSE method. Red lines

excitonic wave functions based on GW+BSE

indicate GW gap.

method. In this project we calculated excitonic

146

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

047401 (2022).

References[3] P. Giannozzi et al., J. Phys. Condens.

[1] R.D. King-Smith et al., Phys. Rev. B

Matter 21, 395502 (2009).

47, 1651(R) (1993).

[4] J. Deslippe et al., Comput. Phys.

[2] H. Katow et al., Phys. Rev. Lett. 129,

Commun. 183, 1269 (2012).

Fig. 1: Supercomputer System B at SCC-ISSP.

147

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Study on structural elementary excitations at
semiconductor surfaces and interfaces
Hiroyuki KAGESHIMA
Graduate School of Natural Science and Technology, Shimane University
1060 Nishi-Kawatsucho, Matsue, Shimane 690-8504

In this project, we have been focused on
physical properties of structural elementary
excitations of semiconductor surfaces and interfaces. In this year, we have focused on
the physical properties of SiO self-interstitialin SiO2 . [1] The calculations were performed
based on the ﬁrst-principles calculation. Program package PHASE/0 was employed. [2]When Si is oxidized, a large volume expansion occurs at the interface, so Si is released
into the oxide ﬁlm in order to relax the generated strain. This is because a slightly denser
and Si-rich region is formed near the interface,and a concentration gradient of excess Si isgenerated, which tends to promote the migration and diﬀusion of excess Si toward the oxide
ﬁlm side. Moreover, the presence of excess Si
is thought to induce and to enhance structuraldeformation of the oxide ﬁlm. Therefore, thebehavior of excess Si in the near-interface oxide
ﬁlm governs strain relaxation in two ways. In
this study, we traced the path of the migrationand diﬀusion of excess Si at the atomic level,
and investigated the energy proﬁle by the ﬁrstprinciples calculations.
A quartz/Si(100) interface model with four
Si layers and four SiO2 layers was used for the
calculation. The front and back surfaces are
terminated by H, and superslab geometry witha suﬃcient vacuum layer is prepared. The in√√plane periodicity is 2 2 × 2 2, which is suﬃciently large. The unit cell contains 142 atoms.
We used plane wave bases with the cutoﬀ of
30 Ry, and norm-conserving pseudopotentials

for Si and H as well as an ultrasoft pseudopotential for O. We also used the exchangecorrelation density functional of generalized
gradient approximation (GGAPBE). We employed the Monkhorst-Pack k-point samplingof 4×4×1. Using the structure with interstitial
SiO placed at the interface as the initial structure (Fig. 1), we searched for migration diﬀusion paths. In the route search, the structure
optimization calculation was performed by ﬁxing one Si layer and H on the back surface. For
comparison, a SiO2 crystal model equivalent to
one in which only the oxide ﬁlm was taken out
and arranged periodically was also used to investigate the characteristics of the interface.
We assumed that the excess Si is interstitial
SiO in the oxide ﬁlm, and that migration diffusion consists of three elementary processes.
These are O vacancy transfer, Si coordination
number conversion, and Si bond order conversion. All of these elementary processes are effective only for migration diﬀusion of interstitial SiO, and are not considered for other formsof excess Si. In particular, O vacancy transfer
and Si coordination number conversion are essential. In order for Si coordination number
conversion to occur, O vacancy transfer must
be repeated to move O vacancies to appropriate positions. Si bond order conversion can besubstituted by these two, but it has the eﬀect
of shortening several steps at once.
Based on these assumptions, we succeeded inconstructing a transport diﬀusion path of theexcess Si from the interface to the oxide ﬁlm

148

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Figure 1: Starting atomic structure for the migration diﬀusion path of the SiO interstitial.
Large, middle, and small spheres indicate Si,
O, and H atoms, respectively.
surface. Moreover, the energy proﬁle is numerically consistent with previous experimental results. It was also found that near theinterface, migration diﬀusion is diﬃcult due tostrong structural constraint from the Si crystal side. The highest energy is 2.37 eV for
the initial structure, and the energy drops to−1.47 eV when interstitial SiO reaches the surface. This diﬀusion path we found consists of
10 steps of O vacancy transfer, 15 steps of Si
coordination number conversion, and 1 step of
Si bond order conversion. It should be notedthat Si and O belonging to SiO interstitaial at
the ﬁnal structure is diﬀerent from those at thestarting structure. SiO interstitial moves withsequentially kicking the neighboring Si and O
like a billiards, and the kicked-out Si and O
become new interstitial SiO, while Si and O
belonging to the old intersititial SiO are absorbed as a part of the oxide.
So far, we have reported that, by the ﬁrstprinciples molecular dynamics method, the migration and diﬀusion of atoms in Si-rich SiO2 isenhanced under compressive strain, [3] and by
the ﬁrst-principles nudged-elastic-band (NEB)

method, the migration and diﬀusion of the O
vacancies in SiO2 is conversely reduced. [4]Therefore, we have speculated that the movement and diﬀusion of atoms in SiO2 , which
has a large Si composition, is governed not by
the movement and diﬀusion of O vacancies butby the Si coordination number conversion due
to interstitial SiO. Our results are numericallyconsistent with these calculation results, which
supports our speculation, and suggests the importance of the behavior of interstitial SiO in
Si oxidation.
In this calculation, the barrier height ineach elementary process is not calculated yet.
For this reason, the comparison of our resultswith the experimental results and our previous computational results is unfortunately
still insuﬃcient. We are planning to calculate barrier heights by using the ﬁrst-principles
NEB method, and to compare numerical values much more in detail.

References[1] H. Kageshima, T. Akiyama, and K. Shiraishi, Matter. Sci. Semicon. Process. 162(2023) 107527 (7 pages).
[2] https://azuma.nims.go.jp[3] H. Kageshima, Y. Yajima, K. Shiraishi,
and T. Endoh, Jpn. J. Appl. Phys. 58(2019) 111004 (11 pages).
[4] K. Yata and H. Kageshima, Jpn. J. Appl.
Phys., 60 (2021) 035504 (6 pages).

149

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Exponent puzzle for metal-insulator transition in
doped semiconductors
Yosuke HARASHIMADivision of Materials Science, Nara Institute of Science and Technology
Takayama-cho, Ikoma, Nara 630-0192

The zero temperature conductivity is zero at
low impurity concentrations, and it becomes ﬁnite at high impurity concentrations. A metalinsulator transition occurs at concentrations in
between. This metal-insulator transition is a
general phenomenon of quantum transport andis known to occur in many semiconductors.
Understanding the mechanism of the metalinsulator transition leads to an understandingof the general theory of quantum transport.
Here, electrons are scattered by randomly
conﬁgurated impurities, and the phases ofwavefunctions are randomly shifted out. Those
waves interfere each other and propagation is
inhibited, resulting in the appearance of localized states. This is called Anderson localization and a metal-insulator transition driven bydisorder is called Anderson transition. Anderson transition is a continuous transition, andthe correlation length ξ diverges at the transition point as ∝ |n − nc |−ν . The critical exponent, ν, which characterizes this divergence,
plays an important role in understanding thephysical characteristics of the system. Since
the critical exponent is universal and independent of the details of the system, the criticalexponent can be used to classify systems. In
other words, when two systems have diﬀerent
critical exponents, it means that they have different intrinsic physical features and are completely diﬀerent physical phenomena.
Although there have been several experimental reports on the critical exponent of themetal-insulator transition, the proposed mech-anism has not yet been clariﬁed. There are
two values of ν ≃ 0.5 and ≃ 1.0–1.3 that havebeen reported experimentally. This problem
is called the ”exponent puzzle” and the origin of descripancy has been studied for longtime. One possible origin is the eﬀect of carrier compensation due to unintentionally introduced impurities or lattice defects, but this has
not been conﬁrmed theoretically. The purposeof this study is to elucidate the exponent puzzle by conducting a theoretical analysis considering the compensation eﬀect in order to clarify
the essential factor that causes the descripancy
in the critical exponent.
Figure 1 is a calculated electronic density ina randomly distributed impurity system. The
calculation is based on the density functional
theory and local density approximation. We
performed electronic structure calculations ofcompensated systems with spin conﬁgurations
by using a program code used in our previous
work. Positive ions and negative ions are randomly distributed in three dimensional space.
They represent donors and acceptors. We solve
the electronic states such that charge neutrality is satisﬁed, i.e., the number of electrons isequal to the diﬀerence between the number ofdonors and acceptors.
We also have examined stable impurity conﬁgurations in doped systems. The results are
opened in Refs. [1, 2].

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Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Figure 1: Total electronic density (left panel) and spin density (right panel) in a three dimensional system. Donor and acceptor ions are shown as blue and green points, respectively. In theright panel, positive and negative values denote up and down spin, respectively. The number ofdonor ions is 100, and that of acceptor ions is 50.

References[1] Y. Harashima,
et. al.:IEEE
Trans.
Semicon.
Man.,
accepted,
DOI:10.1109/TSM.2023.3265658.
[2] Y. Harashima, et. al.: arXiv:2303.14891.

151

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Phase stability of high-entropy alloys
Yoko Yamabe-Mitarai
Frontier Science Graduate School,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8561
comprise

Special Quasirandom Structure was used tomultiple elements with near-atomic composition

simulate random atomic position for ternary

and have high configurational entropy ofalloys as shown in Fig. 1. The internal

constituent elements. HEAs have been attracted

coordinates was optimized using Quantum

as new generation structural and functional

Expresso (QE). The total energy and density ofmaterials since this new paradigm was proposed

statesin 2004 [1]. Most of HEAs have a single face-coordinates. The formation energy calculated

center-cubic (fcc), body-center-cubic (bcc)from the total energy indicated Al, Sn, Hf and Zr

structures or their mixtures. Due to limited slip

stabilized hcp structure, while Nb and Mo

system, hexagonal-close-pack (hcp) structure isstabilized bcc structure.

High-entropy

alloys(HEAs)

wascalculated

on

the

optimized

expected to be high temperature materials. Largesolid-solution hardening is also expected for
HEAs. Then, we are applying to find HEAs withhcp structure experimentally and by using DFT
calculation. Ti is focused on one of constituent
element because Ti is used as high-temperaturematerials due to its small density and highspecific strength. Phase stability of alloys wasFig. 1:BCC (top) and HCP (bottom) SQS model.

experimentally investigated, and a few alloys

X is alloying elements.

were found to be a hcp structure [2]. To

References

investigate the effect of alloying elements and[1] B. Cantor, I. T. H. Chang, P. Knight, A. J. B.

composition dependence on phase stability,

Vincent, Mater. Sci. Eng. A, 375-377, 213phase stability change of bcc and hcp structures(2004).

in Ti by 6 different alloying elements was[2] Y, Yamabe-Mitarai, K. Yanao, Y. Toda, I.

calculated using DFT. Supercell model with 128

Ohnuma, T. Matsunaga, JALCOM, 911, 164849

atoms was used to indicate solid solution phase.

(2022).

152

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analysis of the electronic structure of magnetic shapememory alloy by quasiparticle self-consistent GW approach
Masao OBATA1,2
1

Institute of Science and Engineering, Kanazawa University, Kanazawa, Ishikawa 920-1192
2

Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa,
Ishikawa, 920-1192
Magnetic shape memory (MSM) alloy of Ni-

stoichiometric Ni2MnGa in austenite (cubic) and

Mn-Ga [1] has attracted attention, showing an

non-modulate martensite (tetragonal) phases byenormous magnetic field-induced strain (MFIS)

using the first-principles calculation package

effect of up to around 10%. This unique property

ecalj [3].

comes from transitions among energeticallyAs the result of the QSGW calculation, theclose structures involving nanoscale-modulated

obtained energy level of the Ni eg orbital of thestructures attributed to magnetic and electronic

cubic phase is higher than that of GGA andstats. The MFIS effect is experimentally

almost coincided with the Fermi level. The state

observed in the modulated structure of 10M or

moves from the Fermi level in the tetragonal

14M, which has a long-period crystal structurephase. This result strongly supports martensitic

in the ab plane. Although many investigations oftransformation due to the Jahn-Teller effect.

the electronic structure based on density

Analysis of the Fermi surfaces nesting throughfunctional theory (DFT) within local density

generalized susceptibility revealed that its

approximation

gradient

electronic state of cubic phase possesses

approximation (GGA) were reported, the results

intrinsic instabilities corresponding to 10M anddid not fully incorporate the experimental facts:

14M, which are not observed in the previous

for example, the stabilization mechanism of the

GGA calculation [4].

modulated structures is still unclear. The

References

importance of electron correlation effects in this[1] K. Ullakko et al, Appl. Phys. Lett. 69, 1966

material was recently indicated [2]. Thus, we(1996).

employed one of the post-DFT methods, the[2] M. Zelený et al., Mater. Des., 209, 109917

quasiparticle(2021).

orgeneralized

self-consistentGW(QSGW)

approach, to investigate the electronic structure[3] https://github.com/tkotani/ecalj/

beyond the GGA level. This study investigated[4] M. Obata, T. Kotani, T. Oda, Phys. Rev.

the electronic and magnetic structure of theMaterials 7, 024413 (2023)

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Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Calculation and comparison of adsorption energies ofperfluoro molecules on Cu(111) and Cu(100)using first-principles calculation
Yuji Ohkubo, Misa Nishino, Hiroki Toujima, and Kouji Inagaki
Graduate School of Engineering,Osaka University, 2-1 Yamadaoka Suita, Osaka 565-0871
Recently, increasing frequency of the digital

Our calculations were performed using thesignals is necessary because the amount of

STATE (Simulation tool for atom technology)

information

increasing.

code with plane-wave basis and ultra-soft

However, the higher the frequency is, the greater

pseudopotential[2, 3]. The wave function and thetheTherefore,charge density of cutoff energies were 36 andpolytetrafluoroethylene (PTFE) which has much

400 Ry, respectively. Generalized gradient

low relative dielectric constant and dielectric

exchange-correlation

loss tangent is considered as a suitable dielectricPredew-Burke-Ernzerhof (PBE) was used forof high frequency printed wiring boards.

the exchange-correlation functional and DFT-

However, PTFE has low adhesion property, so

D2 was used for the dispersion correction

adhering PTFE to Cu is difficult. We havemethod[2, 3]. Cu surface was modeled Cu(100)achieved

oxygen-containing

3×3 slab composed of 3 atomic layers. As thefunctional groups and adhesion strength of 0.94

model of as-received PTFE, CF3–CF3 was

N/mm between PTFE and Cu when PTFE wascalculated. In addition, CF3–CF=O, CF3–CF2–

He-plasma-treatedOH,

communicationtransmission

loss

generation

of

at

is.

over

pressure[1].

atmospheric

is

200℃

and

CF3–CF2–OO・

on

were

calculated as the model of plasma-treated PTFE.

calculations of the adsorption energy between

These were the models of molecule containing

Cu(111)theoxygen-containing functional groups observed

functional groups containing COO・ is possible

by C1s-XPS spectrum of the plasma-treatedto generate PTFE surface having high adhesion

PTFE surface. Cu surface, fluorinated molecules,

property. However, the calculations about Cu

and adsorption systems were optimized thensurface having different orientations are nottotal energies were calculated. The adsorption

performed. Therefore, in this study, theenergy was defined as the difference between theadsorption

andsum of total energy of Cu surface and fluorinatedfluorinated molecules was calculated and themolecules and total energy of adsorption system.

fluorinatedenergybetweenfrom

CF2=CF2,

based

the

and

Also,

under

functional

molecules,

Cu(100)effect of orientation was investigated.

Fig. 1 shows the values of adsorption

154

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

(a)

(b)

Fig. 2 Atomic geometries for CF3–CF2OO・
model (a) on Cu(111) and (b) on Cu(100).
(a)

(b)

Fig. 1 Values of adsorption energies.

energies by calculation. The values of adsorption

Fig. 3 Atomic geometries for (a) CF3–CF2O・model and (b) O model.

energies of CF3–CF3, CF3–CF=O, CF3–CF2–OH,
CF2=CF2, and CF3–CF2–OO・ was 0.25, 0.58,

In this study, the functional groups

0.72, 0.80, and 1.95 eV, respectively. In the casecontributing to improvement in adhesionof molecules containing COO・, the adsorption

property were explored by calculating theenergy was the highest and the molecule wasadsorption

stable as with Cu(100). However, in the case ofgenerating the functional groups containingthat of Cu(111). Fig. 2 shows the optimized

COO・ is possible to generate PTFE surface

atomic geometries for Cu(111) and Cu(100). In

having high adhesion property, regardless ofthe case of Cu(111), CF3–CF2–OO・ wasorientations. Also, in order to further improve

dissociated to CF3–CF2–O・ and O, then they

the adhesion property, it is important toadsorbed. However, in the case of Cu(100),
adsorbed

fluorinatedof Cu(111). In the result of calculations,4.73 eV[2]. The value of Cu(100) was lower thanwasbetweenmolecules and Cu(100) and comparing the result

Cu(111), the value of adsorption energy was

CF3–CF2–OO・

energies

dissociate CO・ and O and adsorb to Cu surface.

without

On the other hands, the calculations of Cu(110)dissociation. This is because the adsorption

and copper oxide is not performed. Therefore,

energy of Cu(100) was lower. The adsorption

these calculations are needed in the future.

energy was calculated when CF3–CF2–OO・ was

Referencesdissociated and adsorbed on Cu(100) as shown[1] M. Nishino et al., INTERFINISH2020 Abstract, C-

in Fig. 3. The adsorption energy was 5.27 eV.

SEP06-004 (2021) 210.

This value was close to Cu(111). These results[2] K. Toyoda et al., J. Chem. Phys. 132 (2010) 134703.

suggest that it is important to dissociate CF3–

[3] K. Toyoda et al., J. Nanosci. Nanotechnol. 11 (2011)

CF2–O・ and O and adsorb to Cu surface, in2836–2843.

order to further improve the adhesion property.

155

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of Efficient Evaluation Methods ofBerry-phase-mediated Physical Properties for Large
Scale Systems Using the First-principles LCPAO
MethodNaoya YAMAGUCHI
Nanomaterials Research Institute (NanoMaRi), Kanazawa University
Kakuma-machi, Kanazawa, Ishikawa 920-1192

We did the following researches about thefollowing topics in this subject: (i) development of a linear-combination-of-pseudoatomic-orbital (LCPAO) scheme of a Berryphase method to apply electric fields [1] and(ii) development of a new scheme to theanomalous Hall and Nernst conductivity applicable to metallic systems [2].
For (i), we have developed a first-principles
LCPAO scheme of a homogeneous and finite
electric field method based on the modern theory of polarization and density functional theory (DFT), so that one can consider electricfield effects even for periodic systems such as
bulk insulators. We validated our scheme bycalculating the electronic and static dielectric
constants and Born effective charges of III-V
and II-VI semiconductors and group IV insulating materials. The calculated values coincided with the reported computational values,
and they were an agreement with the experimental values. For the Born effective charges,
we confirmed that the values obtained fromour scheme are consisted with those obtained
from the finite difference method (i.e. numerical differentiation of electric polarization withrespect to atomic positions.) The spin-orbit interaction (SOI) has a non-negligible influenceon the dielectric constants of cases including
the heavy elements. We applied our schemewith the SOI to evaluate the Born effective

charges characterizing the bond properties, covalency and ionicity in new semi-stable phasesof BiTeI including a wide-gap topological insulating phase [3]. Our LCPAO implementation will make it easy to investigate the electronic structures and physical properties under an electric field even for the large system
including hundreds of atoms. In addition, we
also developed the spin texture code for insulators under electric fields through the Berryphase scheme. We did test calculations by applying the spin texture code to bulk diamond.
Bulk diamond is a system keeping the spatial
inversion symmetry, but a strong electric field
can break the symmetry to induce the spin
splitting through the Rashba effect (see Fig.
1 and 2).
For (ii), we also developed the new evaluation scheme for the anomalous Hall andNernst conductivity without constructing theWannier functions or explicit evaluation of the
Kubo formula [2]. We reproduced the intrinsic
contribution of typical anomalous Hall systems
such as body-centered-cubic iron. Our scheme
has advantages of efficiency so that it is the
non-iterative scheme unlike Wannierization.
Therefore, our scheme can easily address not
only large scale cases but also high-throughput
calculations. We applied the scheme to evaluate the peculiar magnetic thermoelectricity inthe ferrimagnetic phases of MnBi2 Te4 layers [4]156Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyoand a ferromagnetic superlattice of tetragonalFe2 Si, that is, Hapkeite [5]. We also developed
another version of the scheme based on the improved tetrahedron method. It is possible todirectly evaluate the pure term of anomalous
Nernst conductivity (ANC) even for systems
with too low the Curie temperature to obtainthe convergent values of the pure term throughthe numerical differentiation of the anomalous
Hall conductivity with respect to the chemical
potential.
We also improved the spin texture code bychanging the eigenvalue solver so that k-spacespin density matrices can be calculated morestably and efficiently. Through the code, weinvestigated a hydroxyl-terminated diamondsurface and found the electronic structure withthe persistent spin helix that is important tospintronic applications [6].
We implemented them to the OpenMX code[7], and they will be released in the future.

Figure 2: Spin texture for the Rashba spin
splitting around the valence band top at the Γpoint induced by an electric field of 3.5 GV/mperpendicular to one of the faces in bulk diamond. The length and direction of arrows
represent the magnitude and direction of the
expectation values of the spin every k-point,respectively.

References[1] N. Yamaguchi, F. Ishii, Comput. Phys.
Commun. 280, 108487 (2022).
[2] H. Sawahata, N. Yamaguchi, S. Minami,
F. Ishii, Phys. Rev. B 107, 024404 (2023).
[3] Y. Zhang, N. Yamaguchi, H. Sawahata, F.
Ishii, Appl. Phys. Express, in press, DOI:
10.35848/1882-0786/acccd3 (2023).
[4] Y. Morishima, N. Yamaguchi, H. Sawahata, F. Ishii, Appl. Phys. Express 16,
043003 (2023).

Figure 1: Band structure with the Rashba
spin splitting around the valence band top at
the Γ-point induced by an electric field of 3.5
GV/m perpendicular to one of the faces inbulk diamond. The momentum shift ∆k was
2.99 × 10−4 Å−1 , and the induced electric polarization was 12.58 µC/cm2 .

[5] T. Tominaga, N. Yamaguchi, H. Sawahata, F. Ishii, Jpn. J. Appl. Phys. 62,
SD1019 (2023).
[6] H. P. Kadarisman, N. Yamaguchi, F. Ishii,
Appl. Phys. Express 16, 023001 (2023).
[7] http://openmx-square.org.

157

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Electronic structure investigation of the Ba2PrBiO6
photocatalyst
Kazume NISHIDATE
Faculty of Science and Engineering, Iwate University
Ueda 4-3-5, Morioka, Iwate 020-8551

The surface electronic states are calculatedusing a slab model, which consists of stacked
three unit cells and the vacuum region of 16
Å . Where Ba2 PrBiO6 has the Ba-O and the
Pr-Bi polar planes alternately stacked in one
direction. The top and the bottom planes
are terminated with the same polar surface toprevent the artiﬁcial dipole-dipole interactions
over the cyclic boundary. The work function ϕis deﬁned as the diﬀerence between the vacuum
level (ϕvac ) and the Fermi level EF (Figure. 1).
We also performed the Born-Oppenheimer
Molecular Dynamics simulations of the slab toinvestigate its reactiveness to the water. In
this stage, we used the PBE functional for theexchange-correlation and employed only the Γ

Φvac
EF

Energy (eV)A large number of double-perovskite oxides, A2 B ′ III B ′′ V O6 , have been studied dueto their intriguing physical and chemical properties originating in their mixed valence nature. Where the small cations occupy theB’ and B” sites with the diﬀerent valencies.
Recently, it was found that the Ba2 PrBiO6
double-perovskite has a photo catalytic activity in the visible light. However, theoreticalanalysis on the electronic properties of its surface has not been performed. In this work, we
perfomed the ﬁrst-principles density functional
computation of the surface of Ba2 PrBiO6 . We
used the Quantum ESPRESSO (QE) package. We applied the Heyd-Scuseria-Ernzerhof
hybrid functional (HSE06) formalism for theexchange-correlation to evaluate the band gap
as well as the work function.

Z

Z (Å)

Figure 1: Averaged electronic potentials for
the Ba-O polar plane along the Z axis of thesuper-cell.
point for the reciprocal space integration to
suppress the computational time. Temperature was regulated to be 300 K throughout thesimulation time steps using the velocity scaling method. And H2 O molecule was placed at
5 Å over the Ba-O surface. There are threestages in the adsorption process. First, a H2 O
molecule approaches the surface as the resultof the Coulomb interaction between the oxygen and the surface Ba atoms (I). Then, theoxygen atom makes a bond with Ba by releasing its hydrogen atom and thereby forming ahydroxyl group. The released hydrogen atomalso makes a bond with the oxygen atom of
the slab (II). In this adsorption process, twohydroxyl groups were created. We have been
focusing on the detailed analysis on the calculated results.

158

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical Study on Electronic Properties
in New Nanoscale Surfaces and Interfaces
Katsuyoshi KOBAYASHI
Department of Physics, Ochanomizu University
2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610
sity calculated for the structure with a V-adsorbed
surface is similar to Fig. 2. But, Fig. 2 better reproduces a characteristic feature of the experimental
band dispersion. Therefore it is concluded that theV5 Se8 monolayers in the experiment of Ref. [2] havethe structure shown in Fig. 1.

Energy (eV)We theoretically studied the photoemission spectra of V5 Se8 monolayers. V5 Se8 is a layered material composed of VSe2 layers and V intercalant layers. It is known that bulk V5 Se8 has an antiferromagnetic structure at low temperatures. However,a recent experiment showed ferromagnetic behavior
in V5 Se8 thin ﬁlms [1]. We studied the electronic
structure of V5 Se8 monolayers in 2022 [2].
It may be assumed that V5 Se8 monolayers havea structure composed of two VSe2 layers and a Vintercalant layer as shown in Fig. 1(a). However, a
recent experiment [3] showed a structure that thesurfaces of V5 Se8 monolayers are covered with theV intercalant layers. In order to investigate the surface structures of V5 Se8 monolayers we performed
a density-functional calculation. We used the program package VASP for density-functional calculations.

Wave Number (Έ-1)

Figure 2: Calculated photoemission intensity of theV5 Se8 monolayer. The origin of energy is the Fermi
energy. The wave number is along the direction
perpendicular to the side view plane in Fig. 1.

Figure 1: Side view of the atomic structure of a
V5 Se8 monolayer.

References

Figure 2 shows the photoemission intensity calculated for the structure shown in Fig. 1. The photoemission intensity is a calculated band structure
weighted by the G∥ = 0 component of wave functions, where G∥ are the components of reciprocallattice vectors parallel to the surface. This is dueto that the wave functions in vacuum regions aremainly connected to the G∥ = 0 component in materials. The band structure is calculated in a nonmagnetic state because the photoemission experiment was performed at room temperatures. Theenergy bands are broadened with a width of 0.1 eV.
The calculated intensity has good agreement withthe experimental one [2]. The photoemission inten-[2] K. Sumida et al.: Phys. Rev. B 106 (2022)
195421.

159[1] M. Nakano et al.: Nano Lett. 19 (2019) 8806.

[3] Q. Meng et al.: Phys. Status Solidi RRL 16(2022) 2100601.

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Interaction of magnetic metal phthalocyanines withmetal surfaces
Tetsuya ARUGA
Department of Chemistry, Kyoto University
Kitashirakawa-Oiwakecho, Sakyo, Kyoto 606-8502

Phthalocyanine (C32 H18 N8 ) is a planarmolecule with an extended π electron system.
Two hydrogen atoms in the central “hole” ofthe molecule can easily be substitutid by a 2+transition metal ion, giving rise to metal phthalocyanine (M Pc), and thus the molecule
has two signiﬁcant electronic motifs, conjugated π electrons of a Pc molecule and an openshell d orbital of the central transition metalion.
In this work, we studied the interaction andinterface structure of the metal phthalocyanine
molecules adsorbed on bi-layer indium ﬁlms
fabricated on Si(111)-(1× 1) substrate [1] andstudied the ordering and the interaction of themolecule with the indium substrate. Experimentally, the adsorbed molecules form a twodimensional close-packed lattice. No second
adsorption layer is formed at room temperature, suggesting that the energy gain associated with the planar stacking is weak. On theother hand, the interaction of phthalocyaninewith In substrate appears to be strong, as implied by the formation of close-packed lattice
and the stability against the temperature increase.
In order to clarify the origin of the molecule–surface interaction, we performed a computational work by using VASP [2, 3, 4, 5]. We used
optB86b-vdW van der Waals density functional (vdW-DF) [6] in order to treat the interaction of the extended π-electron system of themolecule with the sp bands of the In substrate.
We used DFT+U method in order to properly

describe the electronic state of the Fe2+ ion in
the molecule. The value of U was set so thatthe magnetic moment of the Fe2+ ion in a free
FePc molecule is reproduced.
The adsorption structure predicted by thecalculation indicates that the adsorption isgoverned by two diﬀerent molecule–surface interactions. The structure obtained by the minimization of the total energy indicated two signiﬁcant characteristics that are not found in
H2 Pc, which is only weakly bound to the surface by vdW-like interaction with the metallic
substrate. Firstly, the Pc molecule is deformed
to a bowl-like structure with the molecular center down and closest to the substrate. Secondly, the Fe ion in the center of the molecule
protrude further downward and appears to be
associatively interacting with the In atoms below. These characteristics are not found for
H2 Pc and CuPc, suggesting that these arecharacteristic to M Pc molecules with open dshell M ions. The interaction between themolecule and the substrate may diﬀer depending on the number of d electrons. The eﬀect ofthese interaction on the superconductivity of
the In ﬁlm[7, 8] is intriguing.

References[1] E. Rotenberg et al.: Phys. Rev. Lett. 91,
246404 (2003).
[2] G. Kresse and J. Hafner, Phys. Rev. B 47,
558 (1993); ibid. 49, 14251 (1994).

160

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo[3] G. Kresse and J. Furthmüller, Comput.
Mat. Sci. 6, 15 (1996).
[4] G. Kresse and J. Furthmüller, Phys. Rev.
B 54, 11169 (1996).
[5] G. Kresse and D. Joubert, Phys. Rev. 59,
1758 (1999).
[6] J. Klimeš et al., Phys. Rev. B 83, 195131(2011).
[7] T. Zhang et al., Nat. Phys. 6, 104 (2010).
[8] T. Uchihashi et al., Phys. Rev. Lett. 107,207001 (2011).

161

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

In-plane interaction of π-conjugated molecules
Tetsuya ARUGA
Department of Chemistry, Kyoto University
Kitashirakawa-Oiwakecho, Sakyo, Kyoto 606-8502

Phthalocyanine (C32 H18 N8 ) is a planarmolecule with a 2D extended π-conjugatedelectron system. Two hydrogen atoms in thecentral “hole” of the molecule can easily besubstituted by a 2+ transition metal ion, giving rise to metal phthalocyanine (M Pc).
The adsorption of M Pc on single-crystalline
metal surfaces has been studied by several
groups. In these works, irrespective of thesubstrate, M Pc molecules form ordered twodimensional lattice, which has common characteristics as below: (1) the molecule adsorbs
with its molecular plane parallel to the surface, (2) the molecules form nearly square lattice that is commensurate with the substratelattice, (3) the molecules are rotated in planeby ∼ 20◦ from the symmetrical direction of thesubstrates and forms a staggered structure.
The ﬁrst point is understood by the fact thatthe adsorption is mostly governed by the vander Waals interaction between the surface andthe molecule. The second point is due to theshape of the molecule, which prefers squarelike lattice to maximize the coverage. The
third point is not obvious. Previous authors
claimed that this is due to the direct chemicalinteraction of N atoms in the molecule with aparticular atoms of the surface, which however
has not been conﬁrmed by quantitative methods.
In this work, we studied (1) the interaction among metal phthalocyanine molecules
adsorbed on bi-layer indium ﬁlms fabricated on
Si(111)-(1× 1) substrate [1] and (2) the interaction among metal phthalocyanine moleculesin the same geometry as in (1) but without thesubstrate.

The total energy was computed by using
VASP code [2, 3, 4, 5] as a function of azimuthal rotation angle. The total energy forthe case (1) shows decrease with increasing azimuthal angle from 0◦ and get minimum at∼20◦ . Further increase of the azimuthal angle leads to the divergence of the total energy due to the direct contact of the neighboring molecules. The energy minimum at∼ 20◦ is in good agreement with the observation. The case (2) gave rise to an almost thesame angular dependence but with the amplitude 60% ∼ 70% of the case (1).

The results indicates that the rotation of
the molecule is induced by the intermolecular interaction, which most probably is dipoledipole interaction between C-H groups of themolecule. The energy minimum is achieved
when the C-H bonds with opposite directionof neighboring molecules approach with eachother most closely. Our calculation does notindicate any signiﬁcant contribution of the direct interaction of molecular N atom with thesubstrate. The reduced interaction in the case(2) suggests that the image dipoles inducedin the substrate (bilayer In) are smaller instrength, which is most probably due to theultra-thinness of the substrate In bilayer, inwhich the metallicity of the lower In layer ismostly lost due to the bonding with substrate
Si atoms.

162

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

References[1] E. Rotenberg et al.: Phys. Rev. Lett. 91,
246404 (2003).
[2] G. Kresse and J. Hafner, Phys. Rev. B 47,
558 (1993); ibid. 49, 14251 (1994).
[3] G. Kresse and J. Furthmüller, Comput.
Mat. Sci. 6, 15 (1996).
[4] G. Kresse and J. Furthmüller, Phys. Rev.
B 54, 11169 (1996).
[5] G. Kresse and D. Joubert, Phys. Rev. 59,
1758 (1999).

163

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Atomic structures and electronic properties ofnanocarbon-based materials
Yoshitaka FUJIMOTO
School of Engineering, Kyushu University
Moto-oka, Fukuoka-city, Fukuoka 819-0395

Graphene is one of the most promissing
materials for electronics devices such as fieldeﬀect transistors and molecular sensors. It
has been reported that the boron atom ingraphene could act as a reactive site for theadsorptions of environmetally polluting NO
and NO2 molecules. [1] Furthermore, the B
atoms in bilayer graphenes are also reported
to enhance the adsorption properties of several
molecules, leading to the possibility to fabricate the highly sensitive NOx sensors. [2, 3, 4]However, it might be diﬃcult to detect harmful
CO molecules using B-doped graphene. Carbon nanotube (CNT) is also expected to be
one of the most promising materials for development of sensors due to its high surfaceto-volume ratio of one-dimensional nanostructures and its excellent electrical conductivity.
Here, we report the adsorption properties ofenvironmetally polluting NOx and harmful CO
molecules on CNTs. [5]We examine the atomic structures of Bdoped and N-doped (10,0) CNTs without theadsorbed molecules. The zigzag nanotubes
such as the (10,0) CNT have two kinds of CC bonds around each atom. In the B-doped
case, two kinds of the B-C bond lengths arefound to be 1.47 Å and 1.50 Å. In the case of
the N-doped case, the C-N bond lengths are
1.37 Å and 1.40 Å. The B-C bond lengths aremuch longer compared with two kinds of the
C-C bond lengths (1.40 Å and 1.41 Å) in apristine (10,0) CNT, while the two kinds of NC bond lengths are slightly shorter than thecorresponding C-C bond lengths. In addition,
the B-C and N-C bond lengths are longer andshorter than those of B-doped graphene (1.47
Å) and N-doped graphene (1.40 Å), respec-164

tively.
We also examine the adsorption propertiesof various molecules including environmentally
toxic molecules on the B-doped and N-doped(10,0) CNTs. Table I lists the adsorption energy and the distance between the moleculeand the B (C) atom in the B (N)-doped (10,0)
CNTs. For the B-doped cases, CO, NO, NO2
and O2 molecules are found to be strongly
adsorbed with relatively large adsorption energies as well as the short binding distances,while CO2 and N2 molecules are weakly adsorbed. For the N-doped CNT, it is reported
that the adsorption energy of a H atom ata neighboring C atom is larger than that at
the dopant N atom itself. Here, we examine
the adsorption of all six types of molecules
at the C atom sites next to N-dopant atoms
in the N-doped CNTs. It is found that only
NO and NO2 molecules are strongly adsorbed,
while the adsorption energies of the remaining four molecules (CO, CO2 , O2 , and N2 )are relatively small and at the same time
the binding distances between molecule and C
atom are relatively long. It is interesting thatthe adsorption energies of these molecules on
the B-doped and N-doped CNTs are overalllarger than those on the B-doped and N-doped
graphenes, respectively, due to the curvatureeﬀects of the nanotubes.
In summary, we have investigated theadsorption eﬀects of environmentally toxic
molecules on atomic structures and energeticsof B-doped and N-doped (10,0) CNTs based on
the first-principles electronic structure study.
The B-doped CNTs can strongly bind with
CO, NO, NO2 and O2 molecules, while CO2
and N2 molecules are not strongly but weakly

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Table 1: Adsorption energy Ea (eV) and distance d (Å) from the B (C) atom for each molecule
adsorbed on B (N)-doped (10,0) CNTs.
CO2
O2
N2
NO
NO2
CO
B-doped Ea −1.32 −1.82 −0.46 −0.06 −0.36 −0.23
d
1.75
1.56
1.54
2.77
1.59
2.71
N-doped Ea −0.97 −0.91 −0.08 −0.07 −0.13 −0.23
d
1.66
1.53
2.74
2.75
1.70
2.84

adsorbed. The N-doped CNTs can strongly
bind with only NO and NO2 molecules in air.
The environmentally harmful NO and NO2
and toxic CO molecules are individually detectable by using B-doped and/or N-doped
CNTs.

References[1] Y. Fujimoto and S. Saito, Jpn. J. Appl.
Phys. 58, 015005 (2019).
[2] Y. Fujimoto and S. Saito, Chem. Phys.
478, 55 (2016).
[3] Y. Fujimoto and S. Saito, Appl. Surf. Sci.
Adv. 1, 100028 (2020).
[4] Y. Fujimoto, Mod. Phys. Lett. B 35,
2130001 (2021).
[5] Y. Fujimoto and S. Saito, J. Electrochem.
Soc. 169, 037512 (2022).

165

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Effects of Element Substitution on Molecular Packing andBand Structures in Single-component Molecular Conductors
with Canted Antiferromagnetism
So YOKOMORI
Department of Chemistry, College of Science
Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima, Tokyo, 171-8501

We have investigated the syntheses andelectronic

properties

molecular

conductorsofenergy-correction, by exchanging the original

single-component
exhibiting

elements in the crystal structure of thecanteddiethoxybenzene-fusedgolddithiolene

antiferromagnetism (CAF). The occurrence ofcomplex with other elements. As a result, theCAF in molecular conductors is exceedingly

following findings were unveiled: substituting

uncommonthe

Se led to a reversal of the magnitude of J1 andcorresponding structure-property relationships

J2, as well as a decrease in the bandwidth. This

have yet to be fully disclosed. Recently, asuggests

single-component molecular conductor withsignificantly affect the CAF behavior. In the S-

CAF was produced through the use of a

substituted complex, an interaction appeared

diethoxybenzene-fused

dithiolene

along the inter-conducting layer direction andcomplex (see Fig. 1). In this investigation, wethe bandwidth increased. This outcome implies

centered our attention on the high modulatorythat the dimensionality of spin-spin interaction

capability of substituting elements in theis stronger than that of the original complex,

complex. To enable an effective evaluation ofand thus, the transition temperature of CAF

the systematic structure-property relationship inordering transition could be expected. For the

CAF molecular conductors, we computed the

N-substituted complex, no significant changes

band

element-substituted

were observed except for a slight decrease incomplexes to aid in the synthesis of new

the bandwidth. Therefore, it can be concluded

compounds.

that the priority of synthesizing this complex is[1],

structures

and

of

as

a

gold

result,Band calculations for three kinds of element-

that

Se

substitution

would

low. Accordingly, in this investigation, we

substituted complexes (as depicted in Fig. 1)

successfully

were executed using OpenMX 3.9 software.

complexes should be synthesized next.

For these calculations, the crystal structures

Referenceswere optimized by means of the DFT-D3[1] R. Ishikawa et al., J. Phys. Soc. Jpn., 87,

method which involved vdW- and dispersion

064701 (2018).

166

gainedinsights

into

which

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Fig. 1. Structural formula of the complex of CAF molecular conductor and newly designed elementsubstituted complexes, and calculated band structures. An explanation of band structure changes foreach result are shown in the bottom.

167

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First principles study on the band structures of high entropy
compounds
Hidetomo USUI
Department of Physics and Materials Science,
Shimane University, Nishikawatsu-cho, Matsue, Shimane 690-8504

High-entropy alloys are alloys containing

various elements, spectral weight is reduced. It

five or more elements at one site. Recently,

can be understood that substitution by elements

high-entropy compounds have attracted muchin other groups can suppress the quasiparticle

attention not only from a mechanical point oflifetime but can control the band structure

view but also as functional materials such asaround the Fermi level.

thermoelectricmaterials.[1,2]electronic

and
We

have

structureofcompound MTe

superconducting
investigated
a

high

the

entropy(M = Ag, In, Sn, Pb, Bi),

which exhibits robustness of superconductivity
to external pressure[3, 4]. This year, we
calculated the electronic band structure of MTein the rock salt typed crystal structure using the
VASP package within the PBE-exchange
correlation functional with spin-orbit coupling
included. We used a 2×2×2 supercell of MTe(Sn16Pb16Te32,

In11Pb10Bi11Te32,

In8Sn8Pb8Bi8Te32, and Ag8In6Bi6Sn6Pb6Te32).
We calculated the site arrangement of M atoms
using

the

special-quasi

randomFig. 1: Electronic band structure of MTe

References

structure

implemented in Alloy Theoretic Automated[1] B. Jiang et al., Science 371, 830 (2021)

Toolkit. We took a k-mesh spacing of 0.1 Å-1[2] P. Koželj et al., Phys. Rev. Lett., 113,

and a cut-off energy of 330 Ry. The unfolded

107001 (2014).

electronic band structure of MTe is shown in[3] Md R. Kasem et al., Sci. Rep 12, 7789

Fig. 1. It is found that the band structure for(2022)

M=Sn, Pb exhibits sharp spectral lines, but for[4] Y. Mizuguchi et al., Mater. Today Pnys. 32,

M = Ag, In, Sn, Pb, and Bi, due to a mixture of

101019 (2023)

168

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study of interfacial magnetic
structure in topological magnets
Susumu MINAMI†,‡ , Yuta TOGA† , Katsuhiro TANAKA††
Department of Physics, Univeristy of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033‡
Department of Mechanical Engineering and Science,
Kyoto University, Nishikyo-ku, Kyoto 615-8540

Topological magnetic materials such as
Mn3 Sn and Mn3 Ge exhibit unique properties
due to their particular band structures (Berryphase) and have attracted attention as coreelements for antiferromagnetic spintronics devices. Recently, ﬁnite tunneling magnetoresistance (TMR) eﬀects have been observedat room temperature in the magnetic tunneling junctions (MTJs) with Mn3 Sn [1] and
Mn3 Pt [2], increasing the demand for researchon the interface in antiferromagnetic MTJs.
This research project employed the Quantum ESPRESSO, a ﬁrst-principles calculation code, to analyze the Mn3 Ge/MgO MTJ
and its interface, which have the non-collinear
magnetic conﬁguration.
Due to its noncollinear magnetic structure, the computational cost and output data volume signiﬁcantly increased, and the convergence worsened, necessitating the use of the ISSP Supercomputer.
The study presents the magnetic momentsof the Mn layers at the vacuum surface andwithin the MgO multilayer ﬁlm, with energybased optimization of interfacial distances.
Figure 1 shows the layer dependence of themagnetic moments of the Mn atoms. While
the magnetic moments increase at the vacuum
surface due to increased electron localization,
this increase is not observed at the MgO interface for some Mn positions. The diﬀerent
surface states inﬂuence the magnetic momentsof Mn atoms inside the interface.

Figure 1: Magnetic moments of the Mn atoms
near the surface and the interface.
As the performance of MTJs is inﬂuenced by
the magnetic state near the interface, future
research will investigate charge transfer, ﬁlm
thickness dependence, and their relation to thetunnel conductance.

References[1] X. Chen et al., Nature 613, 490 (2023).
[2] P. Qin et al., Nature 613, 485 (2023).

169

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170

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References
D@E# GF# 9)%*3# LF# K,%+2)%3# MF# ]2)%3# %,&# ;F#
G1+*-1)*3#^$/7F#L">F#_ !"3#@@[TNR#8NU@R<F
DNE# `F5KF# K4%-%3# MF# G%S%$%7$*3# 9F# O7$*/%+%3# GF#_1S23#]F#?$*)%*7$*3#?F#OS%&%3#%,&#]F#a%C%,%3#`F#
b1+(2-F#^$/7F###!3#NWWQ#8NU@U<F
DWE# ^F# ^123# ?F# 9F# c$%7"+*3# ^F# `".*,"S3# GF:*=F#N#:1)6"f&*7-%,6"#87"(%)%-*1,<#62)>"#4*-$#-$"# 1(-*+*P"&# 7-)26-2)"7# 10# -$"# ?*# -*(# %,&#?*8@@@<58ABA<#72)0%6"3# 6%.62.%-"&#C/#L?M:GF

171d",17S/3# ?F

c1"&"6S")# %,&Z%,1-"6$,1.1=/#

#$3#

LF

NeTU@[#^")"P3#8NUUQ<F

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

A study of nickelate superconductors in first-principles
Hirofumi SAKAKIBARA
Department of Engineering,
Tottori University, Tottori, Tottori 680-8525
A

recently

discovered

superconductor

theory and first-principles calculation [5]. In the

NdNiO2 [1] attracts broad interests among thetheory, by applying fluctuation exchange

field of low-temperature physics because of its

approximation (FLEX, Ref. 6) on a seven-orbital

cuprate-likemodelelectronic

structure.

Namely,constructedin first-principle

with

NdNiO2 has infinite layered structure to havemaximally localized Wannier orbital [7], it ismonovalent nickel atoms in which the electron

revealed that the first-principles Hubbard U

configuration is 3d9, the same with the copper

obtainedsite of cuprates. This striking similarity

approximation (cRPA, Ref. 8) is much stronger

motivates researchers to compare the nickelates

than that of cuprates. Therefore, the self-energy

and the cuprates for the purpose of unveiling theinduced by spin-fluctuation damps quasi-

high-Tc pairing mechanism [2].

particles weight to degrade Tc. The main reason

in

constrained

randomphase

However, the nickelates also have severalof this larger U in the nickelates is the muchdissimilarity: (1) Tc is lower (up to 20K, wherelarger energetical splitting Δdp between nickelthat of cuprates are up to 135K), (2) no long-

ion and oxygen.

rangemagnetismsuperconducting
temperature

on

the

vicinity

dome

in

the

phase

diagram,ofConsidering the above numerical results, we

carrier-can easily imagine that Tc in nickelates goes up

(3)

no

by applying hydrostatic pressure that may lower

superconductivity in the bulk materials [3]. Even

U and/or U/t values, where t is the hopping

the feature (1) and (3) is still under intense

integrals of the 3dx2-y2 orbitals between nearest

debate, however, some consensus for (2) is being

neighbor sites. In this research, to confirm thisformed. Namely, since the energy bands formed

idea, I have constructed the seven-orbital modelby lanthanoid atoms overlaps with 3d bands ofby obtaining stable crystal structure under

nickelate unlike cuprates, the self-doped holeshydrostaticfrom the lanthanoid site break magnetic order socomputationalthat no magnetic phase is observed [4,5].

package (QE, Ref. 9) and RESPACK [10]pressuredetails,(0GPa--20GPa).
quantumForespresso

A theory is proposed to interpret the feature

officially implemented in the system B are(1) based on the combination of many-body

employed and the bulk crystal structure is172

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

assumed. It is found that the U/t value becomes

it is found that U itself is roughly scaled by thesmaller by hydrostatic pressure, where the value

valence of nickel atom. These results give us aof t is simply scaled by the lattice constant alonghint to optimize U/t value for seeking higher Tc

the a-axis (along the layers). By performing

materials such as cuprates. As a future task, I

FLEX calculation assuming such smaller U/twill challenge to theoretically explain the recent

value, the larger λ, the eigenvalues ofexperimental result of praseodymium nickelate

Eliashberg equation, is obtained. This means

thin firm in which Tc gets significantly higher bythat Tc may get higher if the hydrostatic pressure

applying pressure [11].

is applied on nickelates.

References

Interestingly, the value of U itself remains
almost constant (or, slightly gets larger) when

[1] D. Li et al., Nature (London) 572, 624 (2019).

the applied pressure gets stronger. To give[2] M. R. Norman, Physic 13, 85 (2020).

deeper insight to this result, I have calculated the[3] Q. Li et al., Communications Materials 1,

value of U in cRPA by varying the valence of1(2020).

nickel atoms. Namely, I have performed virtual[4] A. S. Botana and M. R. Norman, Phys. Rev.

crystal approximation (VCA) for two Sr-doped

X 10, 011024 (2020).

systems La1-xSrxNiO2 and Nd1-xSrxNiO2, where[5] H. Sakakibara et al., Phys. Rev. Lett. 125,

the nickel’s valence is simply formulated as 1+x.

077003 (2020).

In this calculation, the value of U gets smaller as[6] N. E. Bickers et al., Phys. Rev. Lett 62, 961

the valence gets smaller. By constructing the so-(1989).

called d-p model considering all of the 3d-[7] N. Marzari and D. Vanderbilt, Phys. Rev. B

orbitals and 3p-orbitals, it is found that Δdp is

56, 12947 (1997).

roughly scaled by the valence of nickel atoms.

[8] F. Aryasetiawan, Phys. Rev. B 70, 195104

To summarized, I have performed mainly(2004).

two types of calculations employing QE+ R[9] P. Giannozzi et al., J. Phys.: Condens. Matter

ESPACK to capture the possible variation of U/t

21, 395502 (2009)

value in the infinite layered nickelates: structural[10] K. Nakamura et al., Comp. Phys. Comun.

optimization

261, 107781 (2021).

underpressureandVCA

calculation nickelates. The value of U/t may[11] N. N. Wang et al., Nat. Commun. 13, 4367

decrease by hydrostatic pressure while U itself(2022).

possibly remains constant. By VCA calculation,

173

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Growth mechanism of MoS2/MoO2 core shell nanowires
studied by DFT calculation
Toshihiro SHIMADADivision of Applied Chemistry, Faculty of Engineering, Hokkaido University,
Kita 13 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628
We have experimentally found that MoS2

concluded that the MoO2 nanowires are grown

nanotubes with rectangular cross sections arefrom some other precursors with excess oxygen.

grown in certain conditions by chemical vapor

Table 1. Surface Energies of Various Faces ofdeposition. After the detailed study of the

MoO2
Faces
(011)
(101)
(110)
(-111)(11-1)(010)(-101)

growth conditions using turbulent flow, wefound that MoO2 nanowires are formed first,
and the surface is sulfurized to make
MoS2/MoO2 core shell nanowires as shown inelectron microscopy images in Fig. 1[1].

Surface energy /Jm-2
2.25
1.84
2.36
2.55
2.55
1.30
1.75

Fig. 1 : Transmission electron microscope
images of MoS2/MoO2 core shell nanowires.
(reprinted with permission: American Chemical
Society[1])In order to elucidate the mechanism of thisgrowth feature, we used DFT calculation

Fig. 2 : Optimized structures of MoO2 surfaces.

(VASP). We studied the surface energies of theReferences

precursor MoO2 (Table 1 and Fig. 2).

[1] M. Goto, I. Yamane, S. Arasawa, T. YAnase,We found that the surface energies do not so

S. Yokokura, T. Nagahama, Y.Chueh, Y. Shin, Y.

differ with each other as to explain the

Kim and T. Shimada, ACS Omega 7, 39362-

nanowire growth by surface stability effect. We

39369 (2022).

174

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles calculation of graphitization of diamondsurface and its exfoliation process
Kouji INAGAKI
Graduate School of Engineering, Osaka University
Yamadaoka 2-1, Suita, Osaka 565-087

Diamond is a material with a highest

not significantly changed by the separation of

mechanical strength and has been applied as

the interface. However, it was found that the C-

cutting tools. However, serious wear occurs in

C bonds at the diamond-Fe interface can be

cutting ferrous materials. As the cause,cleaved by Fe with a low activation barrier ofoxidation of the diamond surface, diffusion ofless than 1 eV, as in catalytic reactions.

carbon atoms into iron, graphitization and its

Furthermore, at the interface where the reaction

exfoliation, etc. have been proposed, but theytakes place, the graphitized layer is found to be

are still unclear. It is well known that graphite

exfoliatedis generally formed on diamond surfaces. The

separation. This study will be submitted forwear is most likely caused by the exfoliation of

publication soon.

this graphite layer. Following the study ofReferences

diamond surface oxidation [1], graphitization[1] J. I. Enriquez, F. Muttaqien, M. Michiuchi,

and its exfoliation on diamond surfaces were

K. Inagaki, M. Geshi, I. Hamada, and Y.

investigated. We found that for a simple

Morikawa Carbon 174, 36-51 (2021).

by

the

subsequentinterfacediamond-Iron interface, the diamond surface is

(a)

(b)

Fig. 1: Peeling of graphitized diamond surface in the separation of diamond and iron interface.
Yellow and red spheres represent carbon and Fe atom. (a) Formed interface between stepped
diamond (111) and Fe (110) surfaces. (b) After interface separated.

175

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

AB type 2D materials database construction by DFT
Masahiro FUKUDA
Institute for Solid State Physics,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8581
Demand for high-throughput calculations
based on the DFT is increasing rapidly due todevelopments in data science and artificial
intelligence. In our previous research, weconstructed a structure map [1] and a webbased database [2] of AB2 type monolayers byhigh-throughput

DFT

calculations

using

Fig.1: Structures map of AB type monolayers.

OpenMX. These data also provided on the ISSP

References

data repository [3].

[1] M. Fukuda, J. Zhang, Y.-T. Lee, T. Ozaki,

In this project, a program code to perform
high throughput electronic and phonon band

Mater. Adv., 2, 4392 (2021).

and DOS calculations by using OpenMX [4][2] Structure map and database of AB2 type 2D

and Alamode [5] with Spglib [6] werematerials (www.openmx-square.org/2d-ab2/).

developed to construct materials database. In[3] Structure map of AB2 type 2D materials byaddition, the developed job scripts for massivehigh-throughput DFT calculations

parallel bulk jobs using GNU parallel package[4] OpenMX, http://www.openmx-square.org

enable us to perform high throughput DFT[5] T. Tadano, Y. Gohda, and S. Tsuneyuki, J.

calculations on the ISSP supercomputer ohtaka

Phys.: Condens. Matter 26, 225402 (2014).

effectively and comfortably.

[6] Spglib package (github.com/atztogo/spglib/).

These developed program codes are[7] OpenMX database of Atoms using standard

applied to the AB type structure map (Fig.1)

basis sets, OpenMX database of bulks using

construction,

standard basis set

basicmaterials

database

construction [7], material search for quaternary[8] R. Koshoji, M. Fukuda, M. Kawamura, T.

metal hydrides [8], and AFM simulations toOzaki, Phys. Rev. Materials 6, 114802 (2022).

determine atomic arrangement of Si adatom on[9] Y. Adachi, Z. Runnan, W. Xinbo, M.

the Silicene/Ag(111) surface [9]. Au2X type

Fukuda, T. Ozaki, Y. Sugimoto, Appliedmonolayer study is currently being carried out.

Surface Science, 157336 (2023).

176

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Exploring dopants aiming at achieving high bulk insulation in
Pb-based topological insulators
Yuki TOKUMOTO
Institute of Industrial Science,
The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8505

PbBi2Te4 topological insulator (TI) is

proposed by Perdew, Burke, and Ernzerhof

considered as one of the promising candidates(PBE) as the exchange correlation energy

for future spintronics material with a large spinfunctional. For all calculations, we included

current density. However, experimental studies

spin-orbit coupling (SOC). We obtained bandof its surface transport properties have not yet

gap of 115 meV for PbBi2Te4, which is muchbeen reported, owing to a lack of bulk

lower than experimentally reported value ~230

insulating crystals. So far, we achieved bulk

meV. In order to estimate band gap moreinsulating states in Pb(Bi,Sb)2Te4 topologicalaccurately,

insulators by tuning compositional ratio of Bi(HSE06) and HSE03 hybrid functional wasand Sb [1]. Furthermore, we recently revealed

employed. As a result, band gap was further

that In doping for Pb(Bi,Sb)2Te4 TI is effective

underestimated. We found that the HSE is not

for further lowering carrier concentrations andeffective for accurate estimation of band gap ofbulk resistivities, which is considered to be dienarrow-gap semiconductors.

theHeyd-Scuseria-Ernzerhof

to a localized impurity band that acts as a

In future, we plan to calculate electronic

charge buffer occurring inside the bulk band

structure of In-doped Pb(Bi,Sb)2Te4 using

gap.

GGA-PBE including SOC.

We carried out band structure calculation of
PbBi2Te4 based on density functional theory

References(DFT)[1] Y. Hattori, Y. Tokumoto, and K. Edagawa:using

Viennaab-initio

simulation

package (VASP) version 6.2.1. We adopted

Phys. Rev. Mater. 1 (2017) 074201.

generalized gradient approximation (GGA)177

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Dielectric function calculations in rare-earth-metal monoxides
Takayuki MAKINO
Research Center for Development of Far-Infrared Region,
University of Fukui, Bunkyo, Fukui, 910-8507

Oxygen in metals is an important and rapidly

be able to determine in ab-initio manner.

expanding field of theoretical and experimental

Second, we should also introduce the Hubbard

study. One of studies is characterization of theenergy on the oxygen. We used a HP

electronic structure of metals containing a

executable

includedindissolved oxygen or ordered oxide phases.

ESPRESSO

package[3].

Compared to the oxygen adsorption metals, anintroduction of the antiferromagnetic order

ordered oxygen is more manageable because it

tends to open the gap even with smaller

can be handled within the framework of band

Hubbard energy. To reconcile with thistheory. Owing to the metastable open-shell

experimental result (paramagnetic), we should

divalent ions, the ground state of rare-earth-assume the antiferromagnetic order is effective

metal monoxides are not trivial. In some cases,

only within a short-range. To check this, we

it results in a metallic ground state, while inconfirmed that the antiferromagnetic insulatingother cases, it yields in an insulator. Theseground state is energetically favored.

monoxides can be viewed as prototypes of thethe

Quantum

Finally,the

The Hubbard energy for the rare-earth islarge number of metallic monoxides which

evaluated to be ca. 1 eV. The calculation underform in the same NaCl structure.

this condition yielded in a metallic ground state.

According to pioneering work [1], lineshape

If we wish to open the gap, the Hubbard energy

analysis of the spectra revealed that a certain

must be 9 eV. This fact made the authors

rare-earth monoxide is an indirect-type narrow-reconsider about a ground state of our rare-

gap Mott-Hubbard insulator, having a gap of ca.

earth-metal monoxide system.

0.2 eV [1]. The author has tried to reproduce

We used a 50 Ry energy cutoff for thethis in the DFT- based calculation. To open theelectronic wave functions and a small smearing

gap, there are representative three knocks. First,

width of 0.02 Ry which required a 6×6×6 k-

we should introduce an on-site Coulomb energy,

point mesh. Adopted pseudopotentials arewhich is otherwise known as the Hubbard

based on the projector augmented-wave method.

energy [2]. Recently this has been turned out to178

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

We introduced that (Up) on the p orbital of thesynthesized in a thin film state. Then, we areoxygen atom. The value of Up (ca. 21 eV) has

interested in the Hubbard energy dependence ofbeen determined by the self-consistent linear

the optical conductivity and dielectric function

response

spectra for this compound.

approach.

To

implementtheantiferromagnetic ordering, we adopted four-

We are now calculating various types of theatom-configuration including two cations with

opticalup and down spins.

spectrafor

thisrare-earth-metalmonoxide. We used the Wannier executable

The judgement for narrow-gap insulator has

included in the Quantum ESPRESSO package

been based on the absorption spectrum. The[3]. By increasing the Hubbard energy in the

Drude edges are less noticeable viewed in thisDFT calculation, the infrared divergence in the

spectrum. It is no longer true in cases ofconductivity spectrum is suppressed. On one

photoconductivity

function,

hand, in addition to the optical absorption

dominated by large Drude tails. The authors [1]spectrum, we are now constructing the opticalhave presented the dependence of the electricalconductivity spectrum based on the same set of

conductivity on the partial oxygen pressure

the measured data, i.e., transmissivity andduring the growth. They identified that thereflectivity.

ordielectric

specimen showing the lowest conductivity
should be classified into a narrow-gap insulator
rather than a (correlated) bad metal. We
speculate that even this one should be a gaplesscompound. In the measurement of thin films, it

References

is impossible to accurately and precisely[1] K. Kaminaga et al., ACS Omega 2018, 3,

quantify the small optical absorption coefficient

10, 12501.

region. Accurate information in the region of[2] B. Himmetoglu et al., Phys. Rev. B. 84,

small coefficients is essential for determining

115108 (2011).

whether it is indirect or direct transitions. This

[3] P. Giannozzi et al., J. Phys.: Condens.

condition cannot be satisfied in the case of ametastable

substance

that

can

only

Matter 21, 395502 (2009).

be

179

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Electronic Structure and Fermiology of d- andf-electron compounds
Isaki Kinjo, Juno Iraha, Yasutomi Tatetsu1 , and Takahiro Maehira2
Graduate school of Engineering and Science, Nishihara, Okinawa 903-0213
1
Center for Liberal Arts Education, Meio University, Nago, Okinawa 905-8585
2
Faculty of Science, University of the Ryukyus, Nishihara, Okinawa 903-0213

TaC
100 [%]

2.0
1.9
1.8
1.7
1.6
1.5
1.4
1.3
1.2
1.1
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0

EF

W
Z

Γ

L
Q

Λ

Γ

X K
Δ

Ta d component

Energy [Ry]The calculation for an energy band structureof TaC was carried out using a relativistic linear augmented-plane-wave (RLAPW) method.
f electrons are assumed to be itinerant andthe calculation is performed in the paramagnetic phase. Note here that relativity should
be taken into account, because of large atomic
numbers of the constituent atoms. The spatial shape of the one-electron potential is determined in the muﬃn-tin approximation, andwe use the exchange and correlation potential
in the local density approximation (LDA)[1].
The crystal structure of TaC is categorized into
the NaCl-type structure, which is characterized by the space group Fm3m[2, 3, 4, 5, 6, 7].
The iteration process for solving the Dirac oneelectron equation starts with the crystal charge
density that is constructed by superposing therelativistic atomic charge densities for neutral atoms Ta([Xe]4f 14 5d3 6s2 ), and C(2s2 2p2 ),where [Xe] symbolically indicate the closed
electronic configuration for xenon. In Figure 1,
we show the energy band structure for TaC
along the symmetry axes in the Brillouin zone
in the range from 0.0 to 2.0 Ryd. First notethat in the vicinity of the Fermi level EF located at 1.2860 Ryd., there occurs hybridization between Ta 5d and C 2p states. The number of the valence electrons in the APW spherepartitoned into the angular momenta is 0.612(s), 0.993 (p), 3.327 (d) and 0.381 (f ) in the
Ta sphere, 0.570 (s), 1.044 (p), 0.006 (d) and
0.000 (f ) in the C sphere. There are 2.012 va-0Σ

Figure 1: Energy band structure for TaC calculated by using the self-consistent RLAPW
method.EF indicate the position of the Fermi
level.The contribution of Ta-5d electrons to theEnergy band is illustrated by color, where redcorresponds to 100% (Ta-5d).

lence electrons outside the APW sphere in theprimitive cell.
Now we discuss the Fermi surfaces of TaC.
Since the lowest four bands are fully occupied,
as shown in Figure 1, the next three bands
are partially occupied, while higher bands are
empty. Namely, the 5th, 6th, and 7th bands
crossing the Fermi level construct the hole orelectron sheet of the Fermi surface, as shown180

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

(a)

0

(b)

100 [%](c)

100 [%]

00100 [%]

Figure 2: Calculated Fermi surfaces of TaC for (a) 5th band hole sheets, (b) 6th band electron
sheets, and (c) 7th band electron sheets. Colors indicate the amount of 5d angular momentum
character on each sheet of the Fermi surface. Red-shift indicate the increase of the admixtureof d electrons. The center of the Brillouin zone is set at the Γ point.
in Figure 2. Note that the Fermi surfaces from
5th, 6th, and 7th bands are shown in (a), (b),and (c). The Fermi surface from the 5th bandconsists of two equivalent small hole sheets
centered at the K points and one large hole
sheet centered at the Γ point. The 5th band
constructs a large hole sheet centered at the Γpoint, which exhibits a complex network consisting of big “arms” which lie along the edgesof Brillouin zone, as observed in Figure 2(a).
The hole sheet centered at the Γ point is shownin Figure 2(b). It looks like a rounded cube
having eight bumps in the <111> directions.
The 7th band constructs a small electron sheet,
which is centered at the Γ point is shown in
Figure 2(c). The total number of holes is notequal to that of electrons, which represents
that TaC is a uncompensated metal. Let us
turn our attention to the analysis of the angular momentum character of the states forming
various sheets of the Fermi surface. Here themost important quantity is the amount of Ta
5d character, which is the partial density ofstates for Ta 5d state for each point in k-spaceon the Fermi surface. This quantity is visualized in Figure 2, where the admixture of the Ta
5d states is increased as the red shift in color,
as shown in the scale diagram. The broad vari-ation of the color from blue to red reflects a
substantial variation of the 5d contribution fordiﬀerent groups of states which change in therange from about 15% to about 80%. However,this distribution is diﬀerent from part to parton the Fermi surface.

References[1] O. Gunnarsson and B. I. Lundqvist: Phys.
Rev. B 13 (1976) 4274.
[2] Nowotny H., and Kieﬀer R.Z.: Metallkd.
38 (1947) 257.
[3] Allen P.B., and Cohen M.L.: Phys. Rev.
Lett. B29 (1972) 1593.
[4] Klein B.M., and Papaconstantopoulos
D.A.: Phys. Rev. Lett. B32 (1974) 1193.
[5] Mulokozi A.M.: J. Less-Common Met. 79(1981) 139.
[6] Allison C.Y., Finch C.B., Foegelle M.D.,
and Modine F.A.: Solid State Commun.
68 (1988) 387.
[7] Frisk K., and Fernandez Guillermet A: J.
Alloys Compd. 238 (1996) 167.

181

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Electronic Structure of 2D Boron Monosulfide
Masayuki TOYODA
Department of Physics, Tokyo Institute of Technology
Ookayama 2-12-1, Meguro-ku, Tokyo 152-8551

Ultrathin two-dimensional (2D) materials
are a class of nanomaterials that exhibit uniquemechanical, physical and chemical properties.
Among them, 2D materials consisting of boron
has been now attracting increasing interest
due to their polymorphic properties. Recently,
ultrathin boron monosulfied (BS) nanosheets
have been successfully synthesized by the physical exfoliation of rhombohedral boron monosulfide (r-BS) [1]. The discovery of the BS
nanosheets raised attention to their bulk layers. We have investigated the electronic andlattice vibrational properties of r-BS by performing first-principles density-functional theory (DFT) and density-functional perturbation theory calculations. The results agrees
well with the experimental measurements including the infrared absorption spectroscopy[2] and microfocused angle-resolved photoemission spectroscopy [3]. By incorporatingwith the experiment, we have revealed the detailed electronic structure of r-BS and its ptype semiconductivity. In this study, we have
utilized the eﬃcient parallel computing powerof ISSP Supercomputer System B (ohtaka).

Figure 1: Calculated electronic structure of rBS. The band dispersion (a and b) and 2D
cross-section at diﬀerent energies (c, d, and e)
are shown.

References[1] H. Kusaka, R. Ishibiki, M. Toyodaet al.,J. Mater. Chem. A 9, 24631-24640 (2021);
J. Mater. Chem. A 10, 4999 (2022).
[2] 0 N. Watanabe, K. Miyazaki, M. Toyoda
et al., Molecules 28, 1896 (2023).
[3] K. Sugawara, H. Kusaka, T. Kawakami etal., Nano Lett. 23, 1673-1679 (2023).

Figure 2: Calculated phonon dispersion of rBS.

182

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Exploration of exotic surface sites for catalyst informatics
Yoyo HINUMA
National Institute of Advanced Industrial Science and Technology (AIST)
1-8-31, Midorigaoka, Ikeda, Osaka 563-8577
Surface point defects of metal oxides, forshown in the setting of a 2x2x2 supercell of theinstance O vacancies, have a dominant effect onheterogeneous

catalysis.

The

cubic 5-atom.

Mars-Van

Krevelen mechanism is one of the mostfrequently encountered catalytic process. In one
example, O vacancies on a metal oxide catalyst
surface act as reaction sites. The energy
minimum required to remove O from a surface,which is denoted as the surface O vacancy
formation energy (EOvac), can be used torationalize and predict catalytic performance in

Fig. 1. Crystallographic conventional cell ofsuch a catalytic process. Calculation of EOvac

CaTiO3 (space group type Pnma, number 62).

requireswith

Orange, blue, and red balls represent Ca, Ti, andsufficient spacing between O vacancies, henceO, respectively. The directions of basis vectors

some estimation of EOvac from less costly

are shown in the orthorhombic (ort) and cubic

calculations, such as slab-and-vacuum model(cubic) settings/aslab-and-vacuum

model

calculations with minimum cell size and evenbulk calculations, will be effective in screening

The following trends were found:materials for a given purpose.

-Metallic compounds had small EOvac; less thanComputational exploration of previously

2 eV and 1 eV for A-cation and B-cation

unknown reactive sites is a powerful strategy for

terminated surfaces, respectively.

emergence of new catalytic reactions. The-Ti-containing compounds had very high EOvac

surface energies of experimentally knownwith more than 4 eV for the B(Ti)-cation layer.

perovskite oxides with B-site cations with redox

Thiscapability (Ti-Fe). The A-cation and B-cation

perovskites are not very reactive.

terminated (100) surfaces were studied. The-Other compounds were in-between, with thesymmetry was reduced by hand to obtain thetrend of higher A-cation layer EOvac when the B-

lowest energy structure. Fig. 1 shows CaTiO3

cation contains more 3d electrons

183

resultimpliesthat

Ti-containing

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Atom correlation of two-dimensional Cu-Ni alloy on theNi(110) and Cu(110) surfaces
Tsuneo FUKUDA
Division of Electronics and Physics, Graduate School of Engineering,Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka 558-8585

Copper-Nickel

alloysareubiquitousin the inset of Fig. 1 and Table 1.

materials, and they are widely used as
construction materials such as piping andvarious coinages. Cu and Ni are both simple fcc
metals and form a uniform solid solution
without any intermetallic compounds. The
Fig. 1: Interaction energy as function of atomic distance.
Red circles are for Cu-Cu pairs on the Ni(110) surface,and blue squares are for Ni-Ni pairs on the Cu(110)
surface. Unit cell is indicated by a red broken rectangle
in inset, and embedded Cu atoms for n=2 are indicatedby green.

interaction energy is, however, known to bepositive, resulting in a spinodal decomposition
which has been established theoretically andexperimentally. However, due to the lack of

Table 1 Parameters for the present calculation

definitive experimental studies, no quantitative

VASP Version
slab geometry
k-points
potential
cut off energy

evaluation of the interaction energy between Cu
and Ni has ever been conducted.
Here we studied atom correlation of two-Fermi level smearing

dimensional alloy on Ni(110) and Cu(110)convergence condition

surfaces. The (110) face of fcc metals have a

SCF mixing
parameters

unique one-dimensional atom chain, and we

6.3.2
1×12 units 9 layers
32×4
PBE [2]384.08 eV
Methfessel & Paxton
 = 0.12(Ni), 0.3 (Cu) eVElectronic:10-6 eVIonic: 0.01 eV/Ang.
AMIX = 0.02,BMIX = 0.0001
AMIX_MAG = 0.08
BMIX_MAG = 0.0001

one-

The results shown in Fig. 1 clearly indicate

dimensional attractive interaction of Cu-Cu on

attractive interaction both Ni-Ni and Cu-Cu

the Ni(110) surface.[1] The aim of this study ispairs, which is direct confirmation of theto evaluate the interaction energy from the first-

clustering behavior of the two-dimensional Cu-

principles. We used VASP, and by changing theNi alloy.

Cu-Cu (Ni-Ni) distance on the Ni(110)

References(Cu(110)) surfaces the interaction energies[1] T. Fukuda, T. Saito, I. Kishida, ACSIN-14,

were extracted as a function of Cu-Cu (Ni-Ni)

Sendai 2019, 23E28.

distance (n). Atomic structures and the[2] J. P. Perdew, K. Burke, and M. Ernzerhof,

calculation parameters are respectively shown

Phys. Rev. Lett. 77 (1996) 3865.

haveexperimentallydemonstrated

184

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Search and realization of novel electronic properties of
surfaces and interfaces and of nanostructures
Takeshi INAOKA

Department of Physics and Earth Sciences, Faculty of Science,
University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213
This academic year, using the van-derWaals density-functional theory, weinvestigated the electronic structure of
the x-form phthalocyanine (Pc) crystal
and the iodine doping effect on thisstructure. The Pc is a planar conjugated macrocyclic molecule which
can include an atom of various species at
its center. The x-form is one of several
typical stacking forms of Pc in whichmolecular planes are perpendicular to thestacking axis. The x-form crystal iscomposed of a simple tetragonal lattice.
In each primitive unit cell of x-LiPc or
x-NiPc, there are two molecules which
are stacked along the c axis with astaggered angle of about 40°. The x-LiPc
or x-NiPc is considered to be a Mott
insulator because of its half-filled band.
On iodine (I) doping, I atoms penetrate
into one-dimensional (1D) open channels
between x-form molecular chains, which
results in x-LiPcI [1] or x-NiPcI [2].
Although x-LiPc or x-NiPc is a Mott
insulator because of its half-filled band,
doped I atoms oxidize partially Pc chains,
shift the band occupancy from half-filling,
and consequently leads to metallic nature[1]. In this analysis, we chosen SiPc and
SiPcI, because a monomer of SiPc has a
Si pz-derived orbital just above the LUMO,
and we expected x-SiPc to be 1D Si metal.
However, as described below, dimerizationof Si turns out to prevent formation of ametallic band.
We employed the program package‘Vienna Ab initio Simulation Package’(VASP) [3,4] on system B to optimize ourstructures.
To visualize our system, we show the
optimized x-SiPcI structure in Fig. 1.
First, we consider the case without I
doping. If we assume one period in thestacking direction, namely, one molecule

185

in each primitive unit cell, we obtain ametallic band with about one-thirdoccupied, and the cohesive energy permolecule of 1.82 eV. However, this is not
the ground state.
In a single SiPc chain with two period,
two Pc molecules in each primitive unit
cell are stacked with a staggered angle
45°where eight C atoms nearest to thecenter Si atom in one molecule accord
with those in the other molecule inprojected position. This angle relation
enables overlapping of pz orbitals ofadjacent molecules at these C-atom
positions. The cohesive energy is 3.41 eV
which is larger than that of the above
one-period system.
In the x-SiPc crystal without I doping,which includes intermolecular interaction,
the staggered angle deviates to 38.4°.
Although this angle is somewhat
unfavorable in terms of the abovementioned overlap of C-atom pz orbitals,
s-orbital overlap occurs between two H
atoms at the outer edges of neighboring
molecule planes, as shown in the total
electron density distribution in Fig. 2. Thisoverlap can be ascribed to the fact that a
number of k-states in some -bonddominant bands about 7 eV below the
(a)

(b)

Fig. 1 Optimized x-SiPcI crystal structure. (a)top view, (b) side view. As for circles, blue: Si,
gray: N, brown: C, white: H, purple: I.

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

x-SiPcx-SiPcI

(a)

(b)

2

2

E-EF (eV)b199

Fig. 2 Total electron-density distribution of
x-SiPc. The purple circle shows s-orbital
overlap between two H atoms.

1b197,198

0-1

Fermi level have local orbitals like H
molecules. The Si atoms dimerize in thestacking direction, as in Fig. 1 (b), which
prevents formation of a metallic band
owing to Si pz orbitals. The moleculecohesive energy is as large as 4.01 eV.
Figure 3 (a) exhibits the band dispersion
along the -Z line in the stacking direction.
The band b185, which is fully occupied,derives from Si pz orbitals. Two almost
degenerate bands, each of which isspin-degenerate, are half-filled ones,
which leads to Mott insulators, according
to the experimental results of x-LiPc [1]or x-NiPc [2].
Iodine (I) doping to x-SiPc turns thisinsulator into a metal. Figure 3 (b) displays
the band dispersion along the -Z line for
x-SiPcI. We can identify the I-derived
bands by following the energy levels
labeled red in this panel. The highest oneof these band dispersions that passes thelevels b199 and b195 decreases rapidly inenergy and intersects the Fermi level.
Since this implies appearance of a metallic
band, we analyzed the electronic
structure. Figures 4 (a) and (b) shows the
top and side views of the electron density
distribution of the state at the Fermi level
which is arrowed and marked b195 in red
in Fig. 3 (b). The metallic states along the I
atomic chains are connected to electron systems extending around theouter edges of Pc molecular planes. We
consider that I doping makes a wide rangeof x-form Pc crystals metallic, including
LiPcI and NiPcI.
To verify existence of 1D metallic bands
due to I atomic chains, we are performing
further calculations taking more k points in

186

1

b190,191
b188,1890

b195,196
b195

b187

b194

b186

-1 b192,193
b188, b191
189

b185

-2

-2



Z



Z

Fig. 3 Band dispersion of (a) x-SiPc and (b)x-SiPcI along the c axis. The bands labeled in
red in (b) stem from the I-atomic chains, andone of these bands crosses the Fermi level, as
is eye-guided by a red broken line.

the Brillouin zone and upgrading the
calculational scheme to the hybrid density
functional method with higher accuracy.
We will report the confirmed results in anear future [5].
(a)

(b)

Fig. 4 Electron-density distribution of the stateat the Fermi level that is arrowed and labeled
b195 in red in Fig. 3 (b). (a) top view, (b) side view.

References[1] R. Teruya et al., Angew. Chem. Int. Ed. 61,
e202206428 (1-6) (2022).
[2] C. J. Schramm et al., J. Am. Chem. Soc. 102,6702-6713 (1980).
[3] G. Kresse and J. Hafner: Phys. Rev. B 47,
558-561 (1993).
[4] G. Kresse and J. Furthmüller: Comput. Mat.
Sci. 6, 15-50 (1996).
[5] T. Inaoka, to be submitted.

Activity Report 2022 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

DFT calculations of organic halogen molecules and their reaction products
on metal surfaces
Noriyuki TSUKAHARANational Institute of Technology, Gunma College, Toriba-machi 580, Maebashi, Gunma,371-0845, Japan.

In this study, DFT calculations were carriedout to clarify the contribution of intermolecular
halogen and hydrogen bonds to the structuresof the 1,3,5-tris(bromophenyl)benzene (TBB)
molecular film on Ag(111) and Si(111)(!3"!3)-Ag surfaces [1]. In combination with
STM experiments, the structure of TBB
molecular

films

and

the

intermolecularinteractions are clarified. Fig. 1 shows thespatial distribution of the differential charge
density for the isolated TBB molecule and TBB
assembly on Ag(111). The difference in theFig. 1: The spatial distribution of the differential charge

distribution between the isolated molecule anddensity for the isolated TBB molecule and the TBB

the TBB assembly is derived from electrostatic

assembly on Ag(111), and the vertical cross section of

attraction with a Br atom in the neighboring

the distribution along the line in (a) and (c). Reprinted

TBB molecule for the TBB assembly. It

with permission from N. Tsukahara and J. Yoshinobu,

indicates intermolecular halogen bond. Similar

Langmuir, 38, 8881 (2022). Copyright 2022, American

calculation

Chemical Society.

indicates

theintermolecularhydrogen bond on Si(111) (!3"!3)-Ag.

References

In addition, STM and DFT calculations
were carried out to clarify the growth[1] N. Tsukahara and J. Yoshinobu, Langmuir,

mechanism of the metal cluster using the metal-

38, 8881 (2022).

organic layer obtained by coupling reaction of[2] N. Tsukahara, R. Arafune, and J. Yoshinobu,

TBB molecules on Ag(111) as a template [2].

Langmuir,

187

to

be

submitted.