3.2

First-Principles Calculationof Material Properties

43

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Mechanisms of Semiconductor Interface Formation and its Electronic
Properties based on Quantum Theory
Atsushi Oshiyama
Institute of Materials and Systems for Sustainability, Nagoya University
Furo-cho, Chikusa-ku, Nagoya 464-8601
in

In the fiscal year of 2019, on the basis of thethefabricationofelectronic

devices.

total-energy electronic-structure calculations andUnderstanding of bond configurations near themolecular

step on the atomistic level is necessary in order todynamics

simulations

within thedensity-functional theory, we have studied atom-

identify thereactivity at

the

step

edges.

scale behavior during the epitaxial growth ofFurthermore, epitaxial graphene can be prepared

power semiconductors, silicon carbide (SiC) andon SiC surfaces, and the surface steps of SiC also

gallium nitride (GaN). The main computa tional

play an important role. Hence, it is certainly

tools are our RSDFT (Real Space Density

important and inevitable from both science andFunctional Theory) code and RS-CPMD (Car-technology viewpoints to identify the atomic steps

Parrinello Molecular Dynamics) code. We haveon SiC and clarify their energetics, that has notclarified 1) the structures and energetics, and thenbeen achieved yet. Our previous calculations [6]the morphology of SiC surface steps [1,2], 2) theshow that the single-bilayer height steps are

liquid-like behavior of the topmost Ga atoms [3]and 3) the mechanism of oxygen incorporation
during the epitaxial growth of GaN [4,5]. The
group identification codes for the achievements
above are k0042 and m0001. Below, I explain theissues 1) and 2).

1. Step structures and morphology of Siface SiC Polar Surface
SiC is now emerging as a promising material
for power electronics. This is due to its physicalFig.1: Schematic view of the five distinct
mono-bilayer steps on SiC (0001) surface. Si
and C atoms are represented by the larger(blue) and smaller (brown) balls, respectively.
The Si2, Si3, C1 and C2 steps along the ⟨1120⟩ direction and the SC step along the ⟨1100⟩ direction are shown all together.

properties superior to Si, a current premiermaterial, such as the wider band gap and thehigher electric break-down voltage. The thin-film
growth of SiC in the step-flow mode is essential

44Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

energetically favorable compared with higher

for 5 distinct steps as a function of Si chemical

steps on SiC(0001) or (111) surface.

potential (Near step edges, the numbers of Si and

Figure 1 shows schematic view of 5 distinct

C atoms are different so that we need thesingle-bilayer height steps. There are two

chemical potential). We have found that Si2 stepdifferent classes of steps: One is [11-20] oriented

toward [1-100] is the most stable and Si3 stepand the other is the [1-100] oriented; further in thefollows.

latter, four different step edges exit which arecomparable with the Si3 step.

The

SC

step

toward[11-20]islabelled by the atomic species at the edge and the

The energetics obtained above predicts somenumber of the dangling bonds before theinteresting morphology of atomic steps on

structural relaxation as Si2, Si3, C1 and C2.

SiC(0001). Experimentally, the (0001) surface isstructuralslightly inclined along either [1-100] or [11-20]

optimization for all the possible atomic steps anddirection. When it is inclined along the [1-100],

determined their structures. Near step edges wethe surface consists of the [0001] terrace andhave found prominent rebonding between theseveral steps among Si2, Si3, C1 and C2, whereas

upper-terrace and the lower terrace Si atoms in

it consists of the terrace and SC steps when

Si2 and SC steps and also a peculiar resonant-likeinclined along [11-20]. In the former, the Si2 orrebonds for Si3 steps, as well as the C

Si3 steps are energetically favorable (Fig. 2).

dimerization for the C2 step.

However, in the latter, the SC step is energetically

We

have

performed

detailed

unfavorable compared with Si2 and also Si3 in

Figure 2 shows calculated formation energies

some range of the Si chemical potential. Hence
we expect that the steps toward [11-20] show zigzag shape consisting of, for instance, Si2 and Si3.
We have indeed found that such zizgzag-shaped
step-edge pairs of Si2 +Si3 is lower in theformation energy than the straight-shape SC stepon the [0001] surface inclined along [11-20]
direction.

2. Two-DimensionalGaliquidon

growing GaN surface
Fig. 2: Calculated formation energies ofthe mono-bilayer atomic steps on
SiC(0001) surface as a function of the Si
chemical potential μSi, measured fromthat in crystalline Si, μSi(bulk). Shaded
areas surrounded by each pair of solidlines represent the uncertainty in thecalculated formation energy.

GaN, a fundamental material worldwide used
for high performing opto-electronic devices, israpidly becoming another candidate to unseat Si
in

45

power

electronics.

Yet,

their

practical

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

realization asks for the realization of thin epitaxial

temperature, the top-layer Ga atoms get together

films of higher quality with respect to what isand exhibit the peak at much shorter distance,

done nowadays for optoelectronic applications. It

indicating some condensed phase of Ga.
By

is thus highly demanded to clarify the nature ofusing

Kubo-formula(velocity-velocity

correlation function), we have computed thethe growing GaN surface at atomistic level.
It is known that under typical conditions of the

diffusion coefficient of the top-layer Ga atom. We

epitaxial growth of GaN, the surface is Ga-rich.

have found that the diffusion coefficient jumps at

Hence we prepare Ga-rich surface and raise the1300 K from its value of 0.382 x 10-5 cm2/s attemperature by CPMD simulations from room

1100 K to the value of 0.492 x 10-4 cm2/s. We thus

temperature. We have found that, when the

conclude that this condensed phase is not a solid

temperature

growthphase but a two-dimensional liquid phase. This istemperature, i.e., 1300 K, the topmost Ga atom

corroborated by the absence of the peaks except

suddenly moves from their original position. The

for the first peak at 1300 K in Fig. 3. The notion

calculated Ga-Ga pair correlation function isthat the GaN surface during the epitaxial growth

shown in Fig. 3. At room temperature, the top-

is 2-diemnsional liquid is unrecognized in the past

layer Ga atoms vibrate around their original

and important to consider mechanism of thepositions. The pair correlation function shows aepitaxial growth.

peak determined by the Ga coverage. Then withRelated Publications

increasing temperature,[1] K. Seino and A. Oshiyama, Appl. Phys. Exp.

reachesthethetypicalpair correlation

function shows the peak at the same position with

13, 015506 (2020).

increasing peak width, showing the enhanced[2] K. Seino and A. Oshiyama, Phys. Rev. B

thermal vibration. However, at the growth(2020) to be published.
[3] K. M. Bui, M. Boero, K. Shiraishi and A.
Oshiyama, Jpn. J. Appl. Phys. 59, SGGK04(2020).
[4] F. Shintaku et al., Appl. Phys. Exp., 13,055507 (2020)[5] D. Yosho et al., Phys. Sta. Solidi - Rapid Res.
Lett. 2000142 (2020).
[6] K. Sawada, J.-I. Iwata, a. Oshiyama, Appl.
Phys. Lett. 104, 051605 (2014).

Fig. 3: Evolution of the Ga-Ga pair correlation function in the top-layer of GaN during
the heating process. The initial distance of 6.4
Å corresponds to the relaxed system fromwhich dynamical simulations were started.

46

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analyses on electronic structure and magnetic property inhigh-performance spintronics and magnetic materials
Tatsuki ODA1,2, Indra PARDEDE1,2, Afrioni Roma RIO2, Achmad Maulana GANI2,
Daiki YOSHIKAWA2, Tomosato KANAGAWA2, Hasan Al RASYID2, 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 anisotropy calculation.

with

an

available

experimental

We have developed a computational

measurement, as shown in Fig.1. Thismethod of magnetic anisotropy energy

agreement implies that our method is(MAE) using the noncollinear spin

promising on the estimation of MAE.

density functional theory (NC-SDFT).

We have established a calculation

This method enables us to estimate themethod of MCAE in the same time. The

MAE including both contributions to the

MCAE part was evaluated from both

MAE from magnetocrystalline anisotropy

methods of total energy (TE) and grand-

energy (MCAE) originating from spin-

canonical force theorem (GCFT) [1]. All

orbit coupling and the shape magnetic

MCAE values from the TE were wellanisotropy energy (SMAE) originating

reproduced by those from the GCFT

from spin dipole-dipole interaction [1]. In

method. The advantage of GCFT methodtheover the TE method makes analysis of thecalculation

of

SMAE,

the

contribution was estimated from the spin

atom-resolved

density distribution that is obtained in thecontributions of MCAE. In Fig.2, one can

NC-SDFT. One can expect an accurate

easily recognize the portions of large

SMAE. Indeed, we have found some

contribution to MCAE. Such figure cancorrections on SMAE coming from thebe compared with the orbital-resolved

quadrupole component of atomic spincomponent of band dispersion curves. As

density [2,3].

a result, the MCAE is deeply understood,

We applied the method to the freestanding

Co/Ni(111)multilayer

andk-resolved

combined with its anisotropy of orbitalthatcomponents. The atom-revolved MCAE

indicates a perpendicular anisotropy [1].

is also very useful to understand the

The results indicated a good agreement

atom/layer alignment giving rise to large

47

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Fig. 1. MAE in Co/Ni multilayer structure
as num. of multilayer.

MCAEs. In the application of Co/Ni(111),

Fig. 2 k-resolved MCAE in Co/Ni(111)multilayer structure.

we recognized that the Co/Ni interface
makes a large perpendicular magnetic

Other contributions.

anisotropy.

We have developed a noncollinear
spin version of van der Waals density

NC-SDFT under magnetic field.

functional scheme [5]. We have also

We implemented a density functional

contributed a theoretical part of thescheme which enables application of a

spintronics application in the system of

uniform external magnetic field. In theinterfacial

implementation, the rotation of the

PtCoO/ZnO [6].

magnetic

anisotropyofmagnetic moment on an atom wasdescribed using the NC-SDFT calculation.

References.

The[1] I. Pardede et al.: J. Magn. Magn. Mater. 500

newschemewassuccessfully

applied to a ferromagnetic slab with a(2020) 166357.

perpendicular magnetic anisotropy and an[2] T. Oda and M. Obata: J. Phys. Soc. Jpn. 87

antiferromagnetic material [4]. These(2018) 064803.

results were discussed along with thesimplemodel.

This

approach[3] T. Oda et al.: IEEE Trans. Magn. 55 (2018)may

1300104.

provide a useful tool in analyzing[4] A. R. Rio et al.: J. Phys. Soc. Jpn. 89 (2020)

magnetic properties of materials. In the

035002.

scheme, the Kohn–Sham equation was
solvedself-consistently

with[5] M. Christivana et al.: J. Phys. Soc. Jpn. 55

the(2019) 104601.

noncollinear spin density in the system.

[6] M. Al-Mahdawi et al.: Phys. Rev. B 100(2019) 054423.

48

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab initio optimization of 4f -3d intermetallic
ferromagnets for permanent magnets
Munehisa Matsumoto
Institute for Solid State Physics, University of Tokyo
Kashiwa-no-ha, Kashiwa, Chiba 277-8581
andInstitute of Materials Structure Science, High Energy Accelerator Research Organization
Oho 1-1, Tsukuba, Ibaraki 305-0801
April 30, 2020

Today’s main-stream commercial permanent
magnets are made of sintered Nd-Fe-B alloys [1], or rapidly quenched alloys with analogous ingredients [2] that is fabricated into hotdeformed magnets. Their main-phase compound is a 4f -3d intermetallic ferromagnet,
Nd2 Fe14 B [3]. Its magnetization of 1.6 Tesla atroom temperature and relatively good temperature dependence of anisotropy field [4] makes
Nd2 Fe14 B a champion magnet compound forpractical applications in the temperature range
from 300 K to 500 K, while its relatively low
Curie temperature at 585 K, almost half of
the Curie temperature of elemental Fe, leaves
only a small temperature margin as compared to Sm-Co magnets whose Curie temperature reaches the range of 1000 K. The hightemperature properties that are not very excellent pose a drawback for the Nd-Fe-B alloy,
leading to various proposals for alternative materials including NdFe12 N [5, 6] and SmFe12 [7],which cannot escape other problem concerning structure instability. In parallel with suchquest for the possible next-generation champion magnets, it is important to better understand today’s champion magnets and verify
if there is any marginal space left for a possible improvement of R2 Fe14 B-based permanent magnets (R=rare earth). Thus we havebeen investigating optimally degined materi-als with a pool of candidate chemical compositions, made of preferrably light rare earth elements and iron-group elements, where a goodcompromise involving all of the desired properties, such as structure stability, magnetization, magnetic anisotropy and Curie temperature, can be reached within a restricted lattice
structure of R2 T14 B (T=Fe or Co).
In order to explore the chemical composition space in a combinatorial way, we run
massively parallel computer simulations forR2 T14 B covering a virtual space spanned by
R’s and T’s utilizing AkaiKKR [8], the opensource package for ab initio electronic structure
calculations based on Korringa-Kohn-Rostoker(KKR) Green’s function method implementing
coherent potential approximation. Once a selfconsistent electronic structure is reached, anestimate of the Curie temperature can be done
as a post-processing to the converged result,based on an approximation to consider the lowmost excitations on the Fermi level dominantly
contributed from the ferromagnetic spin waves.
Atomic-pair wise exchange couplings can be
estimated based on a magnetic force theorem
following Liechtenstein et al. [9] and a realistic
Heisenberg model defined from them can besolved by the mean-field approximation. The
working lattice constants are basically takenfrom past experiments [3].

49Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Curie temperature of R2Fe14B (K)

1400
1200

Calc. (MTA) on the expt. lattice
Expt.

1000
800
600
400

fully utilize the data obtained within the prohibitively crude approximation based on spinmodels even for intermetallics.
More extensive data collections to elucidate
the overall trends have been in progress andwill be published elsewhere.

2000

La Ce Pr Nd

Sm

Gd Tb Dy Ho Er TmYb Lu

References

R[1] M. Sagawa, S. Fujimura, N. Togawa,
H. Yamamoto, and Y. Matsuura,
J. Appl. Phys. 55 (1984) 2083.

Figure 1: Calculated Curie temperature of
R2 Fe14 B (red squqre) based on muffin-tin approximation (MTA). For a comparison, theexperimental data (blue circle) taken from
Ref. [3] are also shown.

[2] J. J. Croat, J. F. Herbst, R. W. Lee, andF. E. Pinkerton, J. Appl. Phys. 55 (1984)
2078.
[3] For a review, see e.g. J. F. Herbst,
Rev. Mod. Phys. 63 (1991) 819.

Calculated Curie temperature in a representative cross section of the overall chemical composition space, (R,T), are shown in
Fig. 1. Here we show the computational data
set based on local density approximation [10]and within muffin-tin approximation. An analogous and more comprehensive data set within
atomic-sphere approximation is published elsewhere [11]. It is seen that the overall trendwith respect to the species of rare-earth elements is described satisfactorily, while thequantitative accuracy is not as excellent. The
systematic deviation is reasonable, considering one of the biggest approximations we havemade in modeling a metallic system only withspin degrees of freedom, as if our target systems were insulators. On top of that, temperature dependence of lattice constants would
not entirely be negligible under the strong influence of the magnetovolume effect in sucha strong ferromagnet [12]. Since the Curie
temperature is mostly contributed from 3delectrons, the relative trend within a materials family where the 3d-electron part is common seems to be well described. As long as
we are aware of the particular way the systematic deviation between theory and experiment comes in, it is expected that we can care-[4] S. Hirosawa, Y. Matsuura, H. Yamamoto,S. Fujimura, M. Sagawa, H. Yamauchi,
J. Appl. Phys. 59 (1986) 873.
[5] T. Miyake, K. Terakura, Y. Harashima,
H. Kino, S. Ishibashi, J. Phys. Soc. Jpn.
83 (2014) 043702.
[6] Y. Hirayama, Y. K. Takahashi, S. Hirosawa, K. Hono, Scr. Mater. 95 (2015) 70.
[7] Y. Hirayama, Y. K. Takahashi, S. Hirosawa, K. Hono, Scr. Mater. 138 (2017)62.
[8] http://kkr.issp.u-tokyo.ac.jp[9] A. I. Lichetenstein, M. I. Katsnelson, V. P. Antropov, V. A. Gubanov,J. Mag. Mag. Mater. 67 (1987) 65.
[10] S. H. Vosko, L. Wilk, and M. Nusair,
Can. J. Phys. 58 (1980) 1200.
[11] MM, H. Akai, Phys. Rev. B 101 (2020)
144402.
[12] for a review, see A. V. Andreev,
Handbook of Magnetic Materials, Ed.
K. H. J. Buschow, Vol. 8, Chapter 2(1995).

50

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Data integration between theory and experiment for
rare-earth permanent magnets
Munehisa Matsumoto
Institute of Materials Structure Science, High Energy Accelerator Research Organization
Oho 1-1, Tsukuba, Ibaraki 305-0801
June 15, 2020

Materials in practical use are characterizedwith macroscopic properties in a space-timescale comparable to the human scale, as rareearth permanent magnets are with remanent
magnetization and coercivity that works in operation environments that are typically out ofthermal equilibrium. It is desirable to have aworking methodology to understand and control those macroscopic properties of materials from the fundamental laws for atoms andmolecules.
We have been in quest for such materials
design scheme spanning over the microscopic
and macroscopic physics. We have recently
constructed an iterative approach between experimental data and theoretical data, taking
as our playground a material of recent interest, namely, SmFe12 with substitution elements such as Ti, Co, and Zr, a candidate material for a new permanent magnet. Effects of
Ti, Co, and Zr for multiple prerequisite properties for permanent magnet utilities, put in
multiple sublattices, are investigated utilizing
both of ab initio theoretical data and experimental data from neutron diffraction. Goingback and forth between the Rietveld analysis
for the latter and ab initio calculations basedon local density approximation (LDA) until afixed point is reached, dual site preference of Zr
in SmFe12 has been newly elucidated, in contrast to the prevailing assumption in the literature that Zr replaces Sm only. This wayof data-integration analysis has been tenta-

tively called “LDA+Rietveld” method [1], as
has been constructed in an analogous spirit to
LDA+DMFT (DMFT =dynamical mean field
theory) [2].
For LDA+Rietveld, we have utilized
AkaiKKR [3] for incorporating the substituteelements with a continuous variables of theconcentration. OpenMX [4] is needed as wellin order to address the structure stability withcalculated formation energy. In LDA+DMFT,
LmtART [5] has been utilized combined witha continuous-time quantum Monte Carlo
impurity solver adapted for our realistic
simulations.
Taking LDA+DMFT as a prototype, wehave made one step forward in constructing a working simulation framework to bridgeover the microscopic scale and the macroscopic
scale.

References[1] MM, T. Hawai, K. Ono, Phys. Rev. Applied 13 (2020) 064028.
[2] MM, Phys. Rev. Materials 4 (2020)
054401.
[3] http://kkr.issp.u-tokyo.ac.jp[4] http://www.openmx-square.org[5] http://savrasov.physics.ucdavis.
edu/mindlab/MaterialResearch/
Scientific/index_lmtart.htm

51

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Physics of Electrochemical Interfaces
Osamu SUGINO

Institute for Solid State Physics,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8581
The

metal-solution

interfacerecognizedasaquantum

exhibits various properties undermechanically extended particle; ourthe influence of the electrical double

first-principles

layer formed around the interface.

simulations

Our group has been elucidating thecapture the crossover, which can bereaction dynamics and adsorption

explained by a lattice gas model withprocesses

microscopic

a quantum hopping term, or theperspective using interface-adapted

Boson-Hubbard model. The results

first-principles

providefromacomputational

path-integral

for

new

of

the

hydrogen

TiO2

has

on

evolution reaction.

twodifferent

themes: (A) the quantum nuclear

(B)

1

into

mechanism

followingandinsights

methods. This year, our lab focusesthe𝜃 = 2/3

Defective

the

been

effect of hydrogen adsorption at therecognized as a future material forPt(111)-solution interface [1] and (B)hydrogen fuel cell catalysts because

the role of defects in the activation ofof coexistence of the stability andoxygen reduction reactions at theactivity, but the mechanism of the

TiO2-solution interface [2].

oxygen reduction reaction (ORR) is(A) Hydrogen atoms are known to

unknown. To search for the active

exhibit large quantum effects, butsite of this material, we took a high-these effects have been investigatedthroughput

only at the full mono-layer coveragethermodynamics. Since important(𝜃 = 1) or the low coverage limit (𝜃 ≪key to the activity is in the relative

1 ). In the former, hydrogen isstability

recognized as a classical particle

intermediates,

modified by the zero-point energy,

investigated how one can control theand in the latter, hydrogen isstability by doping. Contrary to52

approach

of
O

based

on

the

reaction

and

OH,

we

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

many materials like platinum, TiO2

a novel fuel cell.

surfaces were found to bond O andReferencesOH[1] L. Yan et al. Phys.Rev.B101, 165414

differently

when

doped

differently, suggesting it possible to(2020).

sufficiently flatten the potential[2] Y. Yamamoto et al. J.Phys.Chem.C123

energy19486 (2019).

discovery

profile

for

has

ORR.

This

stimulated

experimental collaborators to design

53

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

DFT sampling analysis on interfaces and electrolytes in novel
batteries
Yoshitaka TATEYAMA
Institute for Solid State Physics,
Center for Green Research on Energy and Environmental Materials (GREEN), National
Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
sulfideWe are working on (1) developments ofelectrolyte,

andabufferlayer,

theoretical, computational and data-driven

respectively. For the LCO/LPS interfaces, wetechniques [1,2] as well as (2) understanding ofsampled over 20000 configurations and foundsurface and interface reactions, essential in theseveral stable disordered structures involving

energy and environmental technologies such as

mixing cations and anions, leading to thebattery and catalyst [3-8]. Recently, we haveformation of a reaction layer. On the other hand,made a progress for DFT-based efficient

Li-ion sites that can be preferentially depleted

calculations of solid-solid interfaces, mainly forupon charging always exist around the cathode-all-solid-state batteries [1].

SE interfaces irrespective of the interfacial

We have been exploring the atomistic

order/disorder (See Li Chemical potential inunderstanding of this interfacial resistance

Figure). Therefore, we conclude that themechanism with DFT-based calculations [4].

dynamic Li-ion depletion is likely to be a major

We first devised some systematic ways for thecause that prevents successive Li-ion transport,solid-solid interfaces and discussed possible

leading to resistance.

origins such as the space-charge layer and thereaction layer. Recently, we incorporated the
CALYPSO structure prediction technique with
our method for the interface structure search,
including mismatch treatment and lateral shift
etc [1]. In this way, we have found several
microscopic electrochemistry of the interfacial

Fig. 1 Li chemical potentials around aninterface between LiCoO2 cathode and bLi3PS4 solid electrolyte; Pristine interface(left) and Co-P exchange interface(right).

Li-ion states.
As a representative model, we investigated
the system with LiCoO2 (LCO), β-Li3PS4 (LPS),
and LiNbO3 (LNO) acting as a cathode, a54

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

21 (2019) 13788.

Through investigating the buffer layer
effects and the interfacial electronic states, we[4] Y. Tateyama, B. Gao, R. Jalem, J. Haruyama,

also deduced a probable origin for the

Curr. Opin. Electrochem. 17 (2019) 149.

interfacial Li depletion and a mean to suppress[5] B. Gao, R. Jalem, Y. Tateyama, ACS Appl.

this problematic behavior.

Mater. Interfaces, 12 (2020) 16350.
[6] M. H. N. Assadi, M. Okubo, A. Yamada, Y.

References

Tateyama, Phys. Rev. Mater. 4 (2020) 015401.

[1] B. Gao, R. Jalem, Y. Ma, Y. Tateyama,[7] A. Ishikawa, K. Sodeyama, Y. Igarashi, T.

Chem. Mater. 32 (2020) 85.

Nakayama, Y. Tateyama, M. Okada, Phys.

[2] A. Ishikawa, Y. Tateyama, J. Comp. Chem.

Chem. Chem. Phys. 21 (2019) 26339.

40 (2019) 1866.

[8] A. Ishikawa, Y. Tateyama, J. Phys. Chem. C[3] C. Yamaguchi, K. Natsui, S. Iizuka, Y.

124 (2020) 6054.

Tateyama, Y. Einaga, Phys. Chem. Chem. Phys.

55

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical study on defects in wide-gap semiconductors:
SiC and α-Ga2O3
Yu-ichiro MATSUSHITA
Institute for Innovative Research,
Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550
We have studied the stabilities of defects insucceeded in identifying the atomic structure ofwide-gap semiconductors on the basis of thethe defect as an ad-atom with a dangling bonddensity-functional theory (DFT). In this study,(Pb center) based on the DFT calculations [2].

we focus on SiC and α -Ga2O3 as next-

We have also calculated the formation

generation of power semiconducting materials.

energies of point defects in α-Ga2O3 [3]. We

To clarify the stable defect structures and its

have used the extended FNV method to remove

electronic properties is necessary to move thethe artifacts derived from the backgroundpower device applications forwards.

charge. We have found that Ga interstitials andFirst, we have discussed the energetics of

Ga vacancies are the major defects when the

carbon-related defects in the SiC, SiO2, and justFermi energy approaches to valence andat their interface for the systematic comparison

conduction bands, respectively.

of the stabilities of them in the three regions. As

Referencesa result, we have found that the stable forms of[1] T. Kobayashi and Y. Matsushita: J. Appl.

the carbon defects depend on the oxidation

Phys. 126 (2019) 145302. T. Kobayashi, K.

environment. In the oxygen-rich condition atHarada, Y. Kumagai, F. Oba, and Y. Matsushita:

1600K, nano carbon clusters likely to stay justJ. Appl. Phys. 125 (2019) 125701.

at the SiC/SiO2 interfaces [1]. According to the[2] T. Umeda, T. Kobayashi, M. Sometani, H.

calculations, a high temperature oxygen-poor

Yano, Y. Matsushita, and S. Harada: Appl. Phys.

condition is preferable for reducing theLett. 116 (2020) 071604.

remained carbon defects near the interface.

[3] T. Kobayashi, T. Gake, Y. Kumagai, F. Oba,

Veryrecently,

an

EDMR

and Y. Matsushita: Appl. Phys. Expr. 12 (2019)

experiment091001.

detected carbon-dangling bonds along thedirection perpendicular to the interface. We

56

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles configurational sampling ofhighly-doped ionic conductors
Shusuke KASAMATSU
Faculty of Science, Academic Assembly, Yamagata University
1-4-12 Kojirakawa, Yamagata-shi, Yamagata 990-8560
Ceramic-based

under

be found in that section). For example, Figure 1

intense research for application in battery, fuelshows the percolation of dopants in Y-doped

cell, and electrolyzer applications. TheseBaZrO3 vs. temperature calculated for several

materials are usually prepared by doping

dopant concentrations. A profound temperatureinsulating

charge-dependence is seen at 15%, which is close tocompensating defect is the hole or electron, you

the percolation threshold. Further discussion

have a semiconductor. When the compensating

including successful reproduction of the dopant

defect is a mobile ion (or ion vacancy), youconcentration for maximum conductivity canobtainbe found in Ref. [2].

anelectrolytes

materials.

ionic

When

conductor.

are

the

Often,

thesematerials are used at rather high dopant
percentages of up to ~30% where theconductivity is maximized. There is still muchcontroversy

as

to

what

determines

thismaximum, and computer simulations are
expected to help in this regard.
At such high dopant concentrations, theshort to middle-range order of the dopant
Figure 1 Percolation as functions oftemperature for dopant ratios of 7, 15, 22, and30 mol% in Y-doped BaZrO3.

arrangements should have a profound effect on
the conductivity. To simulate this, i.e., dopant
arrangements as functions of temperature anddopant content, we combined the replica

References

exchange Monte Carlo method directly with

[1] S. Kasamatsu and O. Sugino: J. Phys.:

DFT

Condens. Matter 31 (2019) 085901.

calculations

[1]

(the

softwareforachieving this was selected as this year’s[2] S. Kasamatsu et al., Chemrxiv. Preprint.

Software Advancement Project, so details can

https://doi.org/10.26434/chemrxiv.11786286.v1

57

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analyses of Atomic Structures and Atom Dynamics
at 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

bending is caused by the accumulation of interstitial Li-ions at the metal-Li3 PO4 interfaces,
and the thickness of the Li-ion accumulation
layer is the order of a few Å. For the Li(100)interface, the band bending behavior depends
on the chemical potential of Li, µLi : Slight upward bending occurs for µLi = −2.59 eV, while
downward bending occurs for µLi = −6.11 eVowing to the accumulation of Li vacancies.
Since Au and Li are known to form alloys,
we also performed simulations taking accountof the alloy formation in the form of work function change. Figure 1 shows the calculated
electrostatic potentials and interstitial Li distribution profiles in γ-Li3 PO4 with Au(111),
LiAu3 and Li3 Au(100). In all cases, the potential profiles show upward bending and theaccumulation of interstitial Li ions near the interfaces. However, the amount of interstitial
Li-ions decreases for the alloy cases. From thisresult, we can explain the switching of VOLRAM.

The understanding on atomic structures andatom dynamics at surfaces, interfaces anddefects is crucial to facilitate innovation ofnovel nanoscale information and energy devices. First-principles calculation is a powerful tool to obtain such understanding, but stillinsufficient to tackle with complex models corresponding to real devices.
Keeping the above in minds, we have been
investigating atomic structures and atom dynamics in various systems via first-principles
calculations combined with multi-scale ormachine-learning approaches. In the followings, some of our results in the fiscal year 2018
are described.

2

Structure of interfaces between
metal and solid electrolyte

The distribution and dynamics of Li ions near
the interfaces between metal electrode andsolid electrolyte play important roles in theoperation mechanisms of novel memory device named VOLRAM [1] and all-solid-state
Li-ion batteries. We examined Li ion distribution at the interfaces between γ-Li3 PO4 andmetal electrodes by the method [2] combining
first-principles data of defect formation energies with a one-dimensional continuum model.
Our results [3] show that within the allowed range of the chemical potential of Li in
γ-Li3 PO4 , upward band bending occurs nearAu(111) and Ni(111) interfaces. This upward3

Phonon-related properties of GaN

Conisdering the facts that GaN is promisingfor power semiconductor device and thermal
management is important in power semiconductor device, we have been examining phononband structures and thermal transport properties of GaN. In the fiscal year 2018, we hadconstructed the high-dimensional neural network potential (HDNNP) [4] for crystalline
GaN, and calculated the phonon band structures and thermal conductivities using the58

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

dynamics using the phono3py package. The
calculation results from HDNNP and DFT under the same simulation conditions are in good
agreement, indicating the strong potential of
HDNNP for application in thermal conductivity simulations: The deviation from the DFT
calculation results is within 5.4% from 200 to1000 K.
Then we constructed HDNNP for GaN crystal with N vacancies, and calculated thephonon band structures and thermal conductivities of GaN with N vacancies. In our
preliminary calculations, we obtained reasonable phonon energy bands and thermal conductivities. We will check the reliability of the
HDNNP and examine the effects of N vacancy
on the phonon band and thermal conductivity
in moe detail in the fiscal year 2020.
Figure 1: Calculated electrostatic potential
and the interstitial Li fraction profiles of γLi3 PO4 as a function of the distance from theinterface z, with Au(111), LiAu3 (111), and
Li3 Au(100) (reproduced from Ref. [3]). The
reference of the electrostatic potential corresponds to the Fermi level of metal surfaces.
The chemical potential of Li is set to −2.59 eV.

References[1] I. Sugiyama, R. Shimizu, T. Suzuki, K.
Yamamoto, H. Kawasoko, S. Shiraki, and
T. Hitosugi: APL Mater. 5 (2017) 046105.
[2] S. Kasamatsu, T. Tada, and S. Watanabe:
Solid State Ionics 183 (2011) 20.
[3] K. Shimizu, W. Liu, W. Li, S. Kasamatsu,
Y. Ando, E. Minamitani, and S. Watanabe: Phys. Rev. Mater. 4 (2020) 015402.

constructed HDNNP. Our preliminary results
were described in the Activity Report 2018.

[4] J. Behler and M. Parrinello: Phys. Rev.
Lett. 98 (2007) 146401.

In the fiscal year 2019, we improved the
HDNNP and examined the phonon band
structures and thermal conductivities moreclosely [5]. To obtain data of atomic structures, energies and forces, we performed classical molecular dynamics (MD) simulations witha well-established interatomic potential andthen evaluated the energies and forces by thedensity functional theory (DFT) for structures
sampled from the trajectories of classical MD.
The final root mean square errors of force andtotal energy prediction in the validation data
were 37.8 meV Å−1 and 66.5 meV atom−1 , respectively. The lattice thermal conductivity
were calculated based on anharmonic lattice[5] E Minamitani, M Ogura, and S Watanabe: Appl. Phys. Express 12 (2019)095001.

59

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles molecular dynamics simulation of thewater/air interface using hybrid functionals
Tatsuhiko OHTO
Graduate School of Engineering Science,
Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531
Density functional theory-based molecularcondensed phases. [1]dynamics simulations are increasingly being
used

for

simulating

aqueous

We employed the CP2K code [2], which isinterfaces.

based on the mixed Gaussian and plane wave

Nonetheless, the choice of the appropriate

basis sets.

density functional, critically affecting theoutcome of the simulation, has remained
arbitrary. Here, we assess the performance ofvarious exchange-correlation (XC) functionals,
based on the metrics relevant to sum-frequency
generation spectroscopy. The structure anddynamics of water at the water-air interface aregoverned by heterogeneous intermolecularinteractions, therefore providing a criticalbenchmark for XC functionals. We find that the
revPBE and revPBE0 with the dispersion

Fig. 1: The ability of different functionals tocorrection show excellent performance. The

accurately predict water properties is directly

poor performance of the empirically optimized

compared. The

density-functionalcorresponds to better (worse) predictive power(M06-L)

manifests

theimportance of satisfying exact functional

smaller(larger) score 𝜅of the functional [1].

condition. Understanding the performance ofdifferent XC functionals can aid resolving theReferences

controversial interpretation of the interfacial[1] T. Ohto et al. J. Phys. Chem. Lett. 10, 4914

water structure and direct the design of novel,(2019).

improved XC functionals better suited to[2]

describe the heterogeneous interactions in

http://cp2k.berlios.de/

60

The

CP2K

developersgroup,

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles molecular dynamics simulation of electrondoped graphene/water interfaces
Tatsuhiko OHTO
Graduate School of Engineering Science,
Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531
Ab initio molecular dynamics (AIMD)

To modify the hydrophobic interaction, we

simulation is a powerful tool to describe

calculated

electron-doped-graphenewater

heterogeneous systems such as the water/solidinterfaces using the CP2K code [3]. Althoughinterface. Although AIMD is computationallyI got preliminary results, it seems that theexpensive, it describes electronic states beyond

integer number of electrons is too strongclassical force fields,[1] which is important forelectron doping. It will be required to thinkinterfaces.

about using plane wave codes (though they are

We have simulated sum-frequency generation

computationally demanding).

(SFG) spectra of isotopically diluted water at thewater-graphene and water-hexagonal boronnitride (hBN) sheet interfaces, using ab initio
molecular

dynamics

simulations.

The

simulations themselves were performed using
ISSP several years ago and recently the paper
was published.[2] A sharp ‘dangling’ O-D peakaround ~2640 cm-1 appearing in both simulated

Fig. 1: Structures of the graphene-water

SFG spectra evidences that both graphene andinterface.

hBN are hydrophobic. The dangling O-D peak is
10 cm-1 red-shifted at the water-hBN interface

References

relative to the peak at the water-graphene[1] T. Ohto et al. Phys. Chem. Chem. Phys. 19,

interfaces. This frequency difference manifests a

6909 (2017).

stronger O-D…N intermolecular interaction[2] T. Ohto et al. Phys. Chem. Chem. Phys. 20,

between water and hBN than a O-D…C

12979 (2018)

interaction between water and graphene.

[3]

The

CP2K

http://cp2k.berlios.de/61developersgroup,

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of first-principles electronic-structure
and transport calculation code RSPACE andsimulations for device
Tomoya ONO
Graduate School of Engineering, Kobe University
Rokkodai-cho, Nada, Kobe 657-8501

× 3 ⃗k-point mesh.

Silicon carbide (SiC) has attracted considerable attention owing to its excellent physical properties, such as its high thermal conductivity, high breakdown strength, and large
band gap. It is also advantageous that the oxidation of SiC leads to SiO2 , since it is wellknown that SiO2 exhibits good dielectric properties in Si device technology. However, unlike Si MOSFETs, SiC MOSFETs have unacceptably low carrier mobility. One of the origins of the low carrier mobility is the generation of a large number of interface defects at
the SiC/SiO2 interface during the thermal oxidation. In this study, we carried out density
functional theory calculations to examine theoxidation process of SiC(0001)/SiO2 interfaces
showin in Fig. 1.[2]The oxidation of 4H-SiC is assumed to proceed by the process which we proposed in theprevious study:[3] (a) an O2 molecule arrives
at the interface, splits, and cuts into the Si-C
bonds (2Oif ). (b) One of the O atoms among
the Si-C bonds migrates to a site between the
Si and C atoms connecting the first and second
SiC bilayers (Osub +Oif ). (c) the third O atom
comes by migration between the SiC bonds(Osub +2Oif ) (d) Due to the interface latticemismatch, CO molecule detachment occurs at
the interface (2Oif VC +CO). I found that thelargest energy barrier is 3.21 eV for process(a). Gavrikov et al. [5] employed the interface model, where two- and three-fold structures are mixed, and reported that the activation barrier is larger than 3.5 eV, which is
required for the penetration of an O2 molecule
through the interfacial layer of SiO2 . It isreported by Shen et al. [6] that the barrier
for an O2 molecule penetration is ∼ 4.0 eV.
Akiyama et al. [7] reported the activation barrier of 3.2 eV using the computational model
similar to the 4H-SiC(0001)/β-tridymite SiO2 .
Their reaction path resembles the atomic oxygen mechanism, in which O atoms diﬀuse byhopping from one bond to another, rather thanan O2 molecule penetration. Shen et al. also
reported that the barrier for the atomic oxygen mechanism is ∼ 3.1 eV. Although my reaction process (a) is similar to that proposed
by Akiyama et al., in which the O2 molecule

It is not straightforward to characterize theatomic structure of the SiC(0001)/SiO2 interface because SiO2 at the SiC/SiO2 interface ismainly amorphous. Here, I assume that crystalline structures exist locally at the SiC/SiO2
interface and employ the most possible candidate for the interface atomic structures reported in Ref. 2. RSPACE code[4] is used
for the first-principles calculations. The energy barriers in the oxidation process are computed by the nudged elastic band method. The
lateral lengths of the supercell are chosen to√
be 3a and 3a along the [11̄00] and [112̄0] directions of the 4H-SiC(0001) surface, where ais the lattice constant of SiC, and integration
over the Brillouin zone is carried out using a 2

62Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

is the reaction-limiting process.

is not a molecule after passing the interfacial
SiO2 layer, my process is diﬀerent from theirsituation, in which the interfacial O atom hops
to the SiC bond and Si2 -CO structure is generated. When I assume that the O2 molecule behaves like two O atoms at the oxidation front,
the activation barriers obtained by these theoretical calculations are comparable. Thus, O2
molecules dissociate when they pass the interfacial SiO2 layer with the barrier of ∼ 3.2 eV.
Next, let me discuss the barrier after the O
atoms cut into the SiC bonds. Gavrikov et
al. reported that the CO molecule is emitted
from the Si2 -CO structure with the activation
barrier of 2.8 eV. Since the Si2 -CO structureis less stable than the Osub +Oif structure by
0.6 eV, the total activation barrier from theOsub +Oif structure is 3.4 eV. Köhler et al.
reported the barrier for the CO molecule detachment of 3.1 eV. If the energy diﬀerence
reported by Gavrikov et al. is added, the total barrier from the Osub +Oif structure is 3.7
eV. It is also reported by Akiyama et al. thatthe activation barrier for the CO molecule detachment from the Si2 -CO structure is 1.7 eV,
which is much smaller than the results calculated by Gavrikov et al. and Köhler et al.
If I believe the larger barrier calculated by
Gavrikov et al. and Köhler et al., these results imply that the CO detachment also limits
the reaction. However, in our previous study[3], we reported that the CO desorption preferentially occurs when the interfacial C atom
is surrounded by three O atoms. The activation barriers for the migration of O atoms at
the SiC/SiO2 interface are 2.72 eV for process(b) and 2.08 eV for process (c). It is noteworthy that these barriers vary between 2.0 eV
and 2.8 eV depending on the configuration of
the O atoms at the interface. When the thirdO atom is considered, the barrier for the O2
molecule penetration is still higher than thatfor the CO detachment. Thus, it can be concluded that the CO detachment does not limit
the reaction and the O2 molecule penetration

Figure 1: Interface atomic structure of βtridymite SiO2 on SiC. Blue, brown, and redballs are Si, C, and O atoms, respectively. The
supercell contains 30 Si, 24 C, 14 O, and 8 H
atoms. H atoms are used for termination of
dangling bonds at the surfaces.

References[1] T. Ono et al., Phys. Rev. B 96 (2017)115311.
[2] T. Ono, Mater. Sci. Forum 963 (2019)208.
[3] T. Ono and S. Saito, Appl. Phys. Exp. 4(2011) 021303.
[4] K. Hirose, T. Ono, Y. Fujimoto, and S.
Tsukamoto: First Principles Calculations
in Real-Space Formalism (Imperial College, London, 2005).
[5] A. Gavrikov et al., J. Appl. Phys. 104(2008) 093508.
[6] X. Shen et al., J. Appl. Phys. 114 (2013)
033522.
[7] T. Akiyama et al., Surf. Sci. 641 (2015)
174.
[8] C. Köhler et al., Phys. Rev. B 64 (2001)
085333.

63

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-Principles Study of Excited Electron, Positronand Atom Dynamics and Optical and Thermoelectric
Properties of Nanostructures
Kazuyuki WATANABE, Yasumitsu SUZUKI,
Kazuki UCHIDA, Tomokazu YAMAGUCHI and Masashi YOSHISATO
Department of Physics, Tokyo University of Science
1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601

In this project we investigated the following four topics on the basis of time-dependent
density functional theory (TDDFT). 1) Angleresolved photoemission spectroscopy (ARPES)
in low-dimensional periodic structures, 2)
Stationary-state electron scattering using acomplex injecting potential (CIP), 3) Opticaland thermoelectric properties of low dimensional materials, and 4) Development of theexchange-correlation term in TDDFT.
1) Angle-resolved photoemission spectroscopy
in low-dimensional periodic structures [1]:We proposed a new approach based on
TDDFT for the calculation of ARPES of
low-dimensional periodic structures, such asgraphene, silicene, and polyacetylene. The calculated ARPES spectra reproduced the occupied energy band structures fairly well. We
further investigate the electron doping effect on ARPES by considering Li-intercalated
bilayer graphene and found a shift in the
Fermi energy. These show that the present
method can provide reliable ARPES spectra
for materials for which ARPES experiments
are diﬃcult to perform under some conditions. We note that the present method is simpler and uses a more direct one-shot TDDFT
calculation for ARPES than previous theories. Further applications to time-resolved andspin-resolved ARPES simulations will be presented elsewhere. The simulations have been
conducted by our homemade TDDFT code,

KENS. Parallelized calculations have been performed using System B.
2) Stationary-state electron scattering using acomplex injecting potential [2]:We simulated stationary electron scattering by solving the time-dependent Schrödinger
equation with a CIP. The calculated electron transmission probabilities through onedimensional potentials and the electron interference patterns caused by double slits show
good agreement with analytical results. The
Aharonov–Bohm eﬀect is also clearly demonstrated by the presence of a vector potential
at one side of the double-slit configuration.
Also, from the simulation of the arranged-CIP
method, we predict that this new method canbe applied to BEC interference simulations.
Since the present method can be straightforwardly extended to TDDFT, we can simulate field electron emission, photo-induced
electron emission, secondary electron emission,
thermionic emission, and so on. The simulations have been conducted by our homemadecode, SCIP, using System B.
3) Optical and thermoelectric properties of low
dimensional materials [3]:We studied the optical and thermoelectric
properties of various low dimensional materials
by means of the first-principles method.
First, we applied TDDFT to the calculation of absorption spectra for two-dimensional
atomic-layer materials: mono-layer and bi-

64Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

layer hexagonal boron nitride (h-BN) andmono-layer transition metal dichalcogenides,
MoS2 and MoSe2 . We demonstrated that
the TDDFT approach with the meta GGA
exchange-correlation potential and the bootstrap kernel can capture the characteristicsof the first bright excitonic peak of bi-layerh-BN that is dependent on the layer stacking type. We also revealed that the TDDFT
method can capture the qualitative features of
the absorption spectra for mono-layer transition metal dichalcogenides, although the exciton binding energies are underestimated compared to those obtained by the many-body
pertubation theory (MBPT) calculation. This
study elucidates the usefulness of the TDDFT
approach for the qualitative investigationof the optical properties of two-dimensional
atomic layer materials. MBPT calculations
and TDDFT calculations have been conduced
using EXCITING (http://exciting-code.org/)and ELK (http://elk.sourceforge.net/) code,
respectively. Parallelized calculations havebeen performed using System B.
Next, we calculated the thermoelectric
power factor of pnictogen (P, As, Sb, Bi)nanoribbon structures using the density
functional theory (DFT) and non-equilibrium
Green’s function (NEGF) method. We foundthat the power factor properties strongly
depend on the structure of nanoribbons, i.e.,the buckled nanoribbon generally exhibit
higher power factor than the puckered one.
It was also found that the light pnictogens (P, As, Sb) have an advantage overthe heavy one (Bi) in giving a high power
factor. This study reveals a part of therelationship between the electronic structure
and the thermoelectric property of pnictogen nanoribbons, and provides the useful
information to develop the thermoelectric
devices based on pnictogen nanoribbons. All
DFT calculations and NEGF calculations
have been conduced using Quantum Espresso(https://www.quantum-espresso.org/)
and

WanT (http://www.wannier-transport.org/)code, respectively. Parallelized calculations
have been performed using System B.
4)Development of the exchange-correlation
term in TDDFT:
We developed a machine learning based approach to improve the approximation to theexchange-correlation potential of TDDFT. We
trained the neural-network projection from thetime-varying electron densities to the corresponding correlation potentials in the time dependent Kohn-Sham equation using a few exact datasets for a model system of electronhydrogen scattering. We demonstrated that
this neural-network potential can capture thecomplex structures in the time-dependent correlation potential during the scattering process
and provide correct scattering probabilities,
which are not obtained by the standard adiabatic functionals. This study oﬀers a novel way
to improve the exchange-correlation potentialof TDDFT. The simulations have been conducted by our homemade code. Parallelized
calculations have been performed using System B.

References[1] K. Uchida, Y. Akimoto, K. Einaga, andK. Watanabe, Jpn. J. Appl. Phys. 58,
128001 (2019).
[2] T. Yamaguchi, K. Uchida, K. Varga, andK. Watanabe, J. Phys. Soc. Jpn. 89,
044002 (2020).
[3] Y. Suzuki and K. Watanabe, Phys. Chem.
Chem. Phys. 22, 2908 (2020).

65

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab initio phonon calculation for Ca5Ir3O12
Kazuma NAKAMURA
Quantum Physics Section, Kyushu Institute of Technology
1-1 Sensui-cho, Tobata, Kitakyushu, Fukuoka, 804-8550
4

The title compound has recently attracted
attention as a thermoelectric material because
it has a relatively high Seebeck coeﬃcient.
In this study, we report an ab initio study
about electronic and phononic properties for
Ca5 Ir3 O12 . In particular, we investigated theeﬀect of spin-orbit interaction (SOI) on the
low-energy properties [1].

Energy (eV)

3

(a)

2
1
0
-1
-2
-3
-4
0.6

Energy (eV)Density functional calculations with planewave basis sets were performed using thexTAPP code [2], where the ultrasoft pseudopotential and the generalized gradient approximation (GGA) of the exchange correlation potential were employed. The cutoﬀ energies in
the wavefunction and charge densities were 64
and 900 Ry, respectively, and the SOI was explicitly considered. To study the eﬀects of SOI,
we performed the usual GGA calculation andcompared it with the result including the SOI.
Below, we refer to the former as GGA and to
the latter as SO-GGA. The atomic and lattice
parameters were optimized with an 8×8×8 kpoint sampling, and we found that SO-GGA
reproduces the experimental crystal structure
quite well. The Fermi-surface calculations
were performed with the dense 21×21×63 kpoint sampling to obtain the detailed surface structure [3]. Phonon calculations with afrozen phonon approximation were performed
using the PHONOPY for 1×1×3 and 2×2×1
supercells [5, 6]. For the k-point sampling,
11×11×11 was used for 1×1×3 supercell calculation, and somewhat coarse 9×9×5 was used
for the 2×2×1 supercell calculation.

0.4

(b)

0.2
0

-0.2
-0.4

L

M

(c)

A
L

M

A

H

(d)

Γ

K

Γ

A
L

H

K

Γ

M

H

K

Γ

Figure 1: (Color online) (a) Ab initio electronic band structure considering the SOI in
Ca5 Ir3 O12 . The energy zero is the Fermi level.
(b) A zoom of the low-energy band structure,
where the SO-GGA result (thick red curves)is compared with the usual GGA result (thinblue curve). (c) Calculated Fermi surface for
SO-GGA and (d) GGA.

Figure 1(a) shows our calculated band structure. To see the SOI eﬀect, the SO-GGA band66

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

M points. However, since the calculation conditions for the 2×2×1 calculation are rough, it
is necessary to perform the calculation undermore severe conditions.

(thick red curves) is compared with the GGA
band (thin blue curves) in Fig. 1(b). An appreciable diﬀerence can be observed in the lowenergy bands; the GGA result exhibits metallic bands, particularly along the L-M or H-Klines. When the SOI is switched on, the metallic bands are split and a pocket-like band structure appears. The gap size due to the SOI is
about 0.3 eV, which is comparable to the valence bandwidth 0.5 eV.

700

(a)

600

Energy (cm-1)

500

Figures 1(c) and 1(d) show the Fermi surfaces based on the SO-GGA and GGA, respectively. We see that the GGA Fermi surface
is contributed from the two bands (indicatedin dark-blue and bright-red colors), while the
SO-GGA Fermi surface is basically formed by
the one band; the SOI makes the bright-red
colored GGA Fermi surface disappear. In the
SO-GGA Fermi surface, since the SOI resolves
the band degeneracy, the Fermi surfaces are
seemingly two (dark-blue and bright-blue colored surfaces); however, these two are originated from the same band. Also, in the SOGGA Fermi surface, we see a sheet structure
along the c∗ -axis (the Γ-A line), which indicates a nesting trend along this direction. We
note that the SOI is relevant to the narrowing of the sheet separation between the blue
colored Fermi surfaces.

400
300
200
100
0
-100
600

(b)

500

Energy (cm-1)

400
300
200
100
0
-100
-200

L

M

Γ

A

H

K

Γ

Figure 2: (Color online) Ab initio phonon dispersion with the SOI in Ca5 Ir3 O12 . Panels(a) and (b) show results based on 1×1×3 and2×2×1 superlattice, respectively.

References

Figures 2(a) and 2(b) are our calculated
phonon dispersions with SOI for 1×1×3 and2×2×1 supercells, respectively. It was foundthat the experimental results at the room temperature are better reproduced by the 1×1×3
supercell calculation. The panel (b) is a preliminary phonon calculation on a 2×2×1 supercell. This supercell includes the displacement degree of freedom in an in-plane 2×2 superlattice, and we can investigate the phonon
instability within this superlattice. On theother hand, the 1×1×3 supercell can clarify
the triple-period phonon instability along thec-axis. Within these two supercells, we observe
phonon softening in the 2×2×1 supercell calculation; there is a sign of softening at the K and[1] K. Matsuhira, K. Nakamura, Y. Yasukuni, Y. Yoshimoto, D. Hirai, Z. Hiroi:
J. Phys. Soc. Jpn. 87 (2018) 013703/1-5.
[2] http://xtapp.cp.is.s.u-tokyo.ac.jp[3] http://fermisurfer.osdn.jp[4] https://atztogo.github.io/phonopy[5] T. Hasegawa, W. Yoshida, K. Nakamura,N. Ogita, and K. Matsuhira:: J. Phys.
Soc. Jpn 89 (2020) 054602/1-11.
[6] H. Hanate, T. Hasegawa, S. Tsutsui, K.
Nakamura, Y. Yoshimoto, N. Kishigami,
S. Haneta, and K. Matsuhira1: J. Phys.
Soc. Jpn 89 (2020) 053601/1-5.

67

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab initio derivation of eﬀective low-energy model of
Ca5Ir3O12
Kazuma NAKAMURA
Quantum Physics Section, Kyushu Institute of Technology
1-1 Sensui-cho, Tobata, Kitakyushu, Fukuoka, 804-8550

dxy and dyz orbitals. Here, the notation of
the orbital follows a local coordinate system
ﬁxed to the IrO6 octahedron. Based on thisobservation, we perform parameter derivationof the dxy /dyz model. Figure 1 is a comparison of the Wannier-interpolation band (greendashed curves) and the original band (red-solid
curves). We see that the original band has
been completely reproduced. Note that the initial guess setting is very important for obtaining such reproducibility. We set the dxy anddyz orbitals as initial guesses, where the initial guess orbitals are represented in the local
coordinate system ﬁxed to IrO6 octahedrons,
and additionally rotated the spin quantization
axis. This treatment is very important to satisfy the symmetry of the calculated Wannierorbitals, that is, all 12 Wannier orbitals havethe same spread.

In this report, we report a ﬁrst-principles
derivation of an eﬀective low-energy model for
Ca5 Ir3 O12 . In order to perform the eﬀectivemodel derivation of materials with strong spinorbit interaction (SOI) such as iridium system,
we extended the ﬁrst principle eﬀective-model
derivation software RESPACK [1] to the spinor
type.
The density-functional band-structure calculations for Ca5 Ir3 O12 are performed using
xTAPP [2] with the experimental lattice parameters [3]: a = 9.3490 Å and c = 3.1713
Å. We use the norm-conserving pseudopotential and the generalized gradient approximation (GGA) of the exchange correlation
potential. We use 8×8×8 k-points for sampling in the ﬁrst Brillouin zone. The energy cutoﬀ is set to be 144 Ry for the wave
functions, and 576 Ry for the charge density.
The interaction parameters are calculated using the constrained random-phase approximation method, in which we employ the scheme
for the band disentanglement. The energy cutoﬀ for the dielectric function is set to be 20 Ry.
The total number of bands used in the calculation of the polarization is 300, which includes
the unoccupied states up to ∼ 26 eV with respect to the Fermi level. To study the eﬀects
of SOI, we performed the usual GGA calculation and compared it with the result including
the SOI. Below, we refer to the former as GGA
and to the latter as SO-GGA.

3

Energy (eV)

2
1
0
-1
-2
-3

L

M

Γ

A

H

K

Γ

Figure 1: (a) Ab initio density functional band
structure considering the spin-orbit interaction
in Ca5 Ir3 O12 .

From the fat band analysis, it was found thatthe band structure near the Fermi energy is

68Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

We next show in Fig. 2 the resulting maximally localized Wannier functions for dxy /dyz
model. The panels (a) and (b) indicate the dxy
and dyz Wannier functions, respectively. Notethat in this plot, three independent Wannierfunctions are shown in one panel.

Table 1: Main parameters of dxy /dyz model of
Ca5 Ir3 O12 , where we show 3 nearest-neighbor(NN) transfers, onsite transfers, and largest inNN
NN
terchain electron transfer. txy↑,yz↑
and tyz↑,xy↑
onsiteare nearest neighbor trasnfers. Also, txy↑,yz↓
is the spin-orbital couplings in the same site.
The interaction parameters with the bare (unscreened) and constrained RPA (cRPA) arelisted. VNN is the orbital-averaged value of thenearest-neighbor interactions. Also, VIC is theorbital-averaged value of the interchaicn interaction. The unit of the parameters is eV.
SO-GGA

GGA

NN
txy↑,yz↑

0.167

0.167

NN
tyz↑,xy↑

0.210

0.208

largesttinterchain

0.032

0.039

onsitetxy↑,yz↓

0.213

-

U
U′
V NN
V interchain
J

bare

cRPA

bare

cRPA

9.87
9.19
4.43
2.86
0.27

2.43
1.95
0.99
0.52
0.21

10.03
9.28
4.39
2.86
0.29

2.23
1.68
0.77
0.44
0.23

As another achievement, we calculated theRaman frequency [4] and the phonon dispersion curves [5].

References[1] https://sites.google.com/view/kazuma7k6r[2] http://xtapp.cp.is.s.u-tokyo.ac.jp

Figure 2: Maximally localized Wannier functions of Ca5 Ir3 O12 : (a) dxy and (b) dyz Wannier functions.

[3] M. Wakeshima, N. Taira, Y. Hinatsu, and
Y. Ishii, Solid State Commun. 125, 311(2003).

Our derived model parameters for Ca5 Ir3 O12
are summarized in the Table 1. The spin-orbit
coupling is estimated as 0.213 eV. The nearest
neighbor parameter tN N is 0.167 eV, the onsite interaction U based on constraind RPA is
2.43 eV, and the nearest-neighbor interaction
V is estimated as 0.99 eV. Then, the correlation degree of freedom (U − V )/t is 8.62.

[4] T. Hasegawa, W. Yoshida, K. Nakamura,N. Ogita, and K. Matsuhira:: J. Phys. Soc.
Jpn 89 (2020) 054602/1-11.
[5] H. Hanate, T. Hasegawa, S. Tsutsui, K.
Nakamura, Y. Yoshimoto, N. Kishigami, S.
Haneta, and K. Matsuhira1: J. Phys. Soc.
Jpn 89 (2020) 053601/1-5.

69

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles calculations of thermoelectric
properties in magnetic materials
Fumiyuki ISHII, Susumu MINAMI, Rifky SYARIATI, Akihiro HORI,
Hikaru SAWAHATA, Naoya YAMAGUCHI, Monika NUR
Nanomaterials Research Institute, Kanazawa University
Kanazawa, 920-1192, Japan

1. Development of Methods and Codes
The thermoelectric conversion based on theanomalous Nernst eﬀect (ANE) has attracted
much attention because the ANE realizes thehigh-density integration more easily comparedto that based on the Seebeck eﬀect[1]. The
ANE is the phenomenon that the electric
power is created along the direction perpendicular to both the temperature gradient andthe magnetization in magnetic materials. Thiseﬀect is induced by the anomalous Hall conductivity (AHC), and if the AHC changes drastically as a function of the Fermi level, we expect the large ANE[2]. In our previous firstprinciples study, we predicted that an electron
doped EuO skyrmion crystal shows the large
ANE induced by the finite Chern number at
the Fermi level[3]. For discovery and designof new materials which have the large ANE
via computational high throughput screening,
we need an eﬃcient computational method
to investigate the Fermi level dependence of
the AHC. We have implemented the code ofcomputing the AHC applicable to metallic
systems in OpenMX package[4] by improving
Fukui-Hatsugai-Suzuki method[5]. Using thiscode, we computed AHCs σxy (ε) and transverse thermoelectric conductivities αxy (ε) in
two-dimensional ferromagnetic materials.
2. Applications to 2D Materials
The discovery of magnetism in the twodimensional materials[6] open a way for realizing thermoelectric devices based on anoma-

lous Nernst eﬀect. The surface phonon scattering advantage in the two-dimensional materials can decrease the thermal conductivity
which can increase the thermoelectric figureof merit ZT [7].The magnitude of anomalous
Nernst eﬀect itself depend on Seebeck eﬀect
or anomalous Hall eﬀect[2, 3]. In our previous
study, we reported that the half-metallic materials possess large anomalous Nernst eﬀect[8].
Here, we performed first-principles calculations to explore the anomalous Nernst eﬀect ofhalf-metallic transition-metal dihalides monolayer using OpenMX package[4]. We analyzed its magnitude based on the semiclassical transport theory and found that there islarge anomalous Nernst eﬀect at 100 K. The
large Berry curvature which contributed bybands near Fermi level is the main reason ofits large magnitude. These results suggest thattransition-metal dihalides monolayer can potentially be used in thermoelectric devices.
3. Thermal Conductivity and ZT
To evaluate eﬃciency of thermoelectric materials, it is important to examine the contributionof thermal conductivity to the thermoelectric
figure of merit ZT that represents the performance of the material. Since the thermal conductivity can be described for each electron
and lattice, in this research, we theoreticallycomputed both electronic and lattice thermal
conductivity, and then evaluated ZT . Theoretical analysis of lattice thermal conductivity is conducted by Boltzmann transport the-70Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

ory with relaxation time approximation. In
order to do this, it is necessary to determine
the inharmonic atomic force constant exactly,
and an accurate analysis is carried out by
first-principles calculations based on density
functional theory. As computational codes,
OpenMX package[4] is used as a density functional calculation, and ALAMODE[9, 10] isused as a lattice thermal conductivity calculation. The half-Heusler compounds are ternarycompounds, have composition formula of XYZ,
and are expected as thermoelectric materials
that exhibit high power factor in a medium
temperature range of about 600 to 1000 K. We
analyzed thermoelectricity and thermal conductivity of ferromagnetic half-metallic halfHeusler MnCoSb[8]. We evaluated the ZT for
the Seebeck and anomalous Nernst eﬀect. We
discussed carrier and temperature dependenceof ZT .
4. Surface Structures and Atomic Radii
To design new functional materials, surface
alloying is an eﬀective way to obtain desired materials. Surface alloys are synthesized by inserting atoms into the surface. This
topic has attracted a lot of research attention lately because of some of its applications, such as spintronics[11], where there isa giant spin splitting in Bi/Ag(111) surface
alloys[12, 13]. Many types of surface alloys
have been studied: for example, Ge/Ag(111),
Pb/Ag(111), Bi/Ag(111), and Sn/Ag(111).
One structure that has been observed in ex√√
periments with surfaces is 3 × 3 R 30◦ .
Structural studies for surfaces alloys can provide important information for forming metalsemiconductors interface and metal interfaces.
The metal-semiconductor interface is very important to industry, for example, the Si/Ag
interface is a promising candidate for solar
cells. We systematically explored the structural stability of M /Ag(111) surface alloys by
first-principles calculation using the OpenMX
package[4], where M is group III (B, Al, Ga,
In and Tl), IV (C, Si, Ge, Sn and Pb) and V

atom (N, P, As, Sb and Bi). We focused on thecorrugation parameter d which is determinedby the height of the M atom from the Ag atomin the plane of the top-most atom. We introduced concept of atomic radii to understandthe tendencies of corrugation in M /Ag(111).
The formation energy for each M atom is also
calculated to determine the stability of the surface alloys. We discussed the dependence of M
atoms on corrugation parameters.

References[1] Y. Sakuraba, Scr. Mater. 111, 29 (2016).
[2] Y. P. Mizuta and F. Ishii, Sci. Rep. 6,28076 (2016).
[3] Y. P. Mizuta, H. Sawahata, and F. Ishii,
Phys. Rev. B 98, 205125 (2018).
[4] T. Ozaki et al., http://www.openmxsquare.org/[5] T. Fukui, Y. Hatsugai, and H. Suzuki, J.
Phys. Soc. Jpn. 74, 1674 (2005).
[6] B. Huang et al., Nature 546, 270 (2017).
[7] R. Anufriev, J. Maire, and M. Nomura,Phys. Rev. B 93, 045411 (2016).
[8] S. Minami, F. Ishii, Y. P. Mizuta, and
M. Saito, Appl. Phys. Lett. 113, 032403(2018)[9] T.Tadano, https://alamode.readthedocs.io[10] T. Tadano, Y. Gohda, and S. Tsuneyuki,
J. Phys.: Condens. Matter 26, 225402(2014)[11] C. R. Ast et al., Phys. Rev. Lett. 98,
186807 (2007).
[12] I. M. Mcleod et al., Surf. Sci. 604, 1395
(2010).
[13] N. Yamaguchi, H. Kotaka, and F. Ishii, J.
Cryst. Growth 468, 688 (2017).

71

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Reduction of Rare Metals in Formic Acid Decomposition
Catalysts and Oxygen Storage Materials
Yuji KUNISADA
Center for Advanced Research of Energy and Materials, Faculty of Engineering,
Hokkaido University, Sapporo, Hokkaido 060-8628
We investigated the catalyst adsorption

catalytic activity using a theoretical volcano

and diffusion properties on non-metal element

plot reported in the previous study.[1] From

doped graphene with the aid of the first-

the adsorption energy of intermediates, we

principles calculation based on the density

estimated the reaction activities. We found

functional theory (DFT). We also investigatedthat the embedded Cu atoms in graphene

the corresponding catalytic activity. Besides,

show higher activity than Cu clusters on

wegraphene.

investigatedproperties

of

the

oxygensubstituted

absorption

brownmillerite

Weoxides.

also

investigatedtheoxygenabsorption properties of partially substituted

At first, we investigated adsorption and

Ca2AlMnO5.

We

revealedthat

Mn-sitediffusion properties of Cu clusters on non-substitution is favorable for the oxygen

metal element doped graphene. We also

absorption-desorption process than Al-site

considered Cu oxide clusters and Cu atoms

substitution.

embedded in the graphene basal plane. We

We also studied the isotope effect on theperformed the total energy and electronic

alkene hydrogenation process on Rh-based

structure calculations using The Vienna AbIntermetallic catalyst [2] and the structure andinitiomagnetism of Ca2RuO4 nanofilm.[3]simulation

package(VASP).

We

installed a parallelized VASP with Intel® MPI

References

Library and Intel® Math Kernel Library. We[1] J. S. Yoo, F. A.-Pedersen, J. K. Nørskov, F.

found that the adsorption energies andStudt: ACS Catal. 4 (2014) 1226.

diffusion activation barriers of Cu clusters[2] S. Furukawa, P. Yi, Y. Kunisada, K.

increase by non-metal element doping into

Shimizu, Sci. Technol. Adv. Mater.

graphene lattice. We note that Cu oxide

20 (2019) 805.

clusters also show the same trend, and the[3] H. Nobukane, K. Yanagihara, Y. Kunisada,

embedded Cu atoms in graphene have quite

Y. Ogasawara, K. Nomura, Y. Asano, S.

high stability. We also investigated theTanda, Sci. Rep. 10 (2020) 3462.

72

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Material exploration by advanced first-principles simulation
Shinji TSUNEYUKI
Department of Physics, School of Science,
The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033
Institute for Solid State Physics,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8581
The density functional theory (DFT)-based

X-ray diffraction data from high-pressure

first-principles electronic structure calculation

experiments), we aimed to establish simulation

method has played an important role as amethods that strongly support experimental

powerful research tool in material properties andresearch on materials under extreme conditions,as a predictor of new materials and structures.

new materials with only poor quality crystals,

Weand materials containing hydrogen that are

have

been

developing

fundamental

difficult to observe experimentally.

simulation methods, such as the accurate
calculation of the lattice thermal conductivity

In this method, instead of finding the global

using DFT calculations and the prediction of theminimum of the multi-dimensional potential

superconducting transition temperature using

energy surface 𝐸(𝐑) as a function of the atomic

superconducting

theorypositions R, we define the effective potential(SCDFT), in collaboration with experimentalists.

𝐹(𝐑) by the sum of 𝐸(𝐑) and a so-called

densityfunctional

In this fiscal year, we focused on determining

penaltyfunctionthe crystal structure of unknown materials, andincreases

when

predicting the physical properties of these newintensity 𝐼calc (R)deviates from the experimental

materials in collaboration with the experimental

one 𝐼obs :𝐷[𝐼obs , 𝐼calc (R)],thesimulatedwhich

diffractiongroups of the Grant-in-Aid for Scientific

𝐹(𝐑) = 𝐸(𝐑) + 𝛼𝑁𝐷[𝐼obs , 𝐼calc (R)].

Research on Innovative Areas "Hydrogenomics:

Here, N is the number of atoms in the simulation

Creation of Innovative Materials, Devices, andcell and a is a control parameter. Note that, in

Reactivecase of the powder diffraction. 𝐼obs and 𝐼calc (R)Processes

usingHigher-Order

Hydrogen Functions" (FY 2018-2022) and theare functions of diffraction angle.

Tokodai Institute for Element Strategy. In
particular,bydeveloping

structure

simulation

Previously, as a first trial, we adopted

data-assimilated

methods

based“crystallinity” for the penalty function, in whichon

we used diffraction angles but not the diffraction

incomplete experimental data (e.g., incomplete

intensity [1]. The method is useful when the73

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

relative intensity of diffraction peaks is notprobability. Therefore, we also investigated thereliable. It is, however, not necessarily robust

efficient sampling of the average diffraction

when the crystal symmetry is extremely low, or

pattern of the system (Fig. 1). We are currently

the noise in the experimental data is very large.

working on a test calculation combining thismethod with the neural network potential.

Therefore, in FY 2019, we introduced thecorrelation between 𝐼calc (R) and 𝐼obs for the
penalty function. With this penalty function, we
can treat all the diffraction data, including eventhe noise, on the same footing and utilize as
much information as possible. We found the new
penalty function improves the predictability of
crystal structures.
We also developed a method to search forstructures by treating the potential energy 𝐸(𝐑)
and

the

penaltyfunction𝐷[𝐼obs , 𝐼calc (R)] independently of each other,

Fig. 1 An average structure of the high-using their gradients to avoid local stabletemperature phase of LiCB9H10 determined bysolutions [2].

the data assimilation method.

Using these methods, it is possible to searchfor complex structures containing more than 100

References

atoms in the simulation cell. However, the[1] N. Tsujimoto, D. Adachi, R. Akashi, S. Todo

search becomes difficult when a specificand S. Tsuneyuki, Phys. Rev. Materials 2,

element in a material is disordered, i.e., a053801 (2018).

specific element partially occupies multiple sites[2] D. Adachi, N. Tsujimoto, R. Akashi, S. Todo,or arrangements in a unit cell, or two

and S. Tsuneyuki, Comput. Phys. Commun. 241,

components occupy the same site with a certain

92 (2019).

74

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study for widening the potential of spinpolarized positron experiments
Mineo SAITO
Institute of Science and Technology, Kanazawa University
Kakuma, Kanazawa, 920-1192 JapanSpin

polarized

positronoxides and nitrides are due to thetechniquedetectedfact that the atomic radii of the firstsome spin polarized vacancies in

raw atoms are small and thus thesemiconductors.

spinannihilation

polarized

We

cation

study

spin-

vacanciesindensities

aresubstantiallylocalized at the four nearest anions

wurtzite structure semiconductors

in. the cation vacancies.

(BeO, ZnO, ZnS, CdS, BN,AlN, GaN

Finally, we study the symmetry

and GaP) by using first-principles

lowering effect from C3v to Cs whichcalculations based on the density

reduces the magnetic moments; wefunctional theory. We find that C3v

study

geometries are the most stable andpairing and departing distortions.

are spin-polarized. Two majority

The magnetic moment becomes 0 in

spin electrons occupying the defect E

the case of II-VI semiconductors andlevel lead to the magnetic moment of

the magnetic moments become 1 μB

2

II-VI

in the case of III-V semiconductors.

semiconductors. On the contrary, in

We find that these low spin states

the case of III-V semiconductors,

have higher energies than the C3v

threeelectrons

high spin states due to the fact thatoccupying the defect E and A1 levels

the symmetry lowering effect do not

inducesignificantly stabilize the system.

μ

in

B

the

case

majorityspinof

the magnetic moment of 3

μB.
Theenergies

spin
are

large

polarization
inthesemiconductors consisting of firstrow anions, i.e., oxides and nitrides.
The stabilities in the cases of the

75

the

possibilities

of

both

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Unification of massively parallel quantum material simulationand data-driven science
Takeo Hoshi
Department of Applied Mathematics and Physics, Tottori University,
4-101 Koyama-Minami, Tottori 680-8550, Japan.
(

The present project was carried out for the

https://www.pasums.issp.u-tokyo.ac.jp).

joint research between quantum material

Since the analysis method has a general

simulation and data driven science. Related

mathematical foundation, it is also applicable tomathematical studies and software development

other experiments, such as X-ray or electron

were also carried out. The main collaborators

diffraction

are K. Tanaka (Tottori U, D. student), H.

electronic structure calculations were carried

Imachi (Tottori U, now in Preferred Networks),

out for a 10-nm-scale pentacene thin film as aK. Yoshimi (ISSP), I. Mochizuki, T. Hyodo

foundation of flexible transistor [3]. Semi-(KEK-IMSS), T. Fujita (IMS), T. Fukaya

localized wavefunctions that expand over

(Hokkaido U), Y. Yamamoto (UEC), H. Matsui

several tens of molecules were obtained, which(Yamagata U) and T. Ogita (TWCU).

isexperiments.

consistenttoelectron

(ii)

spin

Large-scale

resonance

The main achievements are explained

experiment. The study was carried out by ourhereafter. (i) The data analysis software wasoriginal code ELSES ( http://www.elses.jp/ ),developedfor

an order-N electronic state calculation code

positrondiffraction

total-reflection

high-energynovelwith a ab initio based tight-binding method. In

experimental technique for surface structure

addition, several fundamental methodologies

determination

using

were developed for large-scale calculation of

TRHEPD are being conducted intensively atorganic flexible device materials [4,5]. (iii)theSeveral fundamental numerical algorithms were

Slow

(TRHEPD),[1,2].

Positrona

Experiments
Facility,

InstituteofMaterials Structure Science, High Energy

investigated [6-8].

Accelerator Research Organization, revealing

published for reviews of our recent researchsurfaceactivities in large-scale electronic structure

structureofinterest.

Figure1demonstrates the structure determination of the(iv) Two books were

calculations with supercomputers [9,10].

Ge(001)-c(4x2) surface [2]. At April of 2020,
thesoftwarepromoted todevelopment

activitywasReferences

Project for Advancement of[1] Development of data-analysis software forSoftware Usability in Materials Science in ISSP

total-reflection high-energy positron diffraction76

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo(TRHEPD), K. Tanaka, T. Hoshi, I. Mochizuki,

Appl. Math. 376, 112830/1-13 (2020)

T. Hanada, A. Ichimiya, T. Hyodo, Acta. Phys.

[8] K𝜔 -- Open-source library for the shifted

Pol. A 137, 188-192 (2020).

Krylov subspace method, T. Hoshi, M.

[2] Two-stage data-analysis method for total-

Kawamura, K. Yoshimi, Y. Motoyama, T.

reflection

Misawa, Y. Yamaji, S. Todo, N. Kawashima, T.

high-energy

positrondiffraction(TRHEPD), K. Tanaka, I. Mochizuki, T.

Sogabe,Hanada, A. Ichimiya, T. Hyodo, and T. Hoshi:

http://arxiv.org/abs/2001.08707

Submitted;[9] Recent progress in large-scale electronic

Preprint:

Submitted;

Preprint:

https://arxiv.org/abs/2002.12165

state calculations and data-driven sciences, T.

[3] Numerical aspect of large-scale electronic

Hoshi and S. Ito, Chap. 14 of Handbook ofstate calculation for flexible device material, T.

SiliconHoshi, H. Imachi, A. Kuwata, K. Kakuda, T.

Technologies 3rd Ed., Elsevier (2020).

Fujita, H. Matsui, Japan J. Indust. Appl. Math[10] Numerical methods for large scale36, 685-698 (2019).

electronic state calculation on supercomputer, T.

[4] Charge-transfer excited states in the

Hoshi, Y. Yamamoto, T. Sogabe, K. Shimamura,

donor/acceptor interface from large-scale GW

F. Shimojo, A. Nakano, R. Kalia, P. Vashishta,

calculations, T. Fujita, Y. Noguchi, T. Hoshi, J.

Chap. 15 of 21st Century Nanoscience - A

Chem. Phys. 151, 114109/1-8 (2019)

Handbook: Nanophysics Sourcebook (Volume[5]

Computational

conductivity

study

for

electricalpropertiesoforganic

Based

MEMS

Materials

andOne), CRC Press (2019).

semiconducting polymers and metal complexhost systems, M. Ishida, M. Arita, S. Nishino, T.
Hoshi, submitted.
[6] EigenKernel - A middleware for parallel
generalized eigenvalue solvers to attain highscalability and usability, K. Tanaka, H. Imachi,
T. Fukumoto, A. Kuwata, Y. Harada, T. Fukaya,
Y. Yamamoto, T. Hoshi, Japan J. Indust. Appl.
Math 36, 719-742 (2019)

Fig.1 (a) Schematic figure of totalreflection high-energy positron
diffraction (TRHEPD) experiment.
(b) The data analysis of experimental
TRHEPD data for Ge(001)-c(4x2) surface[2].

[7] An a posteriori verification method forgeneralized Hermitian eigenvalue problems inlarge-scale electronic state calculations, T.
Hoshi, T. Ogita, K. Ozaki, T. Terao, J. Comp.

77

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Reduction of Rare Metals in Fuel Cell Catalysts andHydrogen Permeable Membrane
Norihito Sakaguchi
Center for Advanced Research of Energy and Materials, Faculty of Engineering,
Hokkaido University, Sapporo, Hokkaido 060-8628
activity of Pt clusters on non-metal element

We investigated the catalyst adsorption
and diffusion properties on non-metal element

doped

doped graphene and hydrogen dissolution anddiagram.[1] We revealed that the Pt clusters

diffusion properties in the interfaces ofshow less support effect than Pt single atoms.

ceramic materials, with the aid of the first-

Wegraphene

also

based

on

investigated

the

the

energyhydrogenprinciples calculation based on the density

dissolution and diffusion properties in thefunctional theory (DFT).

interfaces of TiN containing O impurities.

At first, we investigated adsorption andWe found that H atoms do not prefer the O

diffusion properties of Pt clusters on non-sites.

metal element doped graphene. This year, we

We also studied the tunneling effect on thealso considered Pt atoms embedded in thealkene hydrogenation process on Rh-basedgraphene basal plane. We performed the total

Intermetallic

energy and electronic structure calculations

dynamics simulation of atomic nuclei [2] andusing The Vienna Ab initio simulation

thickness dependence of the structure andpackage (VASP). We installed a parallelized

magnetism of Ca2RuO4 nanofilm.[3]VASP with Intel® MPI Library and Intel®

References

Math Kernel Library. We found that the[1] J. K. Nørskov, J. Rossmeisl, A. Logadottir,

adsorption energies and diffusion activation

L. Lindqvist, J. R. Kitchin, T. Bligaard,

barriers of Pt clusters on graphene increase by

H. Jónsson, J. Phys. Chem. B, 108

substitutional non-metal element doping. This

(2004) 17886.

catalyst

using

quantum

is because of the strong covalent bonds[2] S. Furukawa, P. Yi, Y. Kunisada, K.

between the Pt atom and substitutional

Shimizu, Sci. Technol. Adv. Mater.

dopants. Therefore, we concluded that these20 (2019) 805.

dopants

ingraphenecanprevent

the[3] H. Nobukane, K. Yanagihara, Y. Kunisada,detachment and surface diffusion of Pt

Y. Ogasawara, K. Nomura, Y. Asano, S.

clusters. We also investigated the catalytic

Tanda, Sci. Rep. 10 (2020) 3462.

78

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab-initio analysis of phonon and electron-phonon interaction
Emi Minamitani
Institute for Molecular Science,
Okazaki, Aichi 444-8585
Heat generation in semiconducting materials

DFT calculation results are used as dataset

has become a critical problem in modern

to train HDNNP. We found that thenanoscale electronics. As the size of electrictraining procedure based on force makes

devices decreases, the power density andthe root mean square error between thedevice temperature increase, which is one offorces predicted by HDNNP and DFT less

the

major

degradation

factorsofcontributing

devicetothethan 40 meV/Å. As typical examples, we

performanceandpresent the results of Si and GaN bulk

reliability.

crystals. The deviation from the thermal

The main carrier of heat in semiconductors is

conductivity

the phonon, which is a quantum of lattice

within 1% at 200 to 500 K for Si and within

vibration.

5.4% at 200 to 1000 K for GaN.

Current

theoreticalframeworks

calculated

using

DFT

is

require accurate prediction of the interatomic
force in the solid. Density functional theory(DFT) calculation is one of the most wellestablished techniques for accurate force
prediction, including the effect of changes inthe electronic state with atomic displacement.
However, the high computational cost limits theapplication of DFT calculation in thermal
conductivity simulations.

Fig. 1 Comparison of thermal conductivity
obtained from DFT calculation and HDNNP for

We apply the high-dimensional neuralbulk Si (a) and GaN (b).

network potential (HDNNP). We generated
the random but reasonable structures werefirst generated from the trajectories ofclassical molecular dynamics simulations,

References

and then the energy and forces in each[1] E. Minamitani, M. Ogura, and S. Watanabe,

structure were evaluated by DFT. These

Appl. Phys. Express, (2019) 12, 095001

79Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Electrochemical Reaction Analysis Using Density Functional
Calculation + Implicit Solvation Model
Jun HARUYAMA
Institute for Solid State Physics,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8581
We have studied charge transfer reaction at

Figure 1 (b) shows the grand potential Ω ofelectrode/electrolyte solution interfaces in Li-

pristine, LinC6mHl/hLi2CO3, and VLi + Li+, Lin-ion batteries (LIB) using density functional

1C6mHl/hLi2CO3

theorycalculation combined withfunction of the chemical potential of an

implicit solvation model. This simulation iselectron µe. In the ESM-RISM calculations, µe

called ESM-RISM,1 i.e., the effective screening

is measured from the potential at inner solution

medium (ESM)2 + the reference interaction site

region ΦS. It is possible to compare µe at

model (RISM)3, and implemented in Quantum

different

Espresso package.4

solution directly.5 The difference between two(DFT)+ Li+(1 M LiPF6 EC), as aelectrodes

contacting

the

same

This year, we focused on Li-ion transfer

equilibrium potentials on different electrodes

reaction (R) at the interface of graphite

provides the electromotive force, Eemf, between

electrode/solid electrolyte interphase (SEI)/

the two electrodes as:

solution (1 M LiPF6 EC) as follows:

Eemf = − (µeq − µLi/Li+)/e

LinC6mHl + hLi2CO3 → Lin-1C6mHl + hLi2CO3 +(1),

Li+(1 M LiPF6 EC) (R).

where µeq represent the equilibrium potential of

ESM-RISM calculations were performed on thereaction (R) and e is the elementary charge.

configuration of a vacuum/slab/soltion system

Once an equilibrium potential µLi/Li+ of Li

as shown in Fig. 1 (a), where the DFT slabtransfer reaction at Li metal electrode isdomaingraphite

determined in the ESM-RISM calculation, the(LinC6mHl)/SEI (inorganic lithium carbonic acid,

electromotive force (or electrode potential

hLi2CO3), and the RISM solvent and ions, (EC,relative to the Li/Li+ reference) can beLi+,electrolyte

immediately derived. Because it was obtained

concentration of typically 1.0 M gives a smallµLi/Li+ = −3.06 eV vs ΦS in a previous study,6Debye screening length of several angstroms,

the result of µeq = −3.17 eV vs ΦS gave Eemf =the RISM region (> 40 Å) used in this0.11 V vs Li/Li+, which is in good agreement

calculation was sufficiently long.

with experiment (0.1 – 0.2 V vs Li/Li+).

andrepresentsPF6−).

Li-inserted

Since

the

80

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo(a)Electrode/SEI (DFT)

Additionally, it was confirmed that the

Solution (RISM)〜〜

equilibrium potential of reaction (R) cannot

1 M LiPF6 EC

depend on such as the thickness and componentof SEI. In the next physical year, the activation

Li+

Grand potential Ω (eV)

(b)

PF6−

energy of reaction (R) will be revealed underEC

operated LIB working conditions.
0.8

VLi + Li+µ Li/Li+

0.0

References

-0.8
-1.6

[1] S. Nishihara and M. Otani: Phys. Rev. B 96

Pristineµeq(2017) 115429.

-2.4
-3.2

[2] M. Otani and O. Sugino: Phys. Rev. B 73
-3.5

-3.2

-2.9

-2.6

-2.3

(2006) 115407.

-2.0

Chemical potential µe vs. ΦS (eV)[3] A. Kovalenko and F. Hirata: J. Chem. Phys.

Fig. 1: (a) ESM-RISM configurations of the

110 (1999) 10095 (1999).

vacuum/slab/solvent system: the simulation[4] P. Giannozzi et al.: J. Phys.: Condens.

cells of LinC6mHl/hLi2CO3|1M

Matter 21 (2009) 395502; 29, (2017) 465901.

LiPF6

EC

interfaces. (b) Profiles of Ω as a function of µe.

[5] J. Haruyama, T. Ikeshoji, and M. Otani,

The blue and orange lines show Ω ofPhys. Rev. Mater. 2 (2018) 095801.

LinC6mHl/hLi2CO3 and Lin-1C6mHl/hLi2CO3 +[6] J. Haruyama, T. Ikeshoji, and M. Otani: J.

Li+(1 M LiPF6 EC), respectively.

Phys. Chem. C 122 (2018) 9804.

81

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Van der Waals density functional study of molecules adsorbed on metal
surfaces
Ikutaro Hamada
Department of Precision Science and Technology, Graduate School of Engineering,Osaka University, 2-1 Yamada-Oka, Suita, Osaka 565-0871
Accurate description of the molecule-water clusters from monomer to hexamer, andsurface interaction is prerequisite for precise

found that the pentagonal water cluster is more

understanding of chemical processes at surfaces

stable than the hexagonal one on Cu(110). We

and interfaces in diverse systems including

further constructed larger water clusters such as

electrochemical energy conversion devices

octamers composed of pentamers, nonamerssuch as fuel cell, photoelectrochemical cell, andcomposed of pentagon and hexagon, those withrechargeable battery, as well as heterogeneous

two pentagons plus water monomer, and dimer

catalyst for emission control, name only a few.

composed of pentamers. We found that the

For this purpose, the van der Waals density

clusters

functional (vdW-DF) [1] and its variants haveconsistently more stable and that the calculated

been used to study a variety of systems andwater clusters can explain the high-resolution

proven accurate in describing molecule/surface

noncontact atomic force microscopy images [6].

interfaces, as well as bulk systems.

Furthermore, we found that the 2D ice rulecomposedofpentagons

areapplies to explaining and predicting the

In this project, we have studied quasi one
dimensional chain composed exclusively of

structure of water clusters on Cu(110).

pentagonal water on Cu(110). In particular, weReferences

have studied the small water clusters on[1] M. Dion et al.: Phys. Rev Lett. 92 (2014)

Cu(110) to investigate the origin of the246401.

pentagonal water chain.

[2] J. Wu and F. Gygi: J. Chem. Phys 136(2012) 224107.

All the calculations were performed using
STATE,

ourin-house[3] Y. Hamamoto, I. Hamada, K. Inagaki, and Y.

plane-wave

pseudopotential code. We used an efficient

Morikawa: Phys. Rev. B 93 (2016) 245440.

implementation [2,3] of the self-consistent[4] I. Hamada: Phys. Rev. B 89 (2014)

vdW-DF. The rev-vdW-DF2 functional was

121103(R).

used [5].

[5] A. Shiotari and Y. Sugimoto: Nat. Commun.
8 (2017) 14313.

Previously we constructed and optimized

82

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Energy Transport in Hybrid Organic-Inorganic Thermoelectric Materials
Shenghong JU
Department of Mechanical Engineering, The University of Tokyo
7-3-1 Hongo, Bunkyo, 113-8656
Thermoelectric materials can directly
convert waste heat energy to usefulelectricity. During the last decade, theorganic polymers have shown uniquefeatures such as low density, low thermal
conductivity, easy synthesis and versatile
process ability. Using organic polymers inthermoelectric materials appears to havegreat potential for producing relatively
low cost and high performance
thermoelectric devices. However, little
work on modeling and simulation isreported at present.

which the low lattice thermal conductivity
and the high electrical conductivity at low
chemical potential region contributes themost. The results suggest an effective way
to improve the thermoelectric performanceof Si-based materials.

The first main part of last year work is
about the thermoelectric property
investigation of metastable phases ofsilicon. In this work, the phonon andelectron transport properties of metastable
Si-III and Si-XII are investigated bydensity functional theory, as shown in Fig
1 and 2. The metastable Si-III and Si-XII
show one magnitude lower thermal
conductivity than the stable Si-I phase.
The effect of different three-phonon
scattering processes on the thermal
conductivity of different phases were
evaluated by removing specific scattering
processes from the Brillouin zone. Further
electron transport property calculationsuggests that the metastable Si-III and SiXII phases have higher thermoelectric
figure-of-merit than the Si-I phase in

Figure 1: Comparison of phonon transport
property in Si-I, Si-III and Si-XII.

Figure 2: Comparison of electron transport
property in Si-I, Si-III and Si-XII.

83

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

The second main part of last year work
is about the design of magnetic tunnel
junctions (MTJs) using disordered
MgAl2O4. Through Bayesian optimizationand the least absolute shrinkage andselection operator technique combinedwith first-principles calculations, weinvestigated the tunnel magnetoresistance(TMR)
effectof
Fe/disorderedMgAl2O4(MAO)/Fe(001) magnetic tunnel
junctionsto determine structures ofdisordered-MAO that give large TMR
ratios. The optimal structure with thelargest TMR ratio was obtained by
Bayesian optimization with 1728
structural
candidates,
where
the
convergence was reached within 300
structure calculations. Characterization of
the obtained structures suggested that thein-plane distance between two Al atoms
plays an important role in determining the
TMR ratio. Since the Al-Al distance ofdisordered MAO significantly affects theimaginary part of complex band structures,the majority-spin conductance of the Δ1state in Fe/disordered-MAO/Fe MTJs
increases with increasing in-plane Al-Al
distance, leading to larger TMR ratios.
Furthermore, we found that the TMR ratio
tended to be large when the ratio of thenumber of Al, Mg, and vacancies in the[001] plane was 2:1:1, indicating that thecontrol of Al atomic positions is essential
to enhancing the TMR ratio in MTJs withdisordered MAO. The present work
reveals the effectiveness and advantage ofmaterial informatics combined with firstprinciples transport calculations indesigning high-performance spintronic
devices based on MTJs.

Figure 3: Schematics of designingmagnetic tunnel junction for high tunnel
magneto-resistance ratio by combining
Bayesian optimization and first-principles
calculation.
In summary: (1) We have shown thatmetastable Si-III and Si-XII phases havehigher thermoelectric figure-of-merit thanthe Si-I phase. (2) We have successfully
designed the optimal disordered Fe/
MgAl2O4/Fe (001) structure with thehighest tunnel magnetoresistance ratio
optimal by combining the first-principles
transport calculations and Bayesian
optimization.
References[1] S. Ju, H. Chen, M. Kohno, J. Shiomi:
High thermoelectric performance inmetastable phases of silicon: a density
functional theory study, under preparation.
[2] S. Ju, Y. Miura, K. Yamamoto, K.
Masuda, K. Uchida, J. Shiomi: PhysicalReview Research, accepted, 2020.

84

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Quantum Chemical Analysis for High-Performance Polymer Electret
Yucheng ZHANG, Zetian MAO, and Yuji SUZUKI
Department of Mechanical Engineering
The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656
Electret is dielectric material with quasi-

reaction can act as a strong charge trapping

permanent charges. Vibration Electretsite [2]. Therefore, we investigate charge

Energy harvesting (VEEH) is a clean way

stability of candidates with free amine

to convert environmental energy intofunctional group which can react with -electricity by electrostatic induction more

COOH end group of CTX-A. Electron

efficiently

oraffinity and ionization potential obtained

piezoelectric counterparts [1]. VEEH canfrom quantum chemical calculation are

be applied to low power electronics such as

used to evaluate the electron trap energy

wireless sensors, implantable medical

and hole trap energy of possible candidates

equipment and wearable device. Since theafter dehydration condensation respectively.

thanelectromagnetic

power output of the VEEH is proportional

Electronaffinityiscalculatedbyto the square of surface potential of thecomparing molecular energy at neutral andelectret, it is necessary to discover electret

negatively-charged state while ionizationmaterial with high surface charge density.

potential is computed by comparing

Furthermore, if we could find electret

molecular energy at neutral and positively-

suitable for both negative and positive

charged state. The calculated ionization

charging, the power output of VEEH will

potential of CYTOP based electret is asboom by 4 times theoretically.

follows: 13.12 eV (CTX-S), 12.03 eVCYTOP (AGC Co. Ltd.) is a fluorinated(CTX- A), 9.81 eV (CTX-M) and 7.81 eV

amorphous polymer, with its chemical(CTX-A/TAEA). Figure 2 visualizes the

structures shown in Figure 1. There arethree kinds of commercialized CYTOP, S,
A and M. CTX-A has carboxyl end groups
and CTX-M has alkoxysilane/amide end
groups. According to quantum chemical
analysis of CYTOP series with different

Fig. 1. Chemical structure of CYTOP series.

end groups, the amino bond formed after85

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

This work was partially supported by
JST CREST Grant Number JPMJCR15Q3
and JPMJCR19Q1, Japan. The calculationis performed with SGI ICE XA ISSP
system B and every calculation is held with
1 node (24 CPUs). The energy of theFig. 2. Visualization of hole trapped
orbitals for positive state of CTX-A/TAEA.

molecule is computed by DFT to CAMB3LYP/6-31+G(d,p) levelby using

quantum chemical simulation software
GAUSSIAN[4].

Molecular

dynamic

simulation package GROMACS [5] andsolid-state analysis package VOTCA-CTP
are also used [6] for more accurate
Fig. 3. Normalized TSD spectra of CYTOP
electrets charged to +2 kV.

estimation. In case of CYTOP hexamers,

hole trapped orbitals of positively charged

CPU

the calculation cost is approximately 150
hours

for

quantumchemicalcalculation, 100 CPU hours for MD

CTX-A/TAEA monomer. It is shown thatsimulation and 5 CPU hours for multipole

the hole is located near the amide bond,analysis and solid-state analysis.

which is formed by the reaction between
the carboxy end group and TAEA.

References

Thermally stimulated discharge (TSD)[1] Suzuki Y. IEEJ Trans. Electr. Electr.

measurement is also done for comparison

Eng., Vol. 6, 101-111 (2011).

between calculation and experiment. Figure[2] Kim S., et al. Sci. Technol. Adv.

3 shows the TSD spectra of CYTOPMater., Vol. 19, 486-494 (2018).

polymers for positive charging. It is found[3] Kim S., et al., IEEE Conf. Electr. Insul.

that CTX-A/TAEA has the highest charge

Dielectr. Phenom., Richland, 8-1, (2019).

thermal stability with smallest computed[4] M. Frisch et al., “Gaussian 09, Rev. A.

ionization potential value. In addition, the1,” Gaussian, Inc. Wellingford, CT, 2009.

TSD spectra for positive charging exhibit[5] S. Pronk et al., Bioinformatics, 29,

multiple peaks, indicating the difference in(2013) 845-854.

the charge trapping mechanisms between[6] V. Rulhe et al., J. Chem. Thery Comput.,negative and positive charges [3], which

7, (2011), 3335-3345.

will be analyzed in the future.

86

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical modeling of carrier
localization/delocalization and related phasetransitions
Hannes RAEBIGER
Department of Physics, Yokohama National University79-5 Tokiwadai, Hodogaya-ku, Yokohama 250-8501

1

Introduction

We investigate trends in carrier localizationin defective semiconductor/insulator systems
focusing on phase transitions. We have previously illustrated the mechanistic origin of
the Mott transition and related excitonic insulator phases [1], as well as strain induced
piezomagnetic transitions in magnetic semiconductors [2]. This year, we have clarified carrier-induced magnetic transitions intransition-metal doped Ga2 O3 systems [3, 4],as well as charge trapping in resistive memory(ReRAM) devices [5]. Also, an introductory
review of first principles methods for defects
in semiconductors/insulators was published asa book chapter [6].

2

Ga2 O3 systems

We carry out density-functional calcualtions
using the VASP code with in-house developed corrections for band-gap [7] and selfinteraction [2]. Band-gap correction of Ga2 O3
is achieved applying non-local external potenN LEP =-6.4 eV,tial parameters as follows. VO,sN
LEP
VO,p =-2.0 eV for oxygen [7], and for Ga,
N LEP =10.0 eV, V N LEP =2.5 eV, andwe use VGa,sGa,p
UGa,d =9.0 eV to achieve best fit of several
physical parameters (see Table 1). For Cr 3d,
we set U =2.6 and J=1.0 eV. [7] We further
cross-validate these parameters against selfinteraction corrected VP-SIC in the KKR-CPA

framework (see [3] for details).
Table 1: Physical properties of β-Ga2 O3 . Eg
is band gap energy (eV) and m∗e is effective
electron mass.[3]

a(Å)
b/a
c/a
V (Å3 )∆V (%)β(deg)
Eg∗
me /mepure GGA
12.40
0.250
0.475
219.43
+5.1
103.8
2.0
0.19

GGA+NLEP
11.90
0.251
0.471
197.26
-5.5
104.1
4.7
0.37

Exp.
12.2140.249
0.475
208.85103.824.9
0.28

Carrier-mediated ferromagnetism in Crdoped β-Ga2 O3 .[3] First of all, we find that Cr
prefers the octahedral lattice site in β-Ga2 O3
by ∼1 eV against the tetrahedral site. We thenshow that Cr in the octahedral site has a negative charge transition close to conduction band
minimum, so the system may become charged.
Magnetic interaction among Cr impurities isinvestigated as a function of Cr–Cr distance up
to ∼8.5Å. For nonconductive systems, we finda weak antiferromagnetic coupling for nearest
neighbor Cr–Cr pairs, and zero interaction for
all other pairs investigated. We then include
carrier-electrons, which cause negative charging of Cr impurities. We further find that suchcarrier-doping switches on a strong ferromag-

87netic interaction, which persists up to ∼6ÅCr–
Cr separation.
Optical properties  and κ phases of Ga2 O3
doped with cobalt.[4] In collaboration with experimental work, we investigate the modulation of optical absorption edge in  and κ
phases of Ga2 O3 by Co doping. Co impurity
levels, as well as those of some typical native
impurities, are calculated from first principles.
We then calculate the optical absorbance forseveral Co doped systems at several defect concentrations. This is used to re-interpret experimental observations, which previously asserted
band-gap modulation based on changes in optical gap upon Co doping. However, our calculation shows that the optical gap changes instead are due to Co impurity levels. We further
present a new band diagram to clarify changes
in work function due to Co doping in thesesystems.

3

Low resistivity High resistivity
state
state

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Q>0
CB
eφ(z)

CB
eφ(z)
EF
VB

eVb

Q<0
CB
eφ(z) E
F

VB

+Vb
eφb

EF
VB

e
e
e

–Vb

eVb

e

e
e
e

e
e

eφ(z) CBEF
VB

Figure 1: Band bending solutions of ReRAM
device, and switching by external bias.
241115(R).
[2] H. Raebiger, S. Bae, C. Echeverrı́aArrondo, and A. Ayuela: Phys. Rev.
Mater. 2 (2018) 024402.

Charge trapping in ReRAM
systems[3] K. Ichihashi, H. Shinya, and H. Raebiger:
Appl. Phys. Express 13 (2020), 021002.

We describe resistive memory ReRAM devices by a metal/insulator/metal sandwich
structure, and investigate charge trappingby numerically solving Poisson’s equation.
We develop a self-consistent Poisson solver,where charge stored in device is solved selfconsistently together with potential over device under different bias voltages. We discover
new band-bending solutions characterized bydifferent amount of charged stored in the system, and reversible switching between thesedifferently charged states, illustrated in Figure 1. This electrostatic switching mechanism
provides a novel interpretation for ReRAM operation, and resolves the mystery of extremely
fast sub-nanosecond switching.

[4] K. Yamanaka, H. Raebiger, K. Mukai,
and K. Shudo: J. Appl. Phys. 127 (2020)065701.
[5] H. Raebiger, A. C. M. Padilha,
A. R. Rocha, and G. M. Dalpian:
J. Phys. D (accepted, 2020, DOI:
10.1088/1361-6463/ab7a58).
[6] E. Ertekin and H. Raebiger: Ch. 7 in
Characterisation and Control of Defects
in Semiconductors, ed. F. Tuomisto (IET,
United Kingdom 2019) pp. 289–343.
[7] H. Raebiger, S. Lany, and A. Zunger:
Phys. Rev. Lett. 101 (2008) 027203.

References[1] S. Bae and H. Raebiger: Phys. Rev.
B (Rapid Communications) 94 (2016)88

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab initio study on the metallization andsuperconductivity in metallic superhydrides
Ryosuke Akashi
Department of Physics, University of Tokyo
Hongo, Bunkyo-ku, Tokyo 113-0033

In this project, we studied the mechanism of
the metallic and superconducting properties ofthe superhydrides–the compounds containing
anomalously large formula ratio of hydrogen–recently synthesized under megabar pressures.
The discovery of the 200-kelvin superconductivity in the compressed H2 S (Ref. [1]) has
triggered extensive study on the pressure induced superconductivity of hydrogen compounds. Later studies revealed that the novel
phase containing excess hydrogen atoms, H3 S,
emerges under extreme pressures, which is responsible for the experimentally observed highTc superconductivity. This has motivatedthe exploration of pressure induced hydrogenexcess compounds.
First, we numerically examined the superconducting properties of some crystalline lanthanum and yttrium superhydrides, LaHx andYHx , for possible explanation of the experimentally observed superconducting transition
temperature (Tc ) (260 K and 240 K, respectively) in these systems. We calculated Tc
for theoretically predicted crystal structuresof LaH10 and LaH16 from first principles.
Specifically, we solved the gap equation of thedensity functional theory for superconductors(SCDFT) (Ref. [2, 3, 4])with the Migdal approximation. Also, theelectron-electron Coulomb repulsion that suppresses the pairing is also incorporated. ∆ isthe order parameter and nk labels the KohnSham band index and√crystal wavenumber,2 + ∆2
respectively. Enk =ξnk
nk and β is
the inverse temperature. The non-diagonalpart of the kernel of Eq. (1) K is composedof the phononic and electronic contributions:
K = Kph + Kel . On the other hand, the diagonal part Z includes only the phononic one:
Z = Z ph . To evaluate the phononic parts
we need to calculate the Eliashberg function
α2 F (ω), which is roughly the phonon densityof states weighted by the coupling strength
to the electrons. The electronic part is calculated as the two-particle matrix element of
the screened Coulomb interaction, where theone-particle states and dielectric function arecalculated by the first-principles Kohn-Shamequation. All the components were calculatedwith the plane-wave basis code package quantum espresso (Ref. [5]). The phononic properties of the yttrium compound was supplemented with the anharmonic correction using
the stochastic self consistent harmonic approximation [6].
We show in Table I the values of Tc calculatedwith the SCDFT gap equation [Eq.(1)],βEtanh 2n′ k′2
1∑∆nk = −Znk ∆nk −Knkn′ k′∆n′ k′ . as well as characteristic parameters of α F (ω)
2 nk
En′ k′∫
α2 F (ω)(1)
λ = 2 dω
,
(2)
ω ]
[ ∫
Here, the phonon-mediated Cooper pairing ef2
α2 F (ω)
logω .
(3)ωln = expdω
fect is included within the Eliashberg theoryλω

89Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

(c)

(b)

(a) 20Sulfur-p

15
Energy [eV]10(1)tSpσ-Hs

5
0

Γ

-5

X

-10

Hydrogen-s

M(1)
tSs-Hs(4)tHs-(H)-Hs

-15
-20

Sulfur-s

-25
Γ

X

M

Γ

R

M

X

0.2
0.4
R0
DOS [1/(eV sp unit)](4)
tSs-SsFigure 1: (a) Crystal structure of the high-Tc phase of cubic H3 S and its band structure and DOS.
The thin and bold lines represent the first-principle and Wannier band structures, respectively.
(b) The simple cubic Brillouin zone and positions of the loop-like continuous saddle points inthe band structures. (c) The minimal Wannier model that reproduces the saddle loop aroundthe M point. See Ref. [12] for more details.

Table 1: Coupling constant λ (Eq. (2)), typicalfrequency ωln (Eq. (3)), and the superconducting transition temperature Tc calculated with
the SCDFT gap equation Eq. (1).
LaHx [9]YHx
LaH10 LaH16 YH6Pressure (GPa)
200
200
165
λ
3.75
1.82
1.71
ωln
905
1366 1332
Tc (K)
271
156
156

Experimentally observed Tc for the lanthanum
systems strongly depends on the trials [7, 8].
The synthesis with excess hydrogen yielded Tc
varying from 250 K to 210 K. Our calculation
indicates that the high-Tc phase corresponds to
LaH10 (left column), whereas the low-Tc phase
could be a mixture of LaH10 and LaH16 (middle column). We have published this result
in Ref. [9]. For the yttrium hydride, on theother hand, our calculated Tc (right column)
was substantially lower than the experimental value (∼ 240 K). At this point we have notreached to a plausible understanding of the origin of the discrepancy [10].

state in the sulfur superhydride H3 S. According to preceding studies, it hosts a sharp peakat the Fermi level in the electronic density ofstates (DOS) N (E) (Fig. 1 (a)), which has arole of boosting the Tc via the relation λ ∝N (EF ) with EF being the Fermi level. Its origin has, however, yet been clarified. To elucidate the mechanism of its formation, we first
performed a close analysis of the band structure and found that the DOS peak structure
mainly originates from the loop-like continuous
saddle points around the M point in the primitive cubic Brillouin zone (Fig. 1 (b)). Next, weconstructed the Wannier model using quantum espresso and Wannier90 (Ref. [11] program packages. Our model consists of sulfurs, p and hydrogen-s like orbitals and almost
perfectly reproduces the first-principles band
structure especially around the Fermi level(Fig. 1 (a)). We then calculated the eﬀective
band structures with this Wannier model withomitting the interorbital hopping parameters.
Finally, we found that a simple model reproduces the key feature in the band structure;
the saddle-point loops around the M point. In
this model (Fig. 1 (c)), the simple cubic ScF3
sites and the nearest-neighbor and selected far-

We also addressed the metallic electronic

90

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

ther neighbor hopping parameters have been
extracted from the original Wannier model.
The nearest-neighbor hoppings for the s-likeand p-like orbitals on the simple cubic ScF3
lattice geometry yields a saddle point at the
M point, and in addition, the selected farther
neighbor hopping “pushes down” the state at
the M point to form the continuous loop of thesaddle point. This understanding on the origin of the DOS peak in the celebrated high-Tc
superconductor H3 S has been published [12].
Computational detail.
The generalized
gradient approximation for the exchangecorrelation potential was employed [13] for the
calculations of LaHx , YHx and H3 S. MPI parallelized calculations were performed with respect to k points (-npool option) as implemented in pw.x code. The screened electronelectron Coulomb matrix elements [4] were
calculated with an in-house code with the
openmp parallelization. The calculations weremainly done in System B.

References[1] A. P. Drozdov, M. I. Eremets, and I. A.
Troyan, V. Ksenofontov, and S. I. Shylin,
Nature (London) 525, 73 (2015).
[2] M. Lüders, M. A. L. Marques, N. N. Lathiotakis, A. Floris, G. Profeta, L. Fast, A.
Continenza, S. Massidda, and E. K. U.
Gross, Phys. Rev. B 72, 024545 (2005).

[6] I. Errea, M. Calandra, and F. Mauri,Phys. Rev. B 89, 064302 (2014).
[7] M. Somayazulu, M. Ahart, A. K. Mishra,
Z. M. Geballe, M. Baldini, Y. Meng, V. V.
Struzhkin, and R. J. Hemley, Phys. Rev.
Lett. 122, 027001 (2019).
[8] A. P. Drozdov, P. P. Kong, V. S. Minkov,
S. P. Besedin, M. A. Kuzovnikov, S.
Mozaﬀari, L. Balicas, F. F. Balakirev, D.
E. Graf, V. B. Prakapenka, E. Greenberg, D. A. Knyazev, M. Tkacz, and M.
I. Eremets, Nature (London) 569, 528(2019).
[9] I. A. Kruglov, D. V. Semenok, H. Song,R. Szczȩániak, I. A. Wrona, R. Akashi,
M. M. D. Esfahani, D. Duan, T. Cui, A.
G. Kvashnin, and A. R. Oganov: Phys.
Rev. B 101, 024508 (2020).
[10] D. V. Semenok, R. Akashi et al., in preparation.
[11] A. A. Mostofi, J. R. Yates, G. Pizzi, Y.S. Lee, I. Souza, D. Vanderbilt, and N.
Marzari, Comput. Phys. Commun. 185,
2309 (2014).
[12] R. Akashi: Phys. Rev. B 101, 075126(2020).
[13] J. P. Perdew, K. Burke, and M. Ernzerhof,
Phys. Rev. Lett. 77, 3865 (1996).

[3] M. A. L. Marques, M. Lüders, N. N. Lathiotakis, G. Profeta, A. Floris, L. Fast, A.
Continenza, E. K. U. Gross, and S. Massidda, Phys. Rev. B 72, 024546 (2005).
[4] R. Akashi, M. Kawamura, S. Tsuneyuki,
Y. Nomura, and R. Arita, Phys. Rev. B
91, 224513 (2015).
[5] P. Giannozzi et al, J. Phys.: Condens. Matter 21,
395502 (2009);
http://www.quantum-espresso.org/.

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study on physics of gap-state control
at metal/semiconductor interfaces
Takashi NAKAYAMA

Department of Physics, Chiba University
1-33 Yayoi, Inage, Chiba 263-8522
Due to the break of atomic bonds and the lackof translational symmetry, gap states appear insemiconductor layers around metal/semiconductor
interfaces, which have the energy position in theband gap and are localized around the interface.
These states induce the electron transfer between
metal and semiconductor layers and determine avariety of physical phenomena at the interface,such as Schottky barrier (SB), defect density, andmetal-atom ionization. However, it is still unclear
how to control the gap states. In this works, westudied the SB and tunneling current at various
interfaces and clarify the origins of gap-state
generation/annihilation and deformation using thefirst- principles calculations.
We first consider metal/Ge interfaces, whereFermi energies of most of metals are locatedaround the valence-band top of Ge irrespective of
the kinds of metals. This is called the Fermi-level(FL) pinning and interrupts desirable low-resistive
metal/n-Ge contacts. Although the breakdown of
FL pinning was recently observed at TiN/Ge(001)interfaces, its origin has not been clarified. To
simulate the interfaces, we adopt (1×1)--(3×3)
TiN/Ge(01) repeated-slab models with various
interface structures and calculate their SBs using
local potential profiles.
Figure 1 shows calculated SBs for hole carriers
ate various interfaces. The SBs at Ti-rich interfaces
like abrupt (a-2) are around 0.0eV corresponding to
the FL pinning, while the SBs at N-rich interfaces
such as (b-2) and (c) have large values above 0.3eV,
which is in good agreement with experiments. The
origin of such SB variation is understood byobserving the projected densities of states (PDOS)
of interface atoms, which are shown in Fig.2.

Fig.1. Left: calculated Schottky barriers for holecarriers at various TiN/Ge interfaces. Right:
schematic pictures of interface structures. (a-2):
abrupt Ti-rich interface, (b-2) and (c): N-richinterfaces with TiN2 and Ge3N4 interface layers.

For (a-2) interface, the continuous PDOS, thus thegap states, appear around 0.0eV for interface Ge
atoms due to the orbital hybridization between Ti
and Ge, which induces electron transfer from TiN
to Ge and realizes the FL pinning. On the other
hand, we can see the suppression of gap states in
the PDOS of interface Ge for (b-2) interface, whichis caused by the production of interface N-Ge
bonds. In this way, the interface covalent bonds
eliminate the gap states in interface Ge layers.
Next, we consider how the interface bonds affect
the SBs. We artificially produce metal/X/Ge(001)interfaces with various segregation atoms, X, thatterminate interface Ge, and calculate the SBs, theresults being shown in Fig.3 for Al/X/Ge cases. We
found the chemical trend that the segregation of IIand III-family atoms lowers the SBs, while that ofV- and VI-family atoms raises the SBs. By
analyzing electronic structures in details, it was
shown that such trend reflects the valency of X

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Fig.4. (a): calculated tunneling probability ofelectrons at Si-p/n junction as a function ofelectric field, for the cases with (red line) andwithout (blue) dopants. (b) and (c): energy
distribution of tunneling electrons and resonancestate at doped p/n junction.

Fig.2. Calculated projected densities of statesof interface atoms around TiN/Ge interfaces
with (a-2) and (b-2) structures shown in Fig.1.
Ge(1) and Ge(2) correspond to the first andsecond layer germanium atoms, respectively.

Si-p/n junction. Figure 4(a) shows calculated
current as a function of applied electric field. Whenthe dopant is embedded in p/n junction (red line),
the current is markedly enhanced, which is causedby the tunneling through the dopant state as seen in
the energy spectra in Fig. 2(b). Figure 2(c) shows awavefunction of such dopant state. This state is aresonance state between isolated dopant state andgap state produced by the penetration of
conduction-band state of right-handed bulk Si
layers into the band gap. By changing not only thespacial and energy positions of dopant state but
also the electric field, we can control suchresonance. In this way, the gap-state characteristics
are controlled by the electric field.
All these calculations were performed using thexTAPP, VASP, and pspwf codes. In order to realize
the calculations for the present interface systems,
because the system is made of a large number ofatoms (300-1000 atoms), the advanced computing
facility having multi-task and higher-speed CPU(more than 64 cores × 2.5GHz), larger-size
memory (around 128GB), and larger-size strange(more than 1 TB) is indispensable. These
conditions are realized only by the ISSP
supercomputing systems.

Fig.3. Calculated Schottky barriers for holecarriers at Al/X/Ge interfaces with various
segregation atoms, X. Ec and Ev denote theconduction-band-bottom and valence-band-top
positions of bulk Ge, respectively.

atoms; when X-Ge bonds are produced at theinterface, the electron transfer occurs from X to Ge
for X atoms with less than 4 valence electrons,
while the additional transfer occurs from X to Al
for X atoms having more than 4 electrons. In thisway, not only the termination of interface Ge bonds
but also the kinds of termination atom is important
to deform the gap state and depin the FL.
Finally, we study how the gap states change inelectric field. We consider the tunneling current at

93Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical analysis of ion conduction mechanism of highly
concentrated electrolytes for secondary batteriesAtsuo YAMADA
Department of Chemical System Engineering,
The University of Tokyo, Bunkyo-ku, Hongo, Tokyo 113-8656
Highlyconcentrated

electrolytes

have

imposed

under

NVT

ensemble.

The

recently attracted much attention owing to theirequilibration of 10 ps at 1 fs time interval was

unique electrochemical properties derived fromfollowed by the sampling of 200 ps.

an unusual coordination structure, where theWith increasing the salt concentration, theligand (solvent/anion) exchange reactions areligand exchange reactions become active

responsible for the ion transport, while themainly via FSA anions (Fig. 1). The increased

vehicular-type mechanism is dominant in theion radius (decreased Lewis acidity) of cations

diluted electrolyte [1]. Herein, we theoreticallyalso activates the ligand exchange reactions byinvestigated the salt concentration dependence

weakening the interaction with the ligands.

of ionic conduction mechanism in AFSA/DME

Therefore, both the higher concentration andelectrolyte (A = Li, Na, K) using quantum

increased cation size should promote the ligand

molecular dynamics (MD) simulations.

exchange-type ion transport.

All the calculations were performed using
divide-and-conquer density functional tight-

Referencesbinding (DC-DFTB) method [2]. A modified[1] M. Okoshi, C.-P. Chou and H. Nakai, J.

3OB parameter set based on first-principles

Phys. Chem. B 122, 2600 (2018).

calculations was adopted, and a constant[2] Y. Nishimura, H. Nakai, J. Comput. Chem.,

temperature condition of 298.15 K was

40, 1538 (2019).

Fig. 1 Relationships between frequencies of ligand exchange, A, and salt concentration.

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles Theoretical Study of Chemical
Reactions in Heterogeneous Catalysts
S. E. M. PUTRA, T. N. PHAM, S. A. Wella, F. MUTTAQIEN, Y. J. WONG, H. KIZAKI,K. INAGAKI, Y. HAMAMOTO, I. HAMADA, and Y. MORIKAWA
Department of Precision Engineering, Graduate School of Engineering,Osaka University, 2-1 Yamadaoka Suita, Osaka 565-0871

In 2019-2020, we carried out theoreticalanalysis of chemical processes at surfaces andinterfaces, formic acid adsorption and decomposition on Cu(111) [1], enhancement of CO2hydrogenation by O-C-O bending vibration
mode [2], trimer formation of NO Cu(111) [3],and CO oxidation and oxygen reduction reaction at Pt single atom catalyst supported
by graphene edges [4]. We also investigateddopant in semiconductors, namely, transition
metal doped ZnSnAs2 [5], and As and B codoping in Si [6]. In this report, we report theenhancement of CO2 hydrogenation by vibration excitation [2].
Recently, formic acid (HCOOH) has been
considered as a potential material for hydrogenstorage. Storage of HCOOH is easier and safer
compared with other hydrogen storage material because HCOOH is a non flammable liquid
at STP. HCOOH can be decomposed on metal
surfaces through dehydrogenation process into
CO2 and H2 , or dehydration process into CO
and H2 O. Cu catalysts have been reported to
selectively decompose HCOOH through dehydrogenation process. The decomposition of
HCOOH does not occur on Cu(111) when exposed to the gas phase HCOOH at room temperature. On the Cu(111) surface, HCOOH
was reported to form polymeric structures
when exposed to the gas phase HCOOH at low
temperatures, then the decomposition occurs
by heating those polymeric HCOOH.
In the present study, we have investigated

the adsorption and decomposition mechanismsof monomeric HCOOH on Cu(111) by using
density functionals that account for the vdW
forces and compared with room temperatureexperimental results.
Our calculations were performed using the
STATE (Simulation Tool for Atom TEchnology) code[7]. Here, we compared results obtained using the PBE functional with thoseusing the van der Waals density functionals(vdW-DFs), i.e., optB86b-vdW and rev-vdWDF2 [8] functionals. We also included the dispersion correction proposed by Grimme with
PBE (PBE-D2). The implementation of theself-consistent vdW-DF in the STATE code is
described in Ref. [9].
The reaction path for the decomposition(Edec ) of the OH-perpendicular configurationon the Cu(111) surface is shown in Fig. 1. The
calculated activation energies of decomposition(Edec ’s) with ZPE correction are 0.37 eV, 0.31
eV, 0.32 eV, and 0.30 eV for PBE, PBE-D2,
rev-vdW-DF2, and optB86b-vdW functionals,
respectively, indicating that the Edec are almost independent among the considered functionals in this work. PBE-D2 and vdW-DFs
produce lower Edec than Edes by (0.16−0.27
eV).
Figure 2 shows the calculated desorption
and decomposition rates per surface adsorbate.
In this analysis, we used the calculated results by rev-vdW-DF2 energy functional. At
low temperatures, the decomposition process

95

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

becomes faster than the desorption process,while at higher temperatures, the desorption
process becomes dominant due to large preexponential factor for the desorption process
and the transition temperature between thetwo processes is ∼ 187 K. These results arein very good agreement with the experimental
situation that there is no HCOOH decomposition on Cu(111) by exposing the surface to thegas phase HCOOH at room temperature.

References[1] S. E. M. Putra, F. Muttaqien, Y.
Hamamoto, K. Inagaki, I. Hamada, and
Y. Morikawa: J. Chem. Phys. 150 (2019)154707.

Figure 1: (a) Decomposition process of the
OH-perpendicular configuration. IS, TS, andFS represent initial state, transition state, andfinal state, respectively. (b) Energy profile for
the OH-perpendicular configuration
decomposition on Cu(111).

[2] J. Quan, F. Muttaqien, T. Kondo, T.
Kozarashi, T. Mogi, T. Imabayashi, Y.
Hamamoto, K. Inagaki, I. Hamada, Y.
Morikawa, and J. Nakamura: Nature
Chem. 11 (2019) 722.
[3] T. N. Pham, Y. Hamamoto, K. Inagaki,
D. N. Son, I. Hamada, and Y. Morikawa:
J. Phys. Chem. C 124 (2020) 2543.

Temperature / K
500

250

167

125

100

12

1.0×10Rate per surface adsorbate / s-1

Desorption: lattice gas model
Decomposition[4] S. A. Wella, Y. Hamamoto, F. Iskandar,
Suprijadi, Y. Morikawa, and I. Hamada:J. Chem. Phys. 152 (2020) 104707.

8

1.0×104

1.0×10[5] H. Kizaki and Y. Morikawa: Jpn. J. Appl.
Phys. 58 (2019) 110601.

0

1.0×10-4

1.0×10[6] K. Tsutsui and Y. Morikawa: Jpn. J.
Appl. Phys. 59 (2020) 010503.

-8

1.0×10

0

0.002

0.004

0.006

0.008

0.01

-1

Temperature / K[7] Y. Morikawa: Phys. Rev. B 51 (1995)
14802.

Figure 2: Calculated reaction rates per surface
adsorbate for the desorption and decomposition of OH-perpendicular configuration. Red
dashed line with circle and blue solid line withsquare dots line represent the decompositionand desorption rates obtained by using the 2D
lattice gas, respectively.

[8] I. Hamada:
121103.

Phys. Rev. B 89 (2014)[9] Y. Hamamoto, I. Hamada, K. Inagaki,
Y. Morikawa: Phys. Rev. B 93 (2016)245440.

96

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical Design of Gate Dielectrics of Future GaN Power
DevicesKenji SHIRAISHI
Institute for Materials and Systems for Sustainability,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601
We

performed

thedensity-functionalenergy barriers. The calculated occurrence rate

calculations that clarify atomic and electronic

for the transformation is high enough to assure

structures of the oxygen vacancy VO inthat the thermal annealing at typical temperatureamorphous (Al2O3)1-x(SiO2)x mixed oxides, aand time causes the conversion of thepromising candidate for the gate insulator inelectrically active VO to the inactive VO,

future GaN power devices [1]. We constructed

providing a further advantage of (Al2O3)1-

microscopic models for the amorphous structurex(SiO2)x as the gate insulator over other oxides

by the melt-quench scheme and then examine allsuch as SiO2 and Al2O3.
Density of states

the possible oxygen vacancies and determine thetotal-energy minimized VO structures. We founda clear tendency that the VO formed at theoxygen site surrounded by less Al atoms has

(a)

-20

(b)

-20
-20

lower formation energy. More importantly, we

VO state
-15

-15
-15

-10

-5

0

5

-10

-5

0

5

-10

-5

Energy level (eV)

0

5

10

10

(c)

find that VO surrounded by Si atoms alone
induces no deep levels in the energy gap of GaN,
whereas VO surrounded by more Al atoms
induces a deep level. This theoretical finding
Fig.1: Density of states of the (Al2O3)0.70(SiO2)0.30
mixed oxide containing a single oxygen vacancy VO
obtained by HSE, (a) surrounded by Al atoms and (b)surrounded by Si atoms. The origin of the energy is set
at the valence band maximum. (c) Atomic structure of a
VO surrounded by Si atoms. A Si-Si bond is formed after
removal of the oxygen atom. Silver, blue, and red
spheres represent the Al, Si, and O atoms, respectively.

strongly infers that the majority of VO in
amorphous (Al2O3)1-x(SiO2)x is electricallyinactive and not very harmful in device
operations. We further explore the possibilitiesof the structural transformation from theReferences

electrically active VO to the electrically inactive[1] D. Kikuta, K. Itoh, T. Narita, and T. Mori,
Al2O3/SiO2 nanolaminate for a gate oxide ina GaN-based MOS device, J. Vac. Sci.
Technol. A 35, 01B122 (2017).

VO. We identified reaction pathways for suchtransformation and obtain the corresponding97

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analysis of Thermoelectric Properties of Clathrate
Compounds with Ab Initio Calculations
Masato OHNISHI
7-3-1, Hongo, Bunkyo-ku, The University of Tokyo, Tokyo 113-8656
Clathratecompounds

aredoping level can enhance ZT significantly (seepromisingcandidates for thermoelectric materials in terms

Figure).

of the “electron-crystal phonon-glass” concept.

properties, we obtained possible structures atClathrate compounds are composed of guest

finiteatoms encapsulated in cagelike structures. It is

expansion and Monte Carlo method [1] andexpected that electrons can smoothly transport

thermoelectric properties were averaged forin the frame work while phonons are scattereddifferent possible structures. Phonon properties

by guest atoms. Particularly, in type-I clathrateof the clathrates were calculated with using acompounds, guest atoms vibrate in a strong

self-consistent phonon (SCP) theory based onanharmonic

first-principles calculations [2]. Our state-of-potential

because

they

are

To

investigate

temperature

analysiswithmethodthermoelectric
using

composed of a Weaire-Phelan structure, which

the-artshows

divides a space with the maximum volume withagreement with experimental data.

aclusteragood

the same cross-sectional area. While off-center
clathrates such as type-I Ba8Ga16Sn30, in which
guest

atoms

vibrateinanharmonic

potential,

haveconductivity,

silicon-basedadouble-welllowthermalclathrates

arepreferable for actual use in terms of thematerial cost.

Fig. Temperature-dependent dimensionlessthermoelectric figure of merit (ZT) of type-I Sibased clathrate with different carrier
concentrations.

In this study, we show that aluminum
substitutions

canenhancethermoelectricperformance of silicon-based clathrates, type-I

References

Ba8Ga16Si30.

[1] R. Kubo: J. Phys. Soc. Jpn. 12 (1957) 570.

Comparing

calculated

thermoelectric figure of merits (ZT) with thoseM. Ångqvist, P. Erhart et al., Chem. Mater. 29,

obtained in experiment, we concluded that (a)7554 (2017) and 28, 6877 (2016).

aluminum additive enhances ZT with lowering[2] Tadano et al. Phys. Rev. Lett 120, 105901

doping level and (b) further suppression of(2018).

98

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles calculations of multiferroic interfaces
Yoshihiro GOHDA
Department of Materials Science and Engineering, Tokyo Institute of Technology
J1-3, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8502, Japan

manent magnets [6–8].

To obtain large magnetoelectric coupling in
multiferroic materials, multiferroic interfaces
are promising, because single-phase multiferroic materials exhibit typically antiferromagnetism preventing from having net magnetization [1, 2]. In addition to multiferroic interfaces, many types of magnetic interfaces are offundamental importance to enhance the performance of magnetic materials. Nevertheless,our understanding from electron theory is far
from being satisfactory. Since first-principles
calculations of magnetic interfaces are computationally challenging, such study is also of importance in the sense of large scale computations.

0.4∆O-Ti (Å)

0.3
0.2
0.1
0.0

−0.1
−0.2
−0.3
−0.4

Fe(Y)Si(Z) (Pup)
Si(Y)Si(Z) (Pup)
CoCo
(Pup)

Fe(Y)Si(Z) (Pdown)
Si(Y)Si(Z) (Pdown)
CoCo(Pdown)TiO (1) TiO (2) TiO (3) TiO (4) TiO (5)Figure 1: Relative displacements ∆O−Ti = zO −zTi in the tetragonal BaTiO3 (001) film for each interface. For the Fe(Y)Si(Z) case, average valuesfor ∆O−Ti are shown. The first layer TiO2 (1) is
the interface layer, whereas the fifth layer TiO2 (5)has the bulk atomic positions of BaTiO3 .

In this project, we performed first-principles
calculations of magnetic interfaces related withmultiferroic materials [3–5] and permanent
magnets [6–8]. We demonstrated enhancement of magnetoelectric coupling by insertionof Co atomic layer into Fe3 Si/BaTiO3 (001) interfaces from first principles [3]. As is shownin Fig. 1, the interface Co monolayer helps
the interface ferroelectric polarization exhibit
enough, whereas the interface electric polarization is killed by Si without the Co monolayer at the interface. Other transition-metalmonolayers are also investigated [4]. In addition, crystal-growth mechanism was also clarified for Co2 FeSi and Co2 MnSi films on singlecrystalline oxides by identifying the initial disorder at the deposition and the formation energy of random alloys relative to ordered alloy [5] by using both of OpenMX [9] and AkaiKKR [10]. Substantial progresses were obtained also for microstructure interfaces in per-[1] T. Taniyama, J. Phys.: Condens. Matter 27,
504001 (2015).
[2] K. Fujita and Y. Gohda, Phys. Rev. Appl. 11,024006 (2019).
[3] Y. Hamazaki and Y. Gohda, J. Appl. Phys.
126, 233902 (2019).
[4] R. Costa–Amaral and Y. Gohda, in preparation.
[5] K. Kudo, Y. Hamazaki, S. Yamada, S. Abo, Y.
Gohda, and K. Hamaya, ACS Appl. Electron.
Mater. 1, 2371 (2019).
[6] A. Terasawa, M. Matsumoto, T. Ozaki, and Y.
Gohda, J. Phys. Soc. Jpn. 88, 114706 (2019).
[7] Y. Ainai, Y. Tatetsu, A. Terasawa, and Y. Gohda, Appl. Phys. Express 13, 017006 (2020).
[8] Y. Ainai, T. Shiozawa, Y. Tatetsu, and Y. Gohda, Appl. Phys. Express 13, 045502 (2020).
[9] T. Ozaki, Phys. Rev. B. 67, 155108 (2003).
[10] H. Akai, J. Phys. Condens. Matter 1, 8045
(1989).

99

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Determination of the ionization energy and theelectron affinity of organic molecular crystals fromfirst-principles
Susumu Yanagisawa
Faculty of Science, Department of Physics and Earth Sciences, University of the Ryukyus
Nishihara, Okinawa, 903-0213

Ionization energy (IE) and electron affinity (EA) are fundamental quantities of organic
semiconductors, and understanding the factorsthat determine the energy levels is of primary
importance to the research and development of
the organic electronics materials such as thoseof organic light-emitting diodes, organic fieldeffect transistors, and organic photovoltaics,
dominating energy barrier for injection of acharge carrier (hole and electron).
IE and EA are measured with direct photoemission and inverse photoemission techniques,
respectively. Notice here that the energy ofthe hole or electron injected into the sample is measured, i.e., IE (EA) is the magnitude of the energy difference between the neutral N-electron and the positively-(negatively)charged N−1 (N+1)-electron systems. Thus,
the measured IE and EA implies many-bodyinteraction between the injected charge andthe surrounding polarization clouds inside theorganic solids which screen the injected charge.
A complex of the injected charge and thesurrounding dynamically induced polarization
clouds are referred to as quasiparticles, which
are theoretically well-described with the selfenergy determined by the many-body perturbation theory within the GW approximation.
Given an experimental measurement of a few
organic monolayers on a substrate such as silica and graphite, it is of importance to investigate the electronic structure of an organic filmof a few monolayer thickness with a reliable

theoretical method. For such purposes, a periodic slab model approach is useful. To avoid
the computationally demanding periodic slab
calculation with GW , the electrostatic potential in a periodic slab was described within
DFT-GGA, which was aligned to that in abulk system. In the bulk system, the electronic
polarization upon the injected charge was described within the GW approximation.
In this study, with a combination of theGW approximation suitable in general to solidor bulk systems and a periodic slab approachat the DFT-GGA level, I investigated polymorphs of pentacene (PEN) and perfluoropentacene (PFP). I theoretically demonstrated
that the IE and EA at the surface are dominated by the electronic polarization (Ep ) upon
the injected charge induced by the surrounding
polarization clouds, and the electrostatic energy (S) crucially affected by the orientationof the molecule at the surface of the organic
semiconductor[1].
The geometrical configurations of the organic semiconductor bulk was determined with
the STATE program code, with the lattice constants fixed to the experimental values. For
the crystal structure and the lattice constants,
two typical polymorphs were considered: single crystal and thin film phases of PEN, fabricated on SiO2 and graphene substrates, respectively, and, herringbone and π-stacking motifs
for PFP, that were reported to grow on the
SiO2 and graphene, respectively.

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

For the optimized crystal geometries, I estimated the Ep upon the excess hole and electron, based on the quasiparticle self-energy
within the GW approximation. I used themodified version of the GW space-time code,
which enables highly parallelized calculations.
The resulting ionization energy (Is ) and electron affinity (As ) are displayed by horizontal
dotted dashed lines in Fig. 1. Here, the electronic polarization Ep was obtained as half thedifference between the crystalline fundamental
gap and that in a gas phase, assuming that
Ep+ = Ep− . The Is and As change drasticallywhen the molecular orientation at the surface
is taken into account, and thus, the non-zero
S + and S − contribute. The calculated Is andAs are in agreement with experiments.
Overall, while Ep , which is approximated by
the charge-induced dipole interaction, is quantitatively described within the GW approximation, the present methodology of estimating the electrostatic contribution S seems todescribe well the electrostatic nature of themolecular orientation dependence of Is andAs at the surface, i.e., the charge-quadrupole
interaction[2]. The method lacks descriptionof the decreasing polarization at the surface
which amounts to the change of the quantitiesby ≈ 0.2 eV[3]. Nevertheless, considering thehuge computational cost involved in treatmentof the slab within GW , the method is suitable for quantitative treatment of an organic
semiconductor nano-scale thin film, which is
required for nano-scale or sub-nanoscale control of the materials properties.

References[1] S. Yanagisawa: Jpn. J. Appl. Phys. 59(2020) 031002.
[2] B. J. Topham and Z. G. Soos: Phys. Rev.
B 84 (2011) 165405.
[3] J. Li et al.: J. Phys. Chem. Lett. 7 (2016)
2814.

(a)

Pentacene (5 ML)
A = 1.39 0.44g

Ep=1.36

As= 2.31
Is= 4.77

Ep=1.36
Ig= 6.59

0.04

P−

Ep=1.41

P−

As [w/o mol.ori.]

As= 2.84 As [w/o mol.ori.]

Is [w/o mol.ori.]

Is= 5.23 Is [w/o mol.ori.]

Ep=1.41
0.05

P+

0.46

P+

Single crystal (010)
Lying orientation

Thin film (001)Standing orientation(b)

Perfluoropentacene (5 ML)

Ag= 2.66 0.55

0.28
−

P
Ep=1.28

As= 4.49

Ep=1.33

P−

As [w/o mol.ori.] As= 3.71 As [w/o mol.ori.]

Is [w/o mol.ori.] Is= 5.87 Is [w/o mol.ori.]
Is= 6.78
Ep=1.33
P+
Ep=1.28
P+
Ig= 7.50
0.30
0.56
Herringbone (100)π-stack (010)Standing orientation
Lying orientation

Figure 1: Determination of ionization energy(Is ) and electron affinity (As ) for the pentacene
and perfluoropentacene polymorphs. The experimental gas phase ionization energy (Ig )and electron affinity (As ) are indicated by thehorizontal dashed lines, and the thick horizontal solid lines indicate Is and As at the crystalline surfaces. The vertical dashed lines display the polarization energies P + or P − , which
are comprised of the electronic polarization Ep
displayed by the double-headed arrows and theelectrostatic energies S + or S − indicated by
the thick one-headed arrows. For comparison,
the ionization energy and the electron affinity
without taking into account the molecular orientation at the surface, i.e. S + =S − =0, areshown by horizontal dotted dashed lines.

101

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

DFT Prediction of Bulk Rashba Eﬀect
in Multiferroic Oxide
Kunihiko Yamauchi
ISIR-SANKEN, Osaka University, Ibaraki, Osaka 567-0047

Based on ab-initio approach using massive parallel computer simulations, we studied
Rashba eﬀect, which causes spin splitting ofbands through the spin-orbit interaction. This
year, we focused on multiferroics — the materials which show both ferroelectric and antiferromagnetic orders — in order to investigate
the particular Rashba eﬀect emerging with themagnetic symmetry that contains spin-flipping
symmetry operations.
Density-functional theory (DFT) calculations were performed using the VASP codewith GGA+U method. BiCoO3 crystalizes in
the polar P 4mm crystal structure in which
the Co3+ (d6 ) ion located at the center of
the O6 octahedron is significantly displaced
toward the apical O ion, leading to a pyramidal coordination rather than an octahedral
coordination. The magnetic symmetry with
the C-type antiferromagnetic order (defined bymagnetic space group P 4′ mm′ ) keeps the spindegeneracy of bands at the high-symmetric k
points. As shown in Fig.1, we found that thecharacteristic vortex-like in-plane components of the spin texture of the Rashba eﬀect
developing around the Z point while the outof-plane spin component is negligible [1].
The magnetic symmetry can be reduced
when the Co spins are canted with respect to
the C-AFM configuration in the real space. We
assumed the application of external magnetic
field along the [100] direction, by canting two
Co spins simultaneously. As a result, we observed a distortion of the energy isocontour
along the ky axis and a downward shift of thecenter of spin vortex.

R2

ky

R1

A

kx

Figure 1: Spin texture (shown by magenta arrows) and energy contour plot of the
conduction-bottom band in the kz = 1/2 plane(centered at the Z point) in BiCoO3 .
While the theoretical predictions in thepresent study call for future experimental confirmation, we speculate that this phenomenon
can be rather common among the antiferromagnetic polar systems; in future works, one
can explore the possibility of Rashba eﬀects invarious multiferroic systems, such as BiFeO3
and PbVO3 .

References[1] Kunihiko Yamauchi, Paolo Barone, andSilvia Picozzi, Phys. Rev. B 100 (2019)
245115.

102

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-Principles Molecular-Dynamics Study of Structural andElectronic Properties of Covalent Liquids and Glasses under
Pressure
Fuyuki SHIMOJO, Shogo FUKUSHIMA, and Akihide KOURA
Department of Physics, Kumamoto University, Kumamoto 860-8555
The investigation of the dynamic properties

cost of numerical integration in the TI methodof covalent liquids and glasses under pressureby using an ANN potential compared withis important from perspectives of geophysics as

FPMD-based TI calculations, while keeping

well as fundamental liquid-state science. For

first-principles accuracy. By comparing withthis purpose, it would be important to consider

the results by FPMD, we confirmed that thethe stability of materials states under various

ANN-based TI method gives the free energy

conditions from the viewpoint of free energy.

within the accuracy of less than 0.1 meV/atom

To accurately evaluate which state is mostwith more than 100 atoms.

stable, the thermodynamic integration (TI)
method has been used by calculating the freeenergy [1]. While the TI method based on firstprinciples

molecular

dynamics(FPMD)

simulations can obtain the free energy with
sufficient precision [2], the system size isseverely limited by its high computational cost.
In order to handle adequate system sizes
while retaining first-principles accuracy, weFig. 1: Melting temperature T as a function of
the number of atoms N.

adopt an interatomic potential constructed byartificial neural-network (ANN) models trained
by FPMD simulations. This study aims toReferences

establish a method for the precise evaluation of[1] D. Frenkel and A. J. C. Ladd, J. Chem. Phys.

the free energy using the TI based on the ANN-81, 3188 (1984).

MD simulations. To that end, we have[2] O. Sugino and R. Car, Phys. Rev. Lett. 74,

calculated the size dependence of the melting

1823 (1995).

temperature of rubidium as shown in Fig. 1 [3].

[3] Fukushima et al., Phys. Rev. B 100, 214108(2019)

We successfully reduced the computational

103

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Elucidation of diffusion process of ionic species
in organic solvent
Kazuto AKAGIWPI-AIMR, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi 980-8577
Further improvement of Li-ion batteries

EC” and “43 EC + 3 Li+” systems were used as(LIB) is strongly expected still now. The

training set. “360 EC + n Li+” systems (fromperformance of LIB depends on various factors,

0.1M to 3.0M) were used for production run.

and optimizing transport properties of Li-ion is

The initial generation was prepared from theone of the most important items. The

original parameters of AMOEBA FF with 20%

microscopic transport mechanism in organic

random noise. The parameter sets formed fourelectrolytes, however, remains unclear. To

groups with the evolution, and only one groupelucidate it, we have developed a genetic

survived at 60th generation. Some of themalgorithm based optimized force field (FF)successfully

which achieves large-scale and long-time

coefficient and density calculated by VASP. Not

classical MD simulation.

only the solvation structure of Li-ions but also

reproducedthediffusion

Polarizable FFs such as AMOEBA andpotential of mean force (PMF) for detachment

APPLE&P are potentially applicable to large

and attachment of EC were also reasonably

scale simulation for LIB systems, but theirdescribed. The diffusion of Li-ion becomesreliability is not sufficient as they are. In order

slower at high concentration and it statisticallyto optimize AMOEBA FF and mimic theturned out that the lack of free EC molecules

thermodynamic properties obtained by rev-

decreases attachment/detachment events. The

vdW-DF2 density functional for target systems,

detailed results are prepared for publication.

we made a framework of multi-objective
genetic algorithm, in which not only relative
potential energy but atomic forces on each atomfrom VASP are reproduced by TINKER.
Pure ethylene carbonate (EC) and EC with
Li-ion systems were assessed. The dimension

Fig. 1: (a) Improvement of solvated structure.

of parameter space to be optimized is 132, and(b) PMF along detachment of EC (DFT and FF).

more than 150 MD snapshots sampled from “9104Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study on the stability of magnetic alloys
Yasutomi TATETSU
Meio University, Biimata, Nago, Okinawa 905-8585
Transforming crystal structures of materials

Fe site. There are two different Wyckoffby adding pressure, heat, or other elements is

positions of Pd labelled by 2e and 2g in Z3-

one of the fundamental approaches to discover

FePd3. From detailed analyses, we concluded

novel physical properties. Recently, a new Z3-

that the new Z3-type Fe(Pd,In)3 structure, in

type

was

which a Pd atom at a 2e site is replaced with an

discovered by Teranishi’s group in Kyoto

In atom, is more stable than In-doped L12-

University [1]. The new structure was obtained

FePd3 structures. These results are consistentby introducing a third element of In into L12-

with the experimental results from XRD,

FePd3, which is the thermodynamically stable

EXAFS, and STEM-EDS analyses.

Fe(Pd,In)3

crystalstructure,phase of binary Fe–Pd systems. Although theaddition of In might be the key behind this new
0.4

Eform (eV/u.c. with 8 atoms)

finding, the physical aspects of In in stabilizing
the new structure is unclear and cannot be
understood deeply only through experiments.

Z3ïFe2Pd5In
L12ïFePd6In

L12ïFePd3
Z3ïFePd3

0ï0.4

In this study, we performed theoreticalï0.8

analyses for the stability of an In-doped novel

ï1.2

Fe–Pd phase to check the systems’ formation

ï1.6

energies using OpenMX. The model structures

ï2

for the calculations were based on the chemical

Pd(e)

Fe

Fe

Pd(g)

Pd

In sitecomposition ratio of Z3-FePd3 obtained from

Figure ： The comparison of the formation

experiments. The In sites were chosen byenergies of In-doped Z3- and L12-type FePd3.

replacing Fe or Pd sites with a specialquasirandom-structure method implemented in

References

the Alloy Theoretic Automate Toolkit [3]. We[1] K. Matsumoto et al., in preparation.

investigated stable sites for In in the Z3-FePd3[2] http://www.openmx-square.org

structure by comparing formation energies[3] A. van de Walle et al., Calphad Journal 42,

which is illustrated in the figure. We found that

13 (2013).

an In stably occupies the Pd site rather than the105Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Electrode Properties of Novel Lithium-Ion Secondary
Battery Materials: First-Principles Calculations
Hiroyoshi MOMIDA, Motoyuki HAMAGUCHI, Hiroshi KATSUMOTO, Tatsuya TAKAHASHI
Institute of Scientific and Industrial Research, Osaka University
8-1 Mihogaoka, Ibaraki, Osaka 567-0047

We have studied electrode properties of Liand Na-ion secondary battery materials by
first-principles calculations. The computations
are done by using HiLAPW and Quantum
Espresso codes.
X-ray absorption spectra in NaFeSO4 F
for exploring Na-ion battery reactions
We study electronic and spectroscopic properties of NaFeSO4 F, which has been a candidate cathode material for Na-ion batteries[1, 2]. NaFeSO4 F have been often synthesized experimentally from NaF and FeSO4 , andthe calculated result shows that NaFeSO4 F isslightly stable in energy than the two-phasemixture of NaF and FeSO4 . The average voltage of NaFeSO4 F cathode is calculated to be
3.08 V with respect to the Na anode, andthat comes dominantly from valence changes
as Fe2+ /Fe3+ in NaFeSO4 F/FeSO4 F. X-ray
absorption spectra (XAS) near K-edges at Fe,
Na, and F are calculated for NaFeSO4 F andFeSO4 F as the cathodes in fully-discharged
and fully-charged states, respectively, and also
for NaF and FeSO4 as possible residual materials in real cathodes (Fig. 1). The results
show that XAS near K-edges, especially at F
as well as Fe, provides us useful information toclarify battery reactions and structures in thecathodes.
O-redox and O2 -release reactions in Liexcess cation-disordered rock-salt oxides
Li2+2x Mn1−x Ti1−x O4Thecation-disordered rock-salt oxides
Li2+2x Mn1−x Ti1−x O4 with the Li-excess

amount x are one of promising Li-ion battery
cathodes. We study the cathode properties of
the Li2+2x Mn1−x Ti1−x O4 models (Fig. 2) withx ranging from 0 to 0.3 by the first-principles
calculations, considering cation and anion
redox reactions with O2 -releases [3]. Eﬀects
of x on voltage-capacity curves and electronic
structures are studied, and the results showthat Mn-redox reactions predominate in earlycharging processes. As charging reactions
further proceed, O-redox reactions contributeto the cathode reactions more significantly forhigher x. From the formation energy analyses,
it is found that O atoms tend to be released
from the cathodes especially in late charging
processes with a trend of easier O2 -releasefor higher x, possibly accounting for lower
experimental capacities than the theoreticalvalues.
Na-ion battery performance and reaction mechanism of SnS anodeWe study the Na-ion battery performanceof SnS as an anode material by the firstprinciples calculations [4, 5]. From formationenergy analyses, the discharge reaction processes of the Na/SnS half-cell system are clarified. We calculate the phase diagram of Na–
Sn–S ternary systems by constructing convexhull curves of Na–Sn–S, and show a possible
reaction path considering intermediate products in discharge reactions. Voltage-capacity
curves are calculated based on the Na–SnS reaction path that is obtained from the ternary
phase diagram. It is found that the conver-106

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

XAS intensity (arb. units)

XAS intensity (arb. units)

7105
1.5

7115

7125

7135

7145

(a) x = 0
Ti
O

7155

Fe K-edge
1.0

Li

FeSO4
(experiment)
FeSO4F (C2/c)

Mn

Na0FeSO4F

0.5

a
b

FeSO4

6995

678
1.5

688

7005
7015
Energy (eV)
698
708

7025

7035

718

728

F K-edge
NaF

1.0

b

FeSO4F(C2/c)
Na0FeSO4F

0.5

0.0
650

660

670
680
Energy (eV)

690

700

Figure 1: Calculated x-ray absorption spectra(XAS) near Fe and F K-edges of NaFeSO4 F
materials [1]. Experimental XAS is also plotted with the upper energy scale.

bc(d) x = 0.3aaNaF (experiment)

NaFeSO4Fac(c) x = 0.2

NaFeSO4F

0.06985(b) x = 0.1

c

b

c

Figure 2: Calculated model structures of
Li2+2x Mn1−x Ti1−x O4 [x = (a) 0, (b) 0.1, (c)0.2, and (d) 0.3] with the cation-disorderedrock-salt structures [3].
the insertion and the conversion reactions at
early and late discharging processes, respectively. Based on the estimated reaction formula, voltage-capacity curve is calculated, andthe result well accounts for the experimentallyobserved two-plateau behavior.

sion reactions and subsequently the alloying
reactions proceed in the SnS electrode, contributing to its high capacity compared withthe metallic Sn electrode, in which only thealloying reactions progresses stepwise. To confirm the calculated reaction process, x-ray absorption spectra (XAS) are calculated for Na2 S
and SnS in discharged and charged states, respectively.

References

Conversion-type reaction mechanism of
FeF3 cathodes for Li-ion batteries[3] M. Hamaguchi, H. Momida and T.
Oguchi: Electrochim. Acta 330 (2020)
135286/1-8.

The perovskite-type FeF3 is one of promising cathodes for Li-ion batteries because of its
high capacity, but reaction mechanism has notbeen clarified yet. In this work, we study discharge reaction processes by calculating formation energies of Li–Fe–F materials. We theoretically find that the discharge reaction proceeds as FeF3 + 3Li → Li0.5 FeF3 + 2.5Li →FeF2 + LiF + 2Li → Fe + 3LiF, showing[1] H. Momida, A. Kitajou, S. Okada andT. Oguchi: J. Phys. Soc. Jpn. 88 (2019)124709/1-6.
[2] A. Kitajou, H. Momida, T. Yamashita, T.
Oguchi and S. Okada: ACS Appl. Energy
Mater. 2 (2019) 5968-5974.

[4] H. Kotaka, H. Momida, A. Kitajou, S.
Okada and T. Oguchi: Chem. Rec. 19(2019) 811-816.
[5] H. Kotaka, H. Momida, A. Kitajou, S.
Okada and T. Oguchi: J. Comput. Chem.
Jpn. 18 (2019) 78-83.

107

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study ofquantum transport in nanostructuresNOBUHIKO KOBAYASHI
Department of Applied Physics, University of Tsukuba
1-1-1 Tennodai Tsukuba Ibaraki 305-8573

Introduction50

An understanding of the electron transport
properties of materials has resulted in theemergence of an important and versatile problem, not only for the fundamental research ofscience but also for the applications of electronics. Quantum nature is essential in nanoscale
systems, and atomistic analysis based on detailed electronic states calculations are indispensable to discuss the transport property.
In order to investigate transport properties,
we have developed the nonequilibrium Green’s
function (NEGF) method, and the O(N) timedependent wave-packet diﬀusion (TD-WPD)
method on the basis of the density functional
theory (DFT). Using these methods, we haveinvestigated charge, head and spin transport
properties of materials. [1, 2]

2

O(N) method for transport
calculations

Organic semiconductors have attracted muchattention for their applications to flexible,
printable, lightweight, and low-cost electronic
devices. They are crystals that are assembliesof π-conjugated molecules weakly bonded byvan der Waals interactions, and single crystallization has been achieved, enhancing themobility. It is expected that the mechanismof carrier transport in organic semiconductors
can be elucidated and that materials exhibiting high mobility can be developed by novel
molecular synthesis.[3]We developed the O(N) TD-WPD method
for the quantum transport calculation of hugesystems of up to 100 million atoms a decadeago.We calculated the conductance and the108

Mobility m (cm2 V-1 s-1)

1105Prediction (Calculation for PBE-TS structure)
Experiment (FET mobility)
Calculation for experimental structure
Calculation for MMFF94 structure

1

200

220
240 260 280 300
Temperature T (K)

Figure 1: Temperature dependence of mobility
along the column direction in a C10-DNBDTsingle crystal. For comparison, the experimental values of FET mobilities are also shown as
triangles.

mobility of the system with micron-orderlengths at room temperature at the atomistic levels. Using this method we can study
the transport properties from diﬀusive to ballistic regimes including the eﬀect of realistic
electron-phonon scattering, and determine themean free path and relaxation time from anatomistic viewpoint. We performed DFT calculations of electronic structures and interactions between molecules of single-crystal organic semiconductors including the eﬀect ofthe van der Waals interaction, and applied the
TD-WPD method to the analysis of transport
properties of the organic semiconductors.
Using TD-WPD method, we have proposeda prediction methodology to obtain chargetransport properties of organic single crystals from their structural formula.
Pre-Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

diction of material properties of newly designed molecules is a long-term goal in organic electronics. As a demonstration, we
employ the promising molecule C10-DNBDT.
We succeeded in quantitative evaluation of
charge mobility of the single crystal using
our quantum wave-packet dynamical simulation method. Here, the single-crystal data iscomputationally obtained by searching possible packing structures from structural formulaof the molecule. The proposed methodology
can be a theoretical design technique for efficiently developing new high-performance organic semiconductors, since it can estimate thecharge transport properties at early stage inthe process of material development.[4]hancement in the figure of merit by doping,which is in agreement with experimental work,and show further enhancement by the optimized doping. Furthermore, electronic structures of thin films are examined. It is shownthat calculated electrical conductances reachto twice larger than that in the bulk, and thecalculated Seebeck coeﬃcients in thin films aresuppressed by the metallicity, remain maximally to about a half of the results in thebulk.[6]References
3

NEGF-DFT method

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.[5] We
have applied the method to analyses of thermoelectricity of magnetic semiconductors.
Thermoelectric materials have attracted
considerable attention from viewpoints not
only of materials science but also of applications for energy harvesting by waste heat, andintensive works have been devoted to enhance
conversion eﬃciency from thermal energy into
electricity. The eﬃciency is expressed as afunction of the figure of merit ZT = σS 2 T /κ,where σ, S, κ and T are the electrical conductivity, the Seebeck coeﬃcient, the thermal conductivity and the temperature, respectively,
and the thermoelectric power factor is written
as σS 2 . Enhancement of thermoelectric eﬃciency is not an easy task since the Seebeck
coeﬃcient, the electrical conductivity, and thethermal conductivity are not independent ofeach other. There is the trade-oﬀ between σ
and S, and materials with high electric conductivity tend to have high thermal conductivity.
We analyze the thermoelectric properties ofa magnetic semiconductor using SAKE program. The electronic transport properties,
Seebeck coeﬃcient, and the figures of meritare estimated for doped systems and thinfilms. We theoretically demonstrate the en-

109[1] N. Kobayashi, H. Ishii, K. Hirose,
Jpn. J. Appl. Phys. 57, 08NA01 (2018).
[2] 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.
[3] A. Yamamura, H.Fujii, H. Ogasawara, D.
Nordlund, O. Takahashi, Y. Kishi, H. Ishii, N.
Kobayashi, N. Niitsu, B. Blulle, T. Okamoto,Y. Wakabayashi, S. Watanabe, and J. Takeya,
Commun. Phys. 3 20 (2020)[4] H. Ishii, S. Obata, N. Niitsu, S. Watanabe, H.
Goto, K. Hirose, N. Kobayashi, T. Okamoto,and J. Takeya,
Sci. Rep. 10, 2524 (2020)[5] H.Takaki, N.Kobayashi, K.Hirose,
J. Phys. Cond. Matter. (2020) in press.
[6] H.Takaki,
K.Kobayashi,
M.Shimono,
N.Kobayashi, K.Hirose, N.Tsujii, T.Mori,
Jpn. J. Appl. Phys. 58 SIIB01 (2019).

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Prediction of properties of organic ferroelectrics andpiezoelectrics by ﬁrst-principles calculation
Shoji ISHIBASHI
Research Center for Computational Design of Advanced Functional Materials (CD-FMat),
National Institute of Advanced Industrial Science and Technology (AIST)
Tsukuba, Ibaraki 305-8565

Organic charge transfer complexes show avariety of crystal structures and electronic
properties. Among them, there is a class ofcompounds called“mixed-stack compounds”,
in which electron-donor and electron-acceptor
molecules stack alternatively along a certain
direction. Some of them show ferroelectricity.
Tetrathiafulvalene-p-chloranil (TTF-CA) is atypical example. Kobayashi et al. successfullymeasured spontaneous polarization in TTFCA and obtained a value of 6.3 µC cm−2 [1].
Furthermore, they found that the polarization
value is more than 20 times larger than thatof the point charge model, and their directions
are opposite. To clarify the origin of this exotic
ferroelectricity in TTF-CA, we made theoretical analyses in terms of Born eﬀective chares aswell as maximally-localized Wannier orbitals[2, 3]. We have shown that only 2 bands below
the band gap are responsible for the emergenceof polarization and also that the electron ﬂow
from cell to cell on these electronic states is theorigin of the exotic polarization in TTF-CA.
Recently, Mezzadri et al.
reported
the structure of the low-temperaturephaseof
3,3,5,5-tetramethylbenzidinetetracyanoquinodimethane(TMB-TCNQ)
and pointed out that this phase is potentiallyferroelectric [4]. Similarly to the TTF-CA
case, TMB and TCNQ molecules stack alternately and form one-dimensional columns.
We have applied the above-mentioned
computational methods to investigate theferroelectricity in TMB-TCNQ and foundsimilarities and dissimilarities with TTF-CA[5].
In addition, theoretical calculations to
obtainspontaneous-polarization
vectorsfor organic ferroelectrics D22bpy-Dia andD55dmbp-Dia have been performed.
Theobtained results explain the experimentallyobserved values well [6].

References[1] K. Kobayashi, S. Horiuchi, R. Kumai, F.
Kagawa, Y. Murakami, and Y. Tokura:Phys. Rev. Lett. 108 (2012) 237601.
[2] S. Ishibashi and K. Terakura: J. Phys.
Soc. Jpn. 83 (2014) 073702.
[3] K. Terakura and S. Ishibashi: Phys. Rev.
B 91 (2015) 195120.
[4] F. Mezzadri, N. Castagnetti, M. Masino,
and A. Girlando: Cryst. Growth Des. 18(2018) 5592.
[5] S. Ishibashi, S. Horiuchi, and K. Terakura: unpublished.
[6] S. Horiuchi, S. Ishibashi, K. Kobayashi,
and R. Kumai: RSC Adv. 9 (2019) 39662.

110

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analysis of metal/oxide interfaces with large
mismatches
Hongping LI1 ,Mitsuhiro SAITO2 , Chunlin CHEN1 , Kazutoshi INOUE1 , Kazuto AKAGI1 ,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

Metal/oxide heterointerfaces are widely usedin engineering, and their microstructures govern the macroscopic properties. We investigated the interaction and bonding reconstruction at Pd/ZnO {0001} interfaces with large
mismatches by density functional theory calculations combined with atomic-resolution scanning transmission electron microscopy. It has
been believed that the interfacial interactions
are very weak at incoherent interfaces withlarge mismatches, and metal–oxide interfaces
can be more favorable than metal–metal interfaces.
To gain insight into the local atomic structures of each interface, ﬁrst-principles calculations were performed using the Vienna ab initio Simulation Package (VASP). The electronic
wave functions were expanded by plane waves
up to a kinetic energy cutoﬀ of 400eV. The
generalized gradient approximation in the formof the Perdew–Burke–Ernzerhof exchangecorrelation functional was implemented in our
calculations. A supercell containing seven Pd
lattices matching six ZnO lattices along theinterfaces was constructed to compensate themismatch which agree with the experimental
result. The surface atoms of the ZnO slabs
were passivated by H atoms to eliminate theeﬀects of dangling bonds, and a 15Å vacuum
area was embedded into the outer Pd surfaces
to avoid unwanted interactions. For k-point
sampling, a 1 × 1 × 1 Monkhorst–Pack grid
was applied in the irreducible Brillouin zone
for the supercell calculations. Convergencewith a 2 × 2 × 1 Monkhorst–Pack mesh was
also tested for both interfaces, and the diﬀerences in the total energy and atomic conﬁgu-

rations could be neglected. The convergencethreshold for self-consistent iteration was set
at 1.0 × 10−4 eV/atom, and the atomic positions were fully relaxed until the maximal force
on each atom was less than 0.05eV/Å. To analyze the interfacial stability of the epitaxial
systems, the adhesive energy was calculated by
Ead = [EPd−slab + EZnO−slab –Etotal ]/A, where
Etotal , EPd−slab , and EZnO−slab are the interfacial total energy and the energies of individual Pd and ZnO slabs, respectively, and A
is the interfacial area. Then, we get Ead =2.66J/m2 and 3.52J/m2 for the Zn-terminatedPd (111)/ZnO (0001) and (0001̄) interface, respectively, implying that the nonstoichiometric Zn-terminated Pd (111)/ZnO (0001̄) interface is energetically favorable. The interfacial atoms were located almost at bulk lattice
points for the stoichiometric Zn-terminatedPd(111)/ZnO(0001) interface while the interfacial Pd and Zn atoms underwent relatively large relaxations at the nonstoichiometric Zn-terminated Pd(111)/ZnO(0001̄) interface, making the interface relaxed to release the large interfacial mismatch. The PdZn bonds exhibited site-dependent characteristics and gradually transitioned from covalent
to ionic at the Pd(111)/ZnO(0001) interface,whereas most of Pd-Zn bonds exhibited strong
covalent behavior at the Pd/ZnO(0001̄) interface [1].

References[1] H. Li, M. Saito, C. Chen, K. Inoue, K. Akagi, Y. Ikuhara: Acta Mater. 179 (2019)237-246.

111

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Firefly Oxyluciferin Anions in Aqueous Solutions
Yoshifumi NOGUCHI
Department of Applied Chemistry and Biochemical Engineering, Graduate School ofEngineering, Shizuoka University, Johoku 3-5-1, Hamamatsu, Shizuoka 432-8561, Japan

Oxyluciferin anion, known as a light emitter

indicatedachargeleakagefrom

thein the firefly bioluminescence process, is a key

oxyluciferin anion to the surrounding watermolecule in understanding the mechanism ofmolecules. In addition, we discussed thethe firefly bioluminescence process. Althoughvalidity of a modeled aqueous solution, such as

significant effort has been taken in various

QM/MM or PCM methods, in which the charge

studies targeting the oxyluciferin anion, most oftransfer between solute and solvent is restricted.

its properties still remain unclear. This is

In order to describe the charge leakage from the

because, from the perspective of simulations,

oxyluciferin anion and reproduce our full QM

the environmental conditions surrounding theresults, at least 10 water molecules should be

oxyluciferin anion are too complicated. In

included into QM region.

addition, the oxyluciferin anion is too sensitive
for the environments.
In this study, we applied the first-principles
Born-Oppenheimer

molecular

dynamics

simulations (BOMD) to three possible isomersoftheoxyluciferin anion

(see

Fig.

1)
Phenolate-ketosurrounded by 64 water molecules, andsimulated the photoabsorption spectra for 1000

Fig.

randomly selected molecular geometries from

Phenolate-enol Phenol-enolate

1. Three possible isomers of theoxyluciferin anion.

the trajectory [1].
The simulated spectra are in a good

References

agreement with the experiments. The remaining[1] Y. Noguchi, M. Hiyama, M. Shiga, H.

error is less than 0.1 eV in comparison with the

Akiyama, and O. Sugino: J. Chem. Theory

peak top positions. Our full QM simulations

Compt.,

112

15(2019)

5474.

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles investigation on electronic structure
modulation via coherent phonon excitation
Yasushi SHINOHARA1,2
1

Photon Science Center,

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

Department of Nuclear Engineering and Management,

The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656
Recent progress of coherent light source

representation, all-symmetric, modes. These

technology allows us to observe quantum

results

invokethat

dynamics in time-domain (TD) driven by intense

modulation due to the optical phonon, excited as

and short laser pulses [1,2], rather thancoherent phonon via the IR pump pulse. Eachfrequency-domain (FD) observation such as thepart of the energy-dispersion has a different

standard spectroscopies. The TD information

coupling with the phonon modes. By extracting

usually contains more than complementarya frequency structure |𝑆(𝐸, 𝑘; 𝜔 = 𝜔phonon )| ,information of FD data because of phasemuch finer information of electron-phonon

information, namely time-origin is clearlyinteraction than Raman spectra is expected to be

introduced by the pulse. Very recently, more

extracted. To prove this scenario, we perform an

extreme and flexible pulse shaping is available

ab-initio

such that two-color mixing pulse composing

modulation due to the optical phonon modes

infrared (IR) and ultraviolet (UV) photon

within the density-functional theory (DFT)energies. We have investigated coherent phonon

framework within the abinit code.

simulationelectronic

that

band

structure

structure

excitation encoded in temporal modulation inFirstly, we optimize the atomic position ofangle-resolved photoemission spectra (ARPES)

the Ta2NiSe5 crystal with two functionals,

by using IR pump and UV probe pulses.

Perdew-Wang local density approximation (PW-

We observe TD-ARPES of Ta2NiSe5, a

LDA),

and

Perdew-Burke-Ernzerhof

candidate of the excitonic insulators, pumped bygeneralized gradient approximation (PBE-

1.55 eV pulse. In the time-dependent E-k

GGA). Secondly, we obtain normal modes of thespectral distribution 𝑆(𝐸, 𝑘; 𝑡) , oscillatory

lattice vibration at Γ-point via density-functional

behaviors appear. The frequencies of theperturbation theory (DFPT) with each functional.

oscillation well coincide with the optical phonon

By performing symmetry operations of thefrequencies

crystal, we assign irreducible representation tobelonging

to Ag

irreducible

113

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

the modes. We only pick up Ag irreducible

prominent change around Fermi-level of therepresentation because this mode is only excitedspectra [3]. This mode has been argued as theas the coherent phonon based on displacive

driving mode of insulator-metal (IM) transition

excitation of coherent phonon mechanism. The

via photoexcitation. Our investigation posts an

DFPT computation demands the heaviest

additional clue to understand the mechanism ofcomputational resource. Our crystal is a

the IM transition.

semimetal with PW-LDA and PBE-GGA
functional. To capture small Fermi surface, weneed fine Brillouin zone sampling that has 864
k-points. The existence of Ta requires rather highReferences

energy cutoff, 50 eV, for the plane wave. The[1] F. Krausz and M. Ivanov, Rev. Mod. Phys.

calculation takes 11 hours with 64 nodes, 1536

81 (2009) 163.

cores in the system B. Finally, we evaluate band[2] Stanislav Yu. Kruchinin, Ferenc Krausz, anddispersion with distorted atomic positions along

Vladislav S. Yakovlev, Rev. Mod. Phys.

with the normal modes obtained by DFPT. To

90 (2018) 021002.

compare with the experimental spectra, we[3] Takeshi Suzuki, Yasushi Shinohara, Yangfan

construct

Lu, Mari Watanabe, Jiadi Xu, Kenichi L.

similarspectral

informationasdifferences of k-resolved density-of-state (k-Ishikawa,

DoS) between the optimized atomic position andNaoyuki Katayama, Hiroshi Sawa, Masami

the distorted ones. The comparison between

Fujisawa, Teruto Kanai, Jiro Itatani, Takashi

experimental and theoretical data shows an

Mizokawa, Shik Shin, Kozo Okazaki, submitted,

agreement that a symmetry breaking mode,

arXiv: 2002.10037.

having 2 THz frequency, shows the most

114

Hide

Takagi,

MinoruNohara,Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

first-principles calculation of exchange coupling
constants and investigation of interface magnetism
for various phases and their interfaces of permanent
magnets
Asako TERASAWA
Department of Materials Science and Engineering, Tokyo Institute of Technology
J1-3, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8502, Japan

Improvement of Nd-Fe-B magnets without
heavy rare earth elements is one of the topics of increasing importance in the applied
physics and materials science. The key forhigh-coercivity Nd-Fe-B magnets lies in the
Nd-rich grain boundary (GB) phases [1]. However, the details of structural and magnetic
properties of those GB phases are not clarified yet. Some experiments revealed the relationship between the crystallinity of GB phases
and the relative angles between the interfaces
and the c-plane of neighboring grains [2], whichindicates the complexity of the physics in grainboundary phases in Nd-Fe-B magnets. Particularly, we targeted the exchange couplings inside and between the various phases for a computational study of magnetism in Nd-based
permanent magnets.
For this purpose, we developed “jx”, a postprocess program for OpenMX [3] to calculate
exchange coupling constants between atoms
based on the Liechtenstein formula [4]. The
details of the implementation is explained in
the published paper of [5]. During the development of jx, we found a remarkable problem about the combination of the Liechtensteinmethod and the linear combination of atomic
orbitals (LCAO) approximation. When adopting diagonal elements of non-orthogonal (NO)
Hamiltonian as eﬀective single-site potentials,
the calculated exchange coupling constants do

115

not converge as increasing the number of basis. Figure 1(a) shows the exchange coupling
constants Jij as functions of atomic distancerij for diﬀerent choice of basis sets. Here, thenotation sxpydzfw means that the basis set isconstructed from x types of s orbitals, y typesof p orbitals, z types of d orbitals, and w typesof f orbitals. It is possible to see in Fig. 1 that
the Jij profiles are similar for s2p2d1, s2p2d2,
and s3p2d2 with fluctuations of about a few
meV, whereas the Jij profiles deviate strongly
to negative values for the larger basis sets.
To solve this problem, we introduced a newscheme to orthogonalize the atomic orbitals,
namely the single-site orthogonalization (SO)scheme. In the SO scheme, we derive a basis set {|i⟩i } to orthogonalize only i-th elementfrom the original non-orthogonal orbitals {|i⟩}.
The single-site orthogonlized basis set is defined by the following equations:|i⟩i ≡ |i⟩ −∑|j⟩[S−1S ]i,i i,i ji

(1)

j∈i

|j⟩i ≡ |j⟩, j ̸= i(2)with the definitions of the neighbor set i forsite i as
i ≡ {j | j ̸= i, ⟨i|j⟩ ̸= 0}.

(3)

We found that the Jij profiles calculated with
the SO scheme exhibit a convergent behavior
as increasing the number of bases, while theyActivity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo25

decreases slightly depending on the basis size.
The slight decreases in SO results are well collected by introducing spin population scaling,
namely single-site orthogonalization with spin
population scaling (SOS) scheme:∆ni∆nj (SO)
(SOS)
Jij
≡
J
.
(4)
(SO)
(SO) ij∆nj∆nj

J ij [meV]

20
15
10
5
0
-5
-10

2

3

4

5

6

rij [Å]

7

8

9

10

(SO)

where Jij(a) J ij of bcc Fe by SO scheme(SO)

J ij [meV]

20
15
10
5
0
-5
2

3

4

5

6

rij [Å]

7

8

9

10

(b) Jij of bcc Fe by SOS scheme
s2p1d1s2p2d1s2p2d2Nd

s3p2d2s3p2d2f1
s3p3d2FeB

s3p3d2f1
s3p3d3s3p3d3f1

Jij [meV]
20

25

(SO)

derived by the SO scheme, ∆ni
and ∆ni
are the spin population at site i calculated using the NO basis and SO basis, respectively.
Figure 1 (b) shows the exchange coupling constants as functions of atomic distances calculated with the SOS scheme. We can see a remarkable convergence as increasing the number of bases in Fig. 1(b).
We also applied the newly developed scheme
to larger scale systems. Figures 1(c) and 1(d)show the calculated exchange coupling constants of the model of ab interface, where theamorphous Nd-Fe phase of a few nm are attached to the main phase in ab axis direction.
It can be seen in Figs. 1(c) and (d) that the exchange coupling constants behave diﬀerently inthe main phase and in the amorphous Nd-Fe
phase.
We are now preparing the submission of theabove results to refereed papers, and modified
patch of jx including the SOS scheme for future
release of OpenMX.

25

-10

is the exchange coupling constant30(c) large positive Jij in the ab interface model

References
Nd

Fe

B

Jij [meV]
105(d) negative Jij in the ab interface model[1] K. Hono et al., Scripta Mater. 67, 530 –
535 (2012).

0

Figure 1: Calculated exchange coupling constants Jij of various systems. (a) Jij of bcc Fe
as functions of atomic distance rij for diﬀerent
choices of basis sets when adopting diagonal elements of NO Hamiltonian as eﬀective singlesite potentials and (b) when adopting diagonal
elements of SO Hamiltonian as eﬀective singlesite potentials and applying the spin population scaling to the SO results. (c) and (d) Jij
in the ab interface model of Nd-Fe-B permanent magnet.

116[2] T. T. Sasaki et al., Acta Mater. 115, 269(2016).
[3] T. Ozaki, Phys. Rev. B 67, 155108 (2003).
[4] A. I. Liechtenstein et al., J. Magn. Magn.
Mater. 67, 65–74 (1987).
[5] A. Terasawa, M. Matsumoto, T. Ozaki,
and Y. Gohda, J. Phys. Soc. Jpn. 88
114706 (2019).

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Machine-learning-driven molecular simulations for grainboundary atomic dynamics
Tatsuya YOKOI
Department of Materials Physics,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603
Grain boundaries (GBs), crystalline interfaces

about general or random GBs, which generally

between misoriented grains, often govern

require a large number of atoms for theirmaterial properties in polycrystals, in spite thecomputational cells, in the atomic level.

fact that changes in atomic arrangement andIn order to predict atomic structure andchemicalfew

energetics of GBs while maintaining highnanometers from GBs. Experiments withaccuracy and low computational cost, webicyrstals and theoretical calculations haveconstructed artificial-neural-network (ANN)reported that not only atomic arrangements but

interatomic

also local properties arising from atomic

calculation data, Furthermore, we integrated the

dynamics significantly vary with each GB.

ANN potentials into molecular simulationSuchthermodynamic

algorithms, with the goal of predicting local

stability, diffusivity and thermal conductivity. A

diffusional and lattice vibrational properties atbetter understanding of the connection between

GBs. Here, oxide systems and semiconductor

GB structures and their atomic dynamics is thus

compounds were chosen.

essential

The architecture of ANN potentials was based

composition

properties

for

occur

includesdesigning

withinpolycrystals

withpotentials

trained

with

DFT-

desired properties and functionalities.

on the previous studies by Behler [1]; the feed-

In order to reveal their connection, density-

forwardfunctional-theory (DFT) calculations have beenenvironments were encoded using two- andoften employed. However, DFF calculations are

three-body symmetry functions [1]. Theircomputational demanding as the number ofcutoff radii were set to 5 and 7 Å for oxides andatoms in a computational cell increases, since

compound semiconductors, respectively.

their computational time typically grows with

Training

O(N3) or O(NlnN). Due to this drawback, mostaccounting for various atomic environments to

DFT studies have investigated only GBs withincrease the generalizability of ANN potentials.

simple atomic arrangements, such as symmetric

Here the training datasets contained not only

tilt GBs with low Σ values. Still less is known

single-crystal structures but also lattice defects:

117

networkdatasets

was

employed.

were

AtomicgeneratedbyActivity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

point defects, surfaces and grain boundaries.
DFT total energies and atomic forces were used
to train ANN potentials. DFT calculations were
performed using the VASP code [2].
Figure 1 and 2 show the error of total energies
and atomic forces with respect to the reference
DFT data in the training dataset for Al2O3 and
PbTe, respectively. A data point distributed near
the black dashed line indicates that the ANN
potential accurately learns the training data

Fig. 1 Error of total energies and atomic
forces with respect to the reference DFT
data for (a) Al2O3 and (b) PbTe.

without large error. These figures show that all
the data points are distributed near the diagonalline, without large deviation, for both totalenergies and atomic forces. Thus the ANN
potentials accurately learn the reference DFT
results even for GBs.
The trained ANN potentials were thenintegrated

into

a

structural

optimization

Fig. 2 GB structure obtained from molecularsimulations with the trained ANN potential
for Al2O3.

algorithm and molecular dynamics (MD)simulations to predict energetically favorable
atomic arrangements at GBs not included in the
training dataset. Figure 3 shows an example ofReferences

Al2O3 GBs. The obtained structure was in[1] J. Behler, Int. J. Quantum Chem. 115 (2015)

agreement with an experimental observation1032.

and a theoretical calculation in the literature [3],[2] G. Kresse and J. Hafner, Phys. Rev. B 47

demonstrating excellent predictive ability of(1993) 558.

our ANN potential even for GBs.

[3] H. Nishimura, K. Matsunaga, T. Saito, T.

Finally we examined computational time of

Yamamoto, and Y. Ikuhara, J. Am. Ceram. Soc.

ANN-MD simulations. The computational time86 (2003) 574.

was found to linearly increase with the number[4] H. Guhl, H.-S. Lee, P. Tangney, W.M.C.

of atoms. Ultimately, MD simulations with 104

Foulkes, A.H. Heuer, T. Nakagawa, Y. Ikuhara,steps was finished in an hour even for GB

M.W. Finnis, Acta Mater. 99 (2015) 16.

structures with several thousands of atoms.

118Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study on controlling of electronic
structures and electron-transport properties of
low-dimensional materials
Yoshiyuki EGAMI
Division of Applied Physics, Faculty of Engineering, Hokkaido University
Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-8628

Recently, there has been a lot of energetic research and development of devices using low-dimensional materials. In the ﬁrstprinciples investigations, to estimate electrontransport properties of the nanoscale materials suspended between semi-inﬁnite electrodes,
self-energy matrices of the electrodes are required. The computational cost for obtaining the self-energy matrix is proportional tothe cube of the lateral length of the electrodewhich is a direction perpendicular to the transport direction. Therefore, the computational
cost increases dramatically as the system size
increases.
In this subject, the method to calculate
the self-energy matrices without any approximations and accuracy deteriorating is proposed. [1] In most cases, the electrode has a supercell structure in which a primitive unit cellis repeated in the lateral direction. Exploiting
the repetition, the proposed method calculates
the self-energy matrices of a large electrode byextending the self-energy matrices of the primitive unit cell using the singular-value decomposition. This makes it possible to greatly reduce the computational costs because calculating the inverse of a large matrix (for the supercell structure), which is the most computationally expensive, can be replaced by that of thesmall matrix (for the primitive unit cell). Furthermore, by comparing the self-energy matrix directly obtained from the large-sized electrode structure with that obtained using the

proposed method, it was conﬁrmed that the
self-energy matrices can be reproduced without deterioration in the accuracy.
For demonstration of the proposed method,
the computational time in generating the selfenergy terms for several supercell models is examined. For generating the self-energy terms,
the computational time increases proportional
to N 3 where N means the number of the total grid points in the supercell. In some cases,
the computational eﬃciency exceeds the theoretical value (the square of the supercell size)
because the order of the computational time
for the recursive iteration to generate the selfenergy terms is slightly larger than N 3 . On theother hand, the computational time for reproducing the self-energy terms is notably reducedby the proposed method, and this beneﬁt becomes more remarkable as the supercell size
increases. These works have been performed
on System B and System C.

References[1] Y. Egami, S. Tsukamoto and T. Ono:
Phys. Rev. B 100, 075413 (2019).

119

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Elucidation of Reaction Mechanism of d-sorbitol Dehydrationin High Temperature Water with Metadynamics
1

Tomomi Kondo1,2，Chang Yong Lik1，Takehiko Sasaki1，Motoyuki Shiga2
Department of Complexity Science and Engineering, Graduate School of Frontier Sciences,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8561
2 Center for Computational Science and E-Systems, Japan Atomic Energy Agency
148-4 Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa, Chiba, 277-0871

1 Introduction
Chemical reactions in high temperature pressurized water
without organic solvent or poisonous materials such as metals
are worthy of attention with respect to environmentally friendly
chemistry, i.e., Green Chemistry.

In this study metadynamics

calculation was achieved to elucidate the reaction mechanism
for the cyclodehydration of sorbitol (SBT) [1] (Fig. 1) in highFig. 1. The dehydration reaction of d-sorbitol (SBT).

temperature water (HTW). Reaction pathways were searchedon the free energy surface (FES) and the activation barriers were𝑁𝑁

𝑉𝑉ℎ𝑖𝑖𝑖𝑖𝑖𝑖𝑖𝑖 (𝑡𝑡, 𝒔𝒔) = � � ℎ exp �−compared with the experimental values.

𝜏𝜏<𝑡𝑡 𝑘𝑘=1

(𝒔𝒔𝑘𝑘 (𝑡𝑡) − 𝒔𝒔𝑘𝑘 (𝜏𝜏)) ∙ 𝒘𝒘−1
�
2

(1)

We used PIMD [2] to achieve MTD simulations associated with

2 Methodthe Density Functional based Tight Binding (DFTB) method

In Metadynamics (MTD) simulations chemical reactions
that do not happen in a regular time scale of molecular dynamics
simulations are induced by adding a bias potential proportional
to the appearance frequency on the FES defined with collective
variables (CV).

Bias potential at time t is expressed by aGaussian function (equation (1)) with height h and width wi,

Fig. 2. The reaction pathway and the collective variables (1,4-AHSO6).

where 𝒘𝒘−1 = {1/𝑤𝑤𝑖𝑖 } .

dependent term given by the sum of Gaussian functions (hills)

using DFTB+ [3]. The present system contains one molecule

deposited along the path followed by the fictitious particle (sk)of SBT, 30 molecules of H2O, one proton and one Cl- anion.

on the FES until time t. Sampling is effectively achieved by

The other system containing H2CO3 instead of H+ and Cl- wassumming over N fictitious particles (walkers) which are allowed

also examined. The thermodynamic condition at 573 K andto move simultaneously on the FES. The point corresponding

20 MPa was the same as the experimental results [1]. Fig. 1

to the maximum accumulated potential and the point at the onset

shows structures of SBT molecule and three products (1,4-of the reaction correspond to the minimum point and the saddle

AHSO, 2,5-AHSO and 1,5-AHSO) for the cyclodehydration ofBias potential is the history-

point on the FES, respectively.

120

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

SBT. Considering the reaction pathway of cyclodehydration,
there are two pathways for each product. CV is chosen foreach pathway [4].

For example, there are two reaction

pathways (1,4-AHSO3 and 1,4-AHSO6) for 1,4-AHSO
depending on the position of OH group and the carbon atom
involved in the reaction. Fig. 2 illustrates the pathway 1,4AHSO6 and the associated CV.

Fig. 3. The dehydration reaction of SBT to 1,4-AHSO6.

Here, the oxygen atom O3

in OH group on the carbon atom C3 attacks the carbon atom C6.
In order to describe this reaction pathway the dihedral angleφ（O6-C6 -C5-C4）defined by the O6-C6 bond and the bond C5C4, the difference in the O-C bonds d（= 𝑟𝑟𝑂𝑂3 −𝐶𝐶6 − 𝑟𝑟𝑂𝑂6 −𝐶𝐶6 ）between the O3-C6 bond and the O6-C6 bond, and thecoordination number n of hydrogen atoms toward O6 areselected as CV. The height of the Gaussian function was set as
h = 500 K, and the step width of the variables are set as follows:
wφ= 10.0°, wd = 0.10 Bohr , wn = 0.10 and time step = 0.25 fs.
Fig. 4. The dehydration reaction of SBT to 1,4-AHSO6.

The activation energy with H+ and Cl- was lower than that

3 Results and Discussion

with H2CO3, indicating the activation energy has a negative

Over 3.6 ns of MTD simulations with DFTB along thepathway 1,4-AHSO6 the dehydration reaction was observed

correlation withacidity.

However, relative relationship ofwith the CV atφ= 155°, d = 0.0 and n = 2.1. Fig. 3 shows

calculated activation energies of products was not in agreement

the calculated FES, where the shallow path was observed,

with the experimental results [1]. In order to overcome thisleading to the transition state marked as the red arrow. Withproblem, a method for smoothing FES was developed to

the Molecular Dynamics calculation started from this transition

decrease the sampling error and the calculation with this method

state as the initial state it was found that after the addition ofis under way.

proton to the oxygen atom （Fig. 4 ①）the dehydration （Fig.
4 ②） and the formation of a five-membered ring (C-O bond

References

formation Fig. 4 ③) happened almost simultaneously. Hence,[1] A. Yamaguchi et al. Green Chem., 13, 873 (2011).

it is concluded that the hydroxyl group of SBT is protonated, the[2] http://ccse.jaea.go.jp/ja/download/pimd/index.jp.html.

five-membered ring is formed via SN2 mechanism, and finally[3] https://www.dftbplus.org.

the excess proton is released（Fig. 4 ④）. This mechanism[4] Y. L. Chang, et al., J. Phys Chem. B, 23, 1662 (2019).

is the same as that for our previous study for the
cyclodehydration of polyalcohol [4].

121Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab initio molecular dynamics study of stability of artificial
retina molecule
Satoshi Ohmura
Research Center for Condensed Matter Physics / Department of Environmental and Civil
Engineering
Hiroshima Institute of Technology, Hiroshima, Hiroshima 738-5193
By means of ab initio molecular-dynamics

spectra are different from that of non-substituted

simulations, we have investigated the lightsystem in a sense that there are small peaks at

absorption properties in a photoelectric dye (2-[2-longer wavelength region. In addition to halogen[4-(dibutylamino)phenyl]-3-

atoms, we also substitute Br with [(CF3SO2)2N]−

carboxymetheylbenzothiazolium bromide ) (retina(TFSI) molecule, and investigated the stability andmolecule) coupled to polyethylene. We adopted thelight-absorption properties. Our simulation foundTime-Dependent

Linear-that substitution for TFSI molecule has the

Response Theory (TDDFRT), proposed andpotential for increasing stability of the artificial

formulated by Casida, for calculating light-

retina. For absorption spectrum, the main peak isabsorption spectrum. The absorption spectrum of

maintained, and no additional peak appears at

retina molecule obtained by the simulation have alonger wavelength region. Moreover, we havemain peak at approximately 550, which is ininvestigated effects of the water. Our simulationagreement

indicated that water stabilize the energy around the

with

]

eheny

Density-Functionaltheexperimental

result.

Counterion substitution is considered one of thecounter ion.

effective methods to improve the performance ofretinal molecule. Figure 1 shows absorption
spectra of the non-substituted retina molecule(counter ion = Br-) and substituted retina molecules(counter ion = F-, Cl-, I-). The absorption spectra of
the substituted system also have the main and small
peak, and the profile of spectrum of I-substituted
system is almost the same as non-substituted
Fig1. Light-absorption spectra, inset shows
spatial distribution of wavefuctions for HOMO
and LUMO of non- and F-substituted systemsystem. On the other hand, for F- and Clsubstituted system, the profiles of the absorption

122

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab initio molecular dynamics study of structural properties
and immiscibility of liquid Fe-Si-O mixtures under highpressure
Satoshi Ohmura
Research Center for Condensed Matter Physics / Department of Environmental and Civil
Engineering
Hiroshima Institute of Technology, Hiroshima, Hiroshima 738-5193
Liquid iron is a major constituent of Earth’s

atoms is stronger than those between other atoms,

outer core, but the core density is approximately

which means that a covalent like interactions exists

10 % lower than that of pure iron. Therefore, lightbetween Si and O under outer core conditions.

elements (LE) such as hydrogen, carbon, oxygen,

Moreover, our simulation found that liquid Fe-Si-silicon, and sulfur are expected to exist in the core.

O ternary systems shows immiscible tendency

Under this circumstance, we have studied theunder outer core conditions. Figure 1 shows atomic

effects of light element on the structural andconfiguration of liquid Fe-Si-O at about 140 GPa

transport properties of liquid iron mixtures byobtained from our simulation. As shown in figuremeans of ab initio molecular-dynamics simulations.

1, oxygen atoms confined to the narrow area (redFor Fe-LE binary systems, we clarified thearea in Fig. 1).

structural properties and interactions between LE
atoms at core-mantle boundary condition [1]. The
C–C interactions are stronger than those of otherlight elements. The S–S interactions depend on the
S concentration, in the sense that the shape of pair
distribution functions for the S–S correlation
change with increasing S concentration. In
addition to the binary systems, we haveinvestigated the structural properties of liquid FeFig1. Snapshot of the atomic configuration.
Gray, yellow and red ball show Fe, Si and O
atoms. Red area shows the area in which oxygen
atoms exist.

Si-O ternary systems. From the radial distributionfunction obtained from our simulations, it is foundthat Si and O atoms shows “substitutional” andReferences“interstitial” behavior even in liquid Fe-Si-O[1] S. Ohmura, T. Tsucniya and F. Shimojo:
Physica Status Solidi B, accepted for publication

ternary system. The interaction between Si and O

123

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Construction of Neural Network Force Field for Molecular
Dynamics Simulation in Multicomponent System
Kohei Shimamura
Department of Physics,
Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555
In this study, we aimed to development of an

Even if the interatomic distance approaches

interatomic potential using an artificial neuralduring ANN-MD simulation, the ANN potential

network (ANN) applicable to multicomponent

does not learn such a state, thereby failingsystems such as life systems. This is one of thecontinuing the calculation. For long-term MD

data-driven interatomic potential that takes

simulations,advantagefunctionoversample such rare FP data and let ANN

approximation, and automatically constructs alearn. (Actually, FP data for the relaxation

functional form that represents the input dataprocess from the state where the atoms arethrough training. Since first-principles (FP)close to each other is also needed.)

of

ANN's

universal

it

was

thus

necessary

to

Next, we tried whether the key findings

calculation data is mainly used for the training,molecular dynamics (MD) simulations withobtainedthrough

ANN potentials (ANN-MD) are expected to beconstruction for α-Ag2Se can be applied to theaccessible to large-scale systems or long-term

multicomponent

calculations while maintaining FP accuracy.

glycine taken as an example is a system in

However, the current construction method may

which glycine molecules composed of four

yield less robust ANN potentials, making long-elements H, C, N, and O are irregularly

term MD calculation difficult. Therefore, weaggregated,first have investigated the factors affecting the

between the molecules. In the case of ANN

robustness of ANN potential [1], where the ion-

potential without training rare FP data, the MD

conducting phase of α-Ag2Se is employed as ansimulation cannot be continued for a few fs.

example system.

When it is learned, at least ns order is possible.

and

the

systems.

protonANN
The

potential
amorphoustransport

occursThe most important factor was found in

Although the glycine amorphous system is nottraining data. Generally, it is difficult to preparea living system, we consider that this result is ahighly diverse FP data due to its large

great step forward.

calculation cost. However, minority data can be

Referencephysically very important. That is the FP data

[1] K. Shimamura, et al.: J. Chem. Phys. 151,

with the interatomic distance approaching.

124303 (2019).

124

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Manipulation the cross-plane thermal conductivity of the 2D
hetero-junction materials
Hu Shiqian
Department of Mechanical Engineering,
The University of Tokyo, Hongo, Bunkyo City, Tokyo 113-8654
We have studied the two-path phonon-

packetmolecular-dynamics

simulation.

interference resonance which induces a stop

Compared with thetraditionalband in silicon crystal matrix by embedded

formation(single-path

nanoparticles array [1] and the coherent phonon

scattering), the two-path resonance mechanism

transport in van der Waals graphene-MoS2

has a significant advantage in not requiring thehetero-structure, using the massive parallel

strict periodicity in nanostructures, due to thecomputer simulations.

local origin of the phonon resonance.

mechanismstop-band
Bragg

Massive efforts have been devoted toMoreover, there are growing efforts tocontrol phonon transport in the phononic

control thermal transport via coherent phonons

crystals utilizing phonon interference and in thein the one-dimensional superlattice. However,phononic metamaterials (local nanostructures)in general, the difference in the intrinsic latticeutilizing local phonon resonance. However,structures

since the phononic crystals require strict global

inevitably generate interface disorder during

periodicity and the local resonances in thethe fabrication process, greatly limiting direct

metamaterials only affect phonons with specificexperimental observation of the coherent

discrete frequencies, further development ofphonon transport. The flexible integration andphonon engineering has been a pressing andatomistic interlayer smoothness of van derbaffling challenge. A new mechanism that can

Waals

mitigate the strict requirement of the globally

platform for the coherent phonon transport

periodic nanostructure and can influence a

manipulation. Thus, in the second work, using

broader and continuum range of frequencies

the(the stop band) is urgently needed.

simulations,

of

the

constituent

hetero-structure

non-equilibrium
we

providemolecular

investigate

thematerials

an

ideal

dynamics
coherent

We have studied a new stop-band formation

phonon transport in van der Waals graphene-

mechanism that is the two-path phonon-

MoS2 hetero-structure with different stacking

interference resonance by using the atomistic

order at room temperature. The histogram ofGreen’s function calculation and the wave-

the

125

phonontransmissionsindifferentActivity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

disordered structure exhibits a log-normal
distribution, which reveals a localization of thecoherent phonons. Furthermore, the optimal
stacking order of the graphene and MoS2 isefficiently identified from tens of thousands ofcandidatesbymachinesignificantly

suppressedlearning.
of

the

The

phonontransmission in the low frequency (<5THz)
phonons of the optimized structure lead to asignificant reduction (~95%) of the thermal
conductancecompared

with

the

pristinegraphite. Finally, the effects of the temperatureand strain effect on the thermal conductivity ofgraphite and optimized structures are also
discussed. Our work provides a deep insight
into the coherent phonons transport behavior in
the atomistically smooth van der Waals
structure, which is beneficial for further
development of phononics.

References[1]

Hu, Shiqian, et al. arXiv preprint

arXiv:2001.10321 (2020)

126

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of algorithms in crystal structure
prediction
Tomoki YAMASHITATop Runner Incubation Center for Academia-Industry Fusion,
Nagaoka University of Technology
1603-1 Kamitomioka-machi, Nagaoka, Niigata, 940-2188

We have developed a crystal structure prediction tool, CrySPY as an open source
software [1].
CrySPY is interfaced with
VASP[2], Quantum ESPRESSO[3], soiap[4],and LAMMPS code for structure optimization.
Several searching algorithms are available in
CrySPY, such as random search (RS), evolutionary algorithm (EA), Bayesian optimization(BO), and LAQA. RS is a basic algorithm andwidely used. EA[5, 6, 7] is currently very popular. We have implemented implemented EA
into our CrySPY code. Previously we havedeveloped selection-type algorithms with machine learning. BO can efficiently select potential candidates from a large number of candidate structures by machine learning[8]. LAQA
is one of the refinforcement learning, which can
reduce the computation time[9]. The key point
here is that the selection-type algorithms are
not exclusive with EA. In this study, we develop a hybrid algorithm of BO and EA. Thishybrid algorithm could be the most promising way to find the global minimum structure
in large and complicated systems. Moreover,
we compare searching efficiency among the RS,
EA, BO, and hybrid algorithm.
Searching efficiencies of RS, EA, BO, andthe hybrid algorithm have been investigatedin two systems of Si16 and Si32 . The former isa relatively easy system to find the most stable structure, and the latter is slightly difficult.
For the system of Si16 , we optimized a hundred
structures using interatomic potential calcula-tions with the soiap code in each algorithm.
Here, a hundred structures were selected fromthree hundred structures particularly in BO
and the hybrid algorithm. A hundred structures were obtained by random structure generation and the remaining two hundred structures were generated by EA in the hybrid algorithm. To statistically investigate searchingefficiencies, we carried out simulations of crystal structure prediction 50 times. The successrates to find the most stable structure were64%, 58%, 70%, and 82% for RS, EA, BO,
and the hybrid algorithm, respectively. The
success rates of RS and BO were slightly better
than that of EA. Random structure generation
is sufficiently effective to find the most stablestructure in this small system. The number ofsearching trials (100 structures) might be too
small for EA. The success rate of the hybridalgorithm was the highest in which we generated 200 structures by EA. This is because EA
was able to generate good candidates and BO
efficiently selected the good ones. For the system of Si32 , three hundred structures were optimized in each algorithm. In BO and the hybrid algorithm, three hundred structures wereselected from six hundred structures. Three
hundred structures were obtained by random
structure generation and the remaining half ofthe structures were generated by EA in the hybrid algorithm. The success rates were 46%,
60%, 54%, and 74% for RS, EA, BO, and the
hybrid algorithm, respectively. The success127

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

rate of RS was lower than others since thesystem became complex. Although the success rate of BO was better than that of RS,
BO was not as good as EA. Random structure
generation is no longer effective in this system.
However, the success rate of the hybrid algorithm was still the highest. These results show
the hybrid algorithm is superior to EA and BO
and could be the most promising method forthe crystal structure prediction.

References[1] https://github.com/TomokiYAMASHITA/CrySPY.
[2] G. Kresse and J. Furthmüller, Phys. Rev.
B 54, 11169 (1996).
[3] P.
Giannozzi
J.Phys.:Condens.Matter(2009).

et
21,

al.,
395502[4] https://github.com/nbsato/soiap.
[5] A. R. Oganov and C. W. Glass, J. Chem.
Phys. 124, art. 244704 (2006).
[6] A. R. Oganov, A. O. Lyakhov and M.
Valle, Acc. Chem. Res. 44, 227 (2011).
[7] A. O. Lyakhov, A. R. Oganov, H. T.
Stokes, and Q. Zhu, Comp. Phys. Comm.
184, 1172 (2013).
[8] T. Yamashita, N. Sato, H. Kino, T.
Miyake, K. Tsuda, and T. Oguchi, Phys.
Rev. Materials 2, 013803 (2018).
[9] K. Terayama, T. Yamashita, T. Oguchi,
and K. Tsuda, Npj Comput. Mater. 4, 32(2018).

128

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Large scale ab initio calculations on the fundamental
processes of solar energy convergence devices and on
designing principles for new materials
Koichi YAMASHITA
Elements Strategy Initiative for Catalysts and Batteries (ESICB),
Kyoto University, Nishiｋyo-ku, Kyoto 615-8510, Japan
1. Electron-phonon interactions in tungsten

calculations. An integral approach utilizing 500

oxide photocatalysts

random Q points was used for the electron-

Water-splitting

photocatalysts,

whichphonon interaction calculations. �e results

decompose water into hydrogen and oxygen by

showed that the bandgap of the direct transition

sunlight, are promising for a clean andat the Γ point is larger than the bandgap of therenewable energy source for the next generation

indirect transition. It is suggested that theof hydrogen production. A considerable amountbandgap of the indirect transition is moreof literature has been published on thepreferred and reduce carrier recombination.

photoexcited state of tungsten oxide, and long-

Next, the Eliashberg function was calculated to

lived trapped photocarriers have been found to�nd the phonons that contribute signi�cantly toplay a key role in photocatalytic reactions. Using

the electron-phonon coupling. �e transition

XAFS techniques, Uemura et al. found that thedipole moment on the Γ point of the structure,

photoexcited electrons stay on the tungsten atomwhich is displaced in the direction of the strain

and the local structure is changed [1,2]. However,caused by the phonon, was calculated. It isthere has been no detailed investigation of thesuggested that the strain caused by the phonon,

structural changes caused by photoexcitedwhich is strongly coupling with the electrons onelectrons and the changes in electronic states

the CBM, reduces the transition dipole moment,

associated with these structural changes. In thisand also reduces the recombination of thework, electronic states, phonon, and electron-

photocarriers.

phonon interaction calculations for tungsten
oxide were performed by using �rst-principles

2. Device-Scale Simulations of Organic

calculations based on density functional theory

Photovoltaics for Performance Improvement

in order to discuss the lattice distortions caused

Organic photovoltaics, OPVs, are promisingby photoexcited electrons. �ese calculations

energy harvesting devices, but their power

were performed by using Quantum ESPRESSO

conversion efficiencies are lower than traditional

6.3 and Yambo 4.2.4. GGA-PBE and “on thesilicon ones. For performance enhancement, it ismass shell” approximation were used for theseimportant to control properties of donor and129

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

acceptor materials, such as HOMO and LUMO

and end groups—from SMILES. HOMO andlevels,Fullerene

LUMO levels of indacenodithiophene, IDT,

derivatives, e.g., phenyl-C61 butyric acid methyl

derivatives were evaluated at ωB97X-D/def2-

ester, PCBM, have been used for acceptors, but

SVP level

recently non-fullerene acceptors are attracting

dependence

attentions because of easiness of LUMO level

electronegativities of end groups. In future work,tuning and light harvest. A non-fullerene

it is planned to evaluate other properties such as

acceptor is composed of three units: π-electron mobilities, absorptions spectra, andconjugated core; alkyl side chains, which control

exciton lifetimes.

bymolecular

design.

ofoftheory, which
LUMO

reproduceslevelsonsolubility; and electron-withdrawing end groups,
which control LUMO level. It is however

References

challenging to synthesize and evaluate device[1] Y. Uemura, H. Uehara, Y. Niwa, S. Nozawa,

performances for combinations of donors and

T. Sato, S. Adachi, B. Ohtani, S. Takakusagi, K.

acceptors.

Asakura, Chem. Lett. 43 (2014) 977.

In this work, density functional theory, DFT,

[2] Y. Uemura, D. Kido, Y. Wakisaka, H. Uehara,code as implemented in NTChem was employed

T. Ohba, Y. Niwa, S. Nozawa, T. Sato, K.

to evaluate material properties of donors andIchiyanagi, R. Fukaya, S. Adachi, T. Katayama,non-fullereneWe

T. Togashi, S. Owada, K. Ogawa, M. Yabashi, K.

implemented programs to generate NTChem

Hatada, S. Takakusa, Y. Yokoyama, B. Ohtani, K.

inputs—Cartesian products of cores, side chains

Asakura, Angew. Chem. Int. Ed. 55 (2016) 1364.

acceptorcandidates.

130

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Computational physics and chemistry approach todevelop the artiﬁcial photosynthesis and fuel cell
catalysts
Kazume NISHIDATE
Faculty of Science and Engineering, Iwate University
Ueda 4-3-5, Morioka, Iwate 020-8551

TiO2 is well known as an eﬃcient photo catalytic material and has a wide range of application area from air-puriﬁer to antimicrobial
coating. However, TiO2 uses only the ultraviolet ray which is less than 3 % of the whole
sunlight pouring on the earth surface. Therefore extensive studies have been devoted to develop photo-catalytic materials sensitive to visible light that makes up 50 % of the sunlight.
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.
Above all, Ba2 PrBiO6 was foundto show an eﬃcient photo catalytic activity to dissolve water molecules into oxygen and hydrogen gases under the visible
light. However, detailed theoretical analysis on the electronic structures and the crystal geometries of the double-perovskites has
not been performed. In this work, we study
the structural and electronic properties of
Ba2 BiIII BiV O6 , Ba2 PrBiO6 , and Ba2 PrSbO6
double-perovskites using the ﬁrst-principles
density functional theory [1]. The HeydScuseria-Ernzerhof hybrid functional was applied to the calculations to handle the strong
electron-correlation.
First of all, we evaluate the structuraland electronic properties of Ba2 BiIII BiV O6 as
it gives the basis in analyzing the double
perovskite crystals. Unit cell contains fourBaBiO3 chemical units where the BiIII octahe-

dra and the BiV octahedra are arranged alternately forming the B-site ordering. Where thedistortions of octahedra caused by the mixed
valencies are characterized by breathing distortion and tilting angle as depicted in Figure 1.
We ﬁnd that the BiIII 6s states at the top of

Figure 1: Distorted octahedra of Ba2 BiIII BiV O6 .
valence band of Ba2 BiIII BiV O6 vanish on the
Pr substitution for Bi at B ′ III -site. When Sb
is substituted for Bi at B ′′ V -site, the BiV 6s
states at the bottom of the conduction band
vanish causing additional widening of the bandgap. Further, our calculation suggests thatthe Ba2 PrPrBi O6 is a possible candidate as asource of the PrIV signal observed in the experiment. We ﬁnd that the anti-B-site atomic
conﬁgurations, Ba2 B ′′ V B ′ III O6 , are easily restored to those of the original structures. This
demonstrates the stability of the B-site ordering in the double-perovskite framework.

References[1] K. Nishidate: submitted.

131

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Reveal the mechanism of thermal transport in PbS
quantum dot system
Cheng SHAO
Depart of Mechanical Engineer, University of Tokyo
Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656 JAPANColloidal quantum system has attracted a
lot attention recently due to their controllable
electronic and optoelectronic properties.[1]Therefore, the colloidal quantum dot systems
are promising for a wide range of applications
from solar cells, thermoelectric devices, photodetectors, and many others. [2] Understanding the thermal properties of such quantum
dots system is crucial for the thermo-stability
and the performance of the above-mention application. However, due to the large unit
cell size and complex inter-atomic interaction,
the thermo properties for such system is stillless understood. In this project, we applied
the molecular dynamics simulations to systematically investigate the thermal transport
in PbS quantum dot system. The large-scale
molecule dynamics simulations is carried out
by the open source software LAMMPS withthe computational resource from The Institutefor Solid State Physics (ISSP) of the Universityof Tokyo.

The simulation model used for thermal properties calculations is shown in Fig.1. The sizeof the PbS dots is about 3 nm, which contains
about 600 atoms. C5 H10 S2 ligands are used
to bridging the connection between the quantum dots. The length of the system range from
20-100 nm, while are cross-section of 10 nm ×
10 nm with periodic boundary is used in the
direction perpendicular to the heat flux. The
simulated thermal conductivity from the nonequilibrium molecular dynamics simulations is
as lower as ∼0.1 W/mK at temperature of 300
K. As a reference, the thermal conductivity ofbulk PbS is about ∼5.0 W/mK based on thesame interatomic potential.

Figure 2: Illustration of the non-equilibrium
molecular dynamics simulation for thermal
conductivity calculation in PbS ligand system

Figure 1: Illustration of the non-equilibrium
molecular dynamics simulation for thermal
conductivity calculation in PbS ligand system

To understand the origin of the lower thermal conductivity in such system, we calculated the spectral-resolved thermal conductivity at different temperature and the results
are shown in Fig. 2. From this figure, we132Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

can clearly see that thermal transport in PbS
quantum dots system is dominated by low
frequency phonon in the frequency range of
0.2∼5 THz, while the high frequency vibrational modes are mainly scattered at the PbSligand interface. This explained the ultra-law
thermal conductivity in such quantum dot system.

References[1] Ellingson, Randy J., et al. Nano letters
5.5 (2005): 865-871.
[2] Cao, Yiming, et al. Nature Energy 1.4(2016): 1-6..

133

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Exploration of surface reactions on model real catalyst II
Wataru Mizukami
Center for Quantum Information and Quantum Biology, Institute for Open andTransdisciplinary Research Initiatives,
Osaka University, Toyonaka, Osaka 560-8531, Japan
This year, as in the previous year, we studied

performed a detailed analysis of the reaction. It

two chemical reactions on inorganic surfaces

was found that the adsorption character

using density functional theory (DFT) utilizing

transforms from the chemisorption with theparallel computational resources of ISSP's

physisorption at the reactant and product into thesupercomputer system and the Vienna Ab initio

physisorption at the transition state during the

Simulation Package (VASP) version 5.4.4. On

diffusion.
In addition to the above two studies, we

top of that, we worked on the development of anelectronic

structure

theoryfordeveloped a new quantum chemical method forquantumquantum computing based on the variational

computing.

quantum eigensolver (VQE). The VQE is a

The first reaction was the industriallyrelevant Ziegler–Natta catalysis for olefin

quantum-classicalpolymerization, which is based on titanium

optimized wave-function, where quantum-

chlorides supported by MgCl2. In the previous

circuit parameters are determined variationally.

year, we had revealed that two alkyl aluminum

Our method, called orbital-optimized unitary

molecules are involved during the active-site

coupledformation process. This year, we examined threequantum circuit parameters and molecularpossible reaction paths of the active-siteorbitals

formation in detail, and found a new possible

computing first-order molecular properties

transition state.

easily in the framework of the VQE. Taking

clusterhybriddoubles,simultaneously,

algorithm

optimizes
which

to

both
allowsadvantage of this property, we realized the first

The second reaction was a diffusion of
3,4,9,10-perylene-tetracarboxylic-dianhydride

geometry

optimizations(PTCDA), which is an organic semiconductor

molecules

using

molecule, on the Ge(001) surface. In thederivatives of the VQE.[1]previous year, we had located the transition state

Referencesof this reaction using the climbing-image[1] W. Mizukami, et al., arXiv:1910:11526

nudged elastic band method. This year, we

134

the

of

polyatomic

analyticalenergyActivity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

DFT calculation of atomic displacements captured by energy
dissipation of noncontact atomic force microscope
Toyoko ARAI1, Taichi Shikichi1, Jun-Ichi Iwata2, Atsushi Oshiyama3
1

Graduate school of Natural Science and Technology, Kanazawa University, Kanazawa,
Ishikawa, 920-1192
2
3AdvanceSoft Corporation, Tokyo 101-0062

IMaSS, Nagoya University, Nagoya, Aichi 464-8601
Si(111)-(7×7)

In the last two decades the conservative andsurface,thesimultaneously

non-conservative (dissipative) force interactions

obtained energy dissipation signal increased in

between a tip and a sample in proximity haveclose proximity over the hollow sites surrounded

been examined by non-contact atomic force

by a Si adatom and a Si rest atom with a dangling

microscopy (nc-AFM). In particular, the channelbond per each (Fig. 1) [1]. Based on theof nc-AFM to measure the energy dissipation

experimental results, the dynamic atomic

through the non-conservative force interactions

processes responsible for the dissipation had

has been regarded to have great potential tobeen discussed in regard to breaking of the

explorethe

backbonds of the Si adatom and subsequentdissipation channel gives the change in thebond formation in an alternative atomic

amount of mechanical energy to maintain theconfiguration of the Si surface atoms, including

constant oscillation amplitude of an AFM

the Si atom at the apex of AFM tip. In this study,

cantilever. We had experimentally found that,to elucidate the phenomena, the surface

when the nc-AFM image showed the highdiffusion potentials of a Si adatom wereresolution for the individual adatoms on a

calculated using real-space density functional

nano-mechanicalphenomena;

theory (RSDFT) [2] when the Si tip was broughtcloser to the Si(111)-(7×7) surface. RSDFT is a
first-principles program developed by Oshiyama
and Iwata, which uses a real-space difference
method and a pseudopotential method.
First, we optimized the structure of Si(111)(7×7) reconstructed surface consisting of 298 Si

Fig. 1: Simultaneously obtained nc-AFM
image and the energy dissipation image, withthe structure model of Si(111)-(7×7).

atoms and 49 H atoms by RSDFT, as shown in
Fig. 2. Then, the surface diffusion potential for a

135

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

corner Si adatom was calculated from its

from the adatom site to the hollow site. Thisoriginal position to the neighboring hollow siteenergy of less than 1 eV could be captured as a

(Fig. 3). The hollow site seems metastabledissipation energy in the nc-AFM experiment.

because of a diffusion barrier from the hollow
site to the adatom site, the barrier height ofReferences

which was several tenth of 1 eV. Our preliminary[1] T. Arai, R. Inamura, D. Kura, and M.

calculations anticipated that the diffusion barrier

Tomitori, Phys. Rev. B 97, 115428 (2018).

is lowered and the adatom can move to the[2] J.-I. Iwata, D. Takahashi, A. Oshiyama et al.,hollow site, when the tip is in close proximity to

J. Comput. Phys. 229, 2339 (2010).

the surface [3]. It is deduced that the oscillating[3] B. Enkhtaivan, Y. Sugimoto, and A.

nc-AFM cantilever can provide the Si adatom

Oshiyama, Phys. Rev. B 96, 155417 (2017).

with the kinetic energy to overcome the barrier

Fig. 3: Surface diffusion potential of the Si
adatom from the original position (x = 0,
denoted by Co (corner adatom site)) to theneighboring hollow site (x = 2.25 Å) without
the Si tip.

Fig. 2: Optimized atomic structure of Si(111)(7×7). (a) top view. (b) side view.

136

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Hybrid Ab-Initio/Machine-Learning Computation for Designing
Nano/Molecular Structure
Kenji TSURUTA, Kyosuke SATO, Md. Abdullah Al ASAD, Tadahiro MIMURA, andSatoshi OHMURAa
Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530aDepartment of Civil and Environmental Engineering, Hiroshima Institute of Technology,
Hiroshima 731-5193
Designing and developing functional
materials/molecules often require vast searchingof target properties from extra-large data set,
which is far out of the capability of conventional
computing algorithms. In recent years, theDeep-Learning (DL)-based molecular design
methods have been extensively studied. One of
the recent studies has reported [1] a machinelearning method for predicting molecularproperties by mapping a graph representation ofa molecule to a latent variable space and bylinking the variable to physical property of themolecule. Representing molecules in the latent
space enables an efficient property search within
existing data, because the DL model transforms
the discrete representation of a molecular graphinto a continuous variable space suitable forvarious numerical algorithms.
In the present study, we have developed ahybrid algorithm that combines the continuous
representation of molecules with an
optimization algorithm to predict physicalproperties of organic molecule [2]. Here theGrammar Variational Autoencoder (GVAE) [3]algorithm was adopted for transforming discrete
representation of a molecular graph into
continuous representation. The optimum valueof the HOMO-LUMO gap obtained by an abinitio quantum-chemical calculation waspredicted by searching a molecular structure
within the latent space.
The input of GVAE is a Simplified
Molecular Input Line Entry System (SMILES)
string, which represents a molecular graph. The
GVAE consists of two neural networks: An
encoder and a decoder. The encoder converts
SMILES into latent variables z, whereas the
decoder converts z back to the original SMILES
string. These neural networks are trained so thatan input SMILES coincides with the output
SMILES. The distance between molecules withcloser SMILES is mapped to a closer point in thelatent variable space. By using this method,molecular design with desired characteristics
can be treated as an optimization problem in acontinuous variable space. We have examined
the algorithm for predicting molecules using the
Quantum Machine 9 (QM9) as a training dataset.

Fig. 1 The molecule and its properties predicted by
the present method

Figure 1 shows the molecule possessing atargeted HOMO-LUMO gap among possible
molecular structures with atomic species of C, O,
N, F, and H, predicted by the present algorithm.
In this case, CF4 was predicted to have thewidest gap of 0.62151 hartree among thepossible molecular formula in the QM9 [2].
Parallelly, we have performed an ab-initio
molecular dynamics study on water-molecule
dissociation in a nanostructured perovskite
material (MAPbI3) [4]. These computations
have been done in part by using the Supercomputing System at SCC-ISSP
References[1] R. Gómez-Bombarelli et al, ACS Cent. Sci. 4(2018) 268–276.
[2] K. Sato and K. Tsuruta, Mater. Sci. Forum,in press.
[3] M. J. Kusner, B. Paige, J. M. HernándezLobato, http://arxiv.org/abs/1703.01925.
[4] M.A.A. Asad, K. Sato, and K. Tsuruta, MRS
Adv. 4, 1965 (2019).

137

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analysis of ion conduction in materials of proton-conducting solid electrolyte
and application to catalytic surface reaction with proton conductors
Fumiya Murase, Hiroki Matsuo, Junichiro Otomo
Graduate School of Frontier Sciences,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8561
hydrogen atom dissociate the nitrogen bondstep by step. However, the roles of the cathodic
polarization of the catalyst and protons
supplied from the electrolyte on the nitrogendissociation reaction in the ammonia
electrosynthesis process are still unclear.
In this study, the roles of the cathodepolarization of the catalyst and protons fromthe electrolyte are investigated by theoretical
calculations based on density functional theory(DFT) to reveal the mechanism of theelectrochemical promotion effect of ammonia
formation reaction.

1. Introduction
Ammonia has been regarded as one of theattractive energy carrier for storage andtransport of hydrogen because of its highhydrogen content and high energy density.
Electrosynthesis of ammonia from nitrogen
and water has been studied as a novel processreplacing the conventional Haber-Boschprocess which consumes a lot of energy.
We reported electrosynthesis of ammonia
using an electrolyzer cell with a protonconducting electrolyte and cathode catalyst of
Fe and Ru. We found the ammonia formation
rate is remarkably enhanced with increasing
cathodepolarization(electrochemical
1
promotion effect) . Since dissociation of
nitrogen triple bond is a rate-determining stepin the ammonia formation reaction, we
consider that the application of the cathodic
polarization promoted the dissociation
reaction of nitrogen triple bond.
As for the dissociation reaction of nitrogenmolecule on the metal catalyst, previous
studies based on theoretical calculations
suggested majorly two different mechanisms
for the N2 dissociation reaction on a surface ofthe cathode catalyst metals2,3. One is the direct
dissociation mechanism in which nitrogenmolecule adsorbed on the surface of thecatalyst directly dissociate into two adsorbed
nitrogen atoms. The other is associative
mechanism in which hydrogen atom initiallyreacts with the adsorbed nitrogen molecule toform N2H species and successive reaction with

2. Computational methods
For the calculation of the surface reaction,a slab-and-vacuum model was employed. We
chose BaCeO3 (BCO) with a BaO2-terminated(001) plane as a proton-conducting oxide slab
and a Ru cluster on the surface of the BCO
surface as a catalyst. DFT calculations were
performed

with

VASP5.5.4

code.

The

generalized gradient approximation proposedby Perdew, Burke, and Ernzerhof (GGA-PBE)
represented the exchange-correlation energyfunctional4. Plane-wave cut-off energy of
400 eV was adopted. Monkhorst-Pack k-meshof 2 × 2 × 1 centered at the  point for thegeometry optimized supercells.

138

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

To reveal the effect of the cathodic

configuration

of

the

adsorbed

nitrogenpolarization on the nitrogen dissociation,

molecule was stabilized in the dissociative

density of states (DOS) of the systems withmodel by the addition of an electron. This

one nitrogen molecule apart from the catalyst

result allows us to expect that the dissociationand that with nitrogen molecule adsorbed onmechanism can be promoted by the cathodic

the catalyst were calculated. Moreover, one

polarization.

electron was added to the system withadsorbed nitrogen molecule to reproduce thecathodicpolarization

in

the

ammoniaelectrosynthesis.
Fig. 1. The Ru cluster and the adsorbed N2

3. Results

molecule on the BCO (001) surface withIn the calculation for the model without

BaO2-termination.

adsorbed nitrogen, electron-occupied Ru 4d
state was emerged at around Fermi level after

Table 1. Calculated charges normalized by

the addition of an electron, which suggested

elementary charge for constituent atoms of thethat the cathodic polarization activates an

Ru cluster and the adsorbed nitrogen molecule

electron-donating property of the Ru catalyst.

before and after the addition of an electron

Moreover, the calculation for the model withnormalized by elementary charge.

adsorbed nitrogen showed that an anti-bonding
orbital of the adsorbed nitrogen located aroundthe Fermi level after the electron addition.
Then, charges of constituent atoms of the Rucluster and the adsorbed nitrogen molecule(Fig. 1) were calculated for the system before
and after the electron addition. As summarizedin table 1, the N2 atom and the Ru atoms were
negatively charged after the electron addition.
These results suggested that back donation of

Atom

BeforeAfter

Variation

N1

−0.36

−0.35

0.01

N2

−0.05

−0.15

−0.10

Ru1

−0.42

−0.51

−0.09

Ru2

0.16

0.07

−0.09

Ru3

−0.03

−0.09

−0.06

Ru4

0.09

0.04

−0.05

References

electron from the Ru catalyst to the adsorbed[1] F. Kosaka et al., Sustainable Chem. Eng.,

nitrogen molecule can be promoted by the5, 10439–10446 (2017).

application of the cathodic polarization.

[2] S. Back and Y. Jung, Phys. Chem. Chem.

To clarify the possible nitrogen dissociation

Phys. 18, 9161–9166 (2016).

mechanism, the reaction activation energies[3] D. Bao et al., Adv. Mater., 29, 1604799

for the two mechanisms were calculated with(2017)

the nudged elastic band (NEB) method.

[4] Perdew, J. P. et al., Phys. Rev. Lett. 77, 3865

Though the apparent difference in the(1996).

activation energy was not observed, side-on

139

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Transport and reaction properties of nanographene
Koichi KUSAKABE
Graduate School of Engineering Science, Osaka University
1-3 Machikaneyama, Toyonaka, Osaka 560-8531

1. A cross-correlation transport eﬀect ofa magnetic Ni/h-BN/Ni junction
We found that a thin magnetic Ni/h-BN/Nijunction allows a novel magnetoresistance effect controllable by the external electric-ﬁeld,
i.e. a cross-correlation eﬀect. The eﬀect comesfrom realization of local pyramidal B-N3 structures of the h-BN monolayer. When the antiparallel spin conﬁguration of two ferromagnetic Ni layers is ﬁxed, the spin-polarized tunnel current is reversed in its spin-moment direction by the electric ﬁeld whose ﬁeld strengthis within a realizable range. Switching uprightpyramids to inverted pyramids, the electronic
polarization direction in the h-BN layer andthe spin-moment direction are reversed.[1]2. The strong-correlation eﬀect in anelastic property of defect-free graphite
We developed new DFT-based simulation
methods, i.e. LDA+U+RPA and ACFDTRPA+U, for the explanation of unexpectedly
large elastic constant C33 of the defect-freemonocrystalline graphite by KANEKA, whichis measured by the microscopic picosecond ultrasound method.[2] The short-range correlation eﬀect described by the U term causes unharmonic potential proﬁle raising C33 from thevalue by ACFDT-RPA by more than 20%.
3. Hydrogen production catalyzed bygraphene with vacancies
We found that hydrogenated graphene vacancies promote dehydrogenation processes ofseveral alkane molecules in simulations. Basedon these results, we can propose that creation of atomic vacancy becomes the activa-

140

Figure 1: Calculated C33 by LDA+U+RPA(solid line) and LDA+U.[2]tion of the dehydrogenation catalytic propertyof graphene, which is shown to be realized inexperiments.[3]4. Zero modes in PTM molecules
The counting rule of zero modes by Morishita holds generally in a set of phenalenyl
tessellation molecules (PTM).[4] Based on theruled creation of zero modes, we can constructa certiﬁed ferrimagnetic Hubbard model in two
dimensions. An eﬀective low-energy model becomes a Kondo-lattice model, where extending
orbitals causes the Kondo screening in localized spins of arrayed zero modes.
Acknowledgement
This work was partly supported by KAKENHI (Nos. JP18K03456 and JP19H00862).
References[1] H. Harfar, et al., ACS Appl. Elec. Materials, in press. [2] K. Kusakabe, et al., Phys.
Rev. Materials, 4, 043603 (2020). [3] K.
Kusakabe, et al., Japan patent appl. JP2019135780 [4] N. Morishita and K. Kusakabe, J.
Phys. Soc. Jpn. 88, 124707 (2019).

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyovan der Waals density functional study of image-potential
states at organic-metal interfaces
Yuji HAMAMOTO
Department of Precision Science and Technology, Graduate School of Engineering,Osaka University, Yamada-oka, Suita, Osaka 565-0871
Recent progresses in observation techniques

1
Interaction energy / eVenable us to elucidate the transport properties ofunoccupied states on solid surfaces. Amongthem, image-potential states (IPSs) are ofparticularimportance,

since

they

appearubiquitously on metal surfaces, exhibiting a

0
ï1
ï2
ï3
4.0

Rydberg series with parabolic dispersions. From

top
bridgehollow

4.5

5.0
5.5
6.0
Distance / Å

6.5

7.0

an applicational point of view, IPSs could

Fig. 1: Determination of the equilibrium dis-

influence the properties of molecular-basedtance between PbPc and graphene

electronic devices such as organic light-emitting

as shown in Fig. 1. Experimentally, IPSs of PbPc

diodes, interacting with unoccupied molecularadsorbed on HOPG has been investigatedorbitals of adsorbates. Recently, we have applied

intensively using two-electron photoemission

van der Waals density functional (vdW-DF)

spectroscopy [3-5]. Unlike naphthalene, PbPc

method [1] to naphthalene physisorbed on

has a non-planar shuttlecock structure due to thegraphene and revealed that IPSs are induced onaclose-packed

naphthalene

central lead atom, which results in a dipole

monolayer,

moment. To understand the influence of thehybridizing with graphene IPSs [2]. The

dipole moment on hybrid IPSs, we investigate

resultant hybrid IPSs show an anisotropic

the band structure of PbPc on graphene andeffective mass that reflects the molecularanalyze the effective mass of the IPSs. Our

structure of naphthalene, demonstrating that theresults reveal that the dipole moment reduces thetransport properties of IPSs of metal surfaces

overlap of wave functions between neighboring

can be fine-tuned by molecular adsorption.

molecules, which enhances the effective mass ofAs an extension of our previous study on

the hybrid IPSs. Moreover, unlike the IPSs ofhybrid IPSs at molecular-metal interfaces, we
heretheoreticallyinvestigate

graphene, the hybrid IPSs in PbPc on grapheneleaddisplays an anisotropic effective mass withphthalocyanine (PbPc) physisorbed on graphene141

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

nearly C4 symmetry, which prominently reflects[3] M. Shibuta, K. Miyakubo, T. Yamada, and T.

the molecular structure of PbPc [6].

Munakata, J. Phys. Chem. C 115, 19269 (2011).
[4] N. Kawakita, T. Yamada, M. Meissner, R.

References

Forker, T. Fritz, and T. Munakata, Phys. Rev. B[1] M. Dion, H. Rydberg, E. Schröder, D. C.

95, 045419 (2017).

Langreth, and B. I. Lundqvist, Phys. Rev. Lett.

[5] T. Yamada, N. Kawakita, C. Okui and T.

92, 246401 (2004).

Munakata, J. Phys.: Condens. Matter 31, 044004[2] S. A. Wella, H. Sawada, N. Kawaguchi, F.

(2019).

Muttaqien, K. Inagaki, I. Hamada, Y. Morikawa,[6] Y. Hamamoto, H. Sawada, S. A. Wella, K.

and Y. Hamamoto, Phys. Rev. Materials 1,

Inagaki, I. Hamada, and Y. Morikawa, in

061001(R) (2017).

preparation.

142

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

STM simulations for Fe-adsorbed Si(111) surfaces
Kei TANIMOTO and Ken HATTORI
Graduate School of Science and Technology, Nara Institute of Science and Technology
Takayama, Ikoma, Nara 630-0192

Using scanning tunneling microscopy(STM), author’s group has been studied
iron-silicides formation on Si(111) [1] prepared in ultra-high vacuum. In the initialstage of Si(111)7×7 with isolated Fe atoms,
we observed 5 diﬀerent adsorption types inexperimental STM images [2]. In order tounderstand (meta) stable actual structures of
Fe/Si(111)7×7, we carried out ﬁrst principles
calculations using the super computing systemin the institute for solid state physics.
We utilized the calculation package of Simulation Tool for Atom TEchnology (STATE)Senri [3] for 17 models of Fe single-atom adsorption including atop, ins, T4 , and H3 sites,
based on a Si(111)4×4 surface-substrate model[4]. The 4×4 model (i.e., 4 Si adatoms on
2×2 T4 sites, and 2 of 4 restatoms terminatedwith H atom, in a unit) has an advantage offast calculation, because of smaller number ofatoms compaired to that in the 7×7 model,
maintaining the speciﬁc Si surface property of
the 7×7 model of the dimer–adatom–stackingfault, though the 4×4 model is not equal to
the 7×7 model.

The clean Si(111)4×4 model consisting of a
Si adatom-layer, six Si-layers, and a bottom
H-terminated layer has 118 atoms, while 7×7
has 347 atoms. The top-view and side-view
schematics in Fig. 1 show the atomic structure of the clean 4×4 model; upper adatom(brawn ball) corresponds to center adatom(CEA) with two neighbored restatoms (purple
ball, note another restatom is terminated by Hatom), and lower adatom corresponds to corner adatom (COA). The bottom panel represents STM simulation images of ﬁlled (empty)
states at -0.5 (+0.5) V in bias voltage, displaying clear adatom images.
In the simulation, the atoms in the top six
layers were relaxed with the spin polarization,from the converged conﬁgurations without the
spin polarization.

Figure 2: A model of Si(111)4×4 surface withFe atom near a H3 site and STM simulation
results.

Figure 1: A model of Si(111)4×4 clean surface
and STM simulation results.

143

During the 17 models, the stable conﬁguration was Fe atom close to H3 site as shown in
Fig. 2; Fe atom (pink ball) locates between
CEA and restatom, with the formation energyof -7.59 eV. The STM images showed darken
adatom at ﬁlled states at -0.5 V while no drastic change at empty states at +0.5 V. The sec-

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyoond (meta) stable conﬁguration was also nearH3 site COA and restatom with the formationenergy of -7.55 eV. The third meta-stable conﬁguration group was near T4 sites with -6.87
eV to -6.35 eV in formation energy. The fourthgroup was ins sites with -6.34 eV to -6.28 eV,
and the last (much unstable) group was atop
sites with -5.32 eV to -5.28 eV.
The authors thank Profs.
Morikawa,
Hamada, and Inagaki in Osaka University, andProf. Yanagisawa in Ryukyu University for
their great support in STATE-Senri calculations.

References[1] K. Kataoka, K. Hattori, Y. Miyatake,and H. Daimon, Phys. Rev. B 74 (2006)
155406.
[2] K. Kataoka, Dr.. Thesis, Nara Institute of
Science and Technology, Nara (2006).
[3] Y. Morikawa, Phys. Rev. B 63 (2001)
033405, and references therein.
[4] Guo-Xin Qian and D. J.Chadi, Phys. Rev.
B 35 (1987) 1288.

144

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Analysis on atomic and magnetic structure in magnetic
molecular complex, crystal and interface and investigation of
external field effectMasao 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 investigated the weak-boundproportional to minus cube of distance. It canmagnetic material systems such as magnetic

be estimated using spatial spin density obtained

molecular

fromcrystalandmagnetic-layered

DFT calculation.

Weappliedthismaterial. They have received a lot of attention

approach to antiferromagnetic molecular crystal

due to their unique physical properties, such as[1] (monoclinic crystal solid oxygen 𝛼𝛼 phase:external field-controllable its magnetization andcrystal structure. Since prediction of structural

𝛼𝛼 -O2) and ferromagnetic thin film and chain

and energic properties with high accuracy is

MA is comparable to those of Spin-Orbit

essential

for weak-bond magnetic materials,

Interaction. Moreover, the spatial distribution

we have enhanced the computational accuracyof intra-atomic spin density occasionallyof density functional theory (DFT) by including
physical interactions, e.g. van der Waals (vdW)

contributes to MDI energy. For solid oxygen 𝛼𝛼-interaction and magnetic dipole-dipole (MDI)

DF method, which developed in our previous

energy, which were neglected in standard DFT

work [2], was employed. External magnetic

calculation. While MDI energy is often

field effect due to Zeeman interaction can beconsidered as weak, it plays important role formagnetic anisotropy (MA) and diamagnetic

considered for oxygen 𝛼𝛼-phase case, in order tofield. Moreover, we also attempt to build a[3].

framework to investigate the external magnetic

References

field effect.

[1] M. Obata et al., AIP Adv. 8, 10149 (2018).

We developed

the method(Fe, Co, Ni). We found that its contribution tophase case, noncolinear spin-dependent vdW-

investigate the effect towards its magnetization[2] M. Christivana et al., JPSJ 88, 104601

for eachmaterial dimensionality (chain, film, bulk) to(2019).

estimate[3] A. R. Rio et al., JPSJ 89, 035002 (2020)

their

MDI

energy,

since

MDI

interaction is basically long-range interaction

145

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Eﬀects of electron-phonon scattering on electronic
structure of half-metallic Heusler alloys
H. Akai
Institute for Solid State Physics, University of Tokyo
Kashiwa-no-ha, Kashiwa, Chiba 277-8581

In some Heusler alloys, despite the fact that
there exists a band gap in one of spin channels
expected, established through ﬁrst-principles
calculations, the half-metallicity of the materials often turns out fragile under realistic situations such as in device structures. It has
been pointed out that chemical disorders anddefects might easily degrade the half-metallic
nature of such materials. These degradations
are structure oriented, and therefore, static.
This means, once a perfect structure is attained, there exists no reason of this kind of
degradation for the half-metallicity. However,there still exist another source of degradation,i.e., dynamical eﬀects. The main sources ofsuch eﬀects are phonons and magnons at ﬁnite
temperature. In the present research, we discuss the eﬀects of electron-phonon scatteringon the half-metallicity of Co2 MnSi, as a typicalexample, on the basis of ﬁrst-principles calculations. The phonons are treated as giving local and static (adiabatic) eﬀects [1], where correlations of the displacements between neighboring sites as well as dynamical eﬀects are neglected, i.e. we take a quasi-dynamical treatment. The phonons are expressed as random
displacements of atoms from their equilibrium
positions. Using the distribution of the atomic
displacements, the electronic structures of thesystem at ﬁnite temperature are calculated byregarding the system as a disordered systemwith randomly distributed atomic positions.
This kind of randomness can be treated using KKR-CPA code [2]. The results show

146

that even at 300 K, the perfect half-metallicity
is lost (Fig.1), showing that the eﬀects ofphonons are important at usual operating temperatures of devices. The eﬀects on the GMR
is also discussed. It turns out that, though
the half-metallicity is lost at ﬁnite temperature, the conductivity of the spin-down stateis much lower than that of the spin-up state
by virtue of the strong electron-phonon scattering. Thus, the system can still be used in
GMR devices at ﬁnite temperatures.

Figure 1: DOS of Co2 MnSi with an average
displacement hu2 i = 0 (left) and 0.046 (right)
in units of Bohr2 .

References[1] S. Kou and H. Akai, Solid State Commun.
276, 1 (2018).
[2] H. Akai, AkaiKKR, http://kkr.issp.
u-tokyo.ac.jp/ (2002).

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Systematics of Curie temperature in rare earth
permanent magnet materials
H. Akai
Institute for Solid State Physics, University of Tokyo
Kashiwa-no-ha, Kashiwa, Chiba 277-8581

References

Calc.
Calc. lmd
Expt.

R2Fe14B

TC (K)

1000

500

0
La

Ce

Pr

Nd Sm Gd Tb Dy Ho Er
Rare-earth elements

Tm Yb

Lu

Y

Figure 1: Calculated TC of R2 Fe14 B comparedwith experiments.
R2Co14B

Calc.
Calc. lmd
Expt.

TC (K)

1000

500

0
La

Pr Nd Sm Gd Tb
Rare-earth elements

Y

Figure 2: Calculated TC of R2 Co14 B comparedwith experiments.
Calc.
Calc. lmd
Expt.

R2Fe171000

TC (K)

Curie temperatures TC ’s of permanentmagnet materials R2 (Fe,Co)14 B, R2 (Fe,Co)17 ,and RFe11.5 Ti0.5 (R = La, Ce,. . . , Lu, Y),
are calculated within the mean field approximation using the exchange coupling constants Jij ’s that are obtained by first-principles
KKR–Green’s function method[1]. While theagreement between the calculations and experiments is rather well for the Co-based systems,
there arise some discrepancies in the case of
Fe-bases systems. Despite these discrepancies,
however, the systematic changes seen in TC
as the rare earth element R changes acrossthe lantanoid are fairly well reproduced by thecalculation. In the case of R2 Fe14 B, the discrepancies can be largely diminished by using
Jij ’s that are calculated for local-moment disordered states (LMD), which is considered tocorrespond to the paramagnetic state above
TC , as is shown in Fig.1 and 2. However, this is
not the case in general: the discrepancies seenin R2 Fe17 (FIg. 3), cannot be remedied. From
the analyses of calculated and experimental
data, it is concluded that data assimilations
are possible and necessary to make reasonablepredictions of TC for rare earth permanentmagnet materials, in particular, the Fe-based
ones.

500

0
Ce

[1] H. Akai, AkaiKKR, http://kkr.issp.
u-tokyo.ac.jp/ (2002).

147

Pr

Nd Sm Gd Tb Dy Ho Er
Rare-earth elemets

Tm Yb

Lu

Y

Figure 3: Calculated TC of R2 Fe17 comparedwith experiments.

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Electronic state of water under various environments
Ryosuke YAMAMURA, Kento AKIHIRO, Nozomu FUTAMATA, and Osamu
TAKAHASHI
Graduate School of Science, Hiroshima University, kagamiyama, Higashihiroshima,
Hiroshima 739-8526
We have studied aqueous solution using
massive parallel computer simulations. This
year, we focus on aqueous oxalic and malonicacid observed by X-ray absorption and

Fig. 1: (a) XAS and (b) XES spectra ofemission spectroscopy [1]. To obtain the

aqueous oxalic acid (solid line: experiment,

theoretical spectra of an aqueous solution, adash: theoretical, black: pH 1.1, red: pH

molecular dynamics (MD) simulation based

2.7, green: pH12.9).

density functional theory (DFT) was adopted toemission spectra. The core excited dynamics

simulate the structure of the solution. The MD

and relative peak intensities of the spectra were

simulations ware performed using the Vienna

calculated within the framework of DFT using

ab initio simulation package (VASP). The MD

deMon2k code.

simulations ware performed for 5 ps, with 0.2-

We found that the theoretical XAS and XES

fs time steps. Cluster sampling was performed

spectra of cluster models reproduced theusing python and fortran code for the results oftrends of the experimental spectra with

the MD simulations. From the cluster obtained

respect to emission energy compared withby structure sampling, a carboxylic acidsingle molecular models. We found that themolecule at the center of the cluster was used todependence of XAS and XES spectra on pH

model the OC=O,1s and OC-O-,1s core-holeis different from monocarboxylic acid.

and core excited state dynamics. The time steps

Referencesused for these simulations were 0.25 and 20 fs,[1] R. Yamamura, T. Suenaga, M. Oura, T.

respectively. During the core excited state

Tokushima, and O. Takahashi: Chem. Phys.

dynamics, each snapshot was used to calculate

Lett. 738 (2020)13689

the relative line intensities of the X-ray

148

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Temperature-Dependent Optical Properties in Rare-earth
Sesquioxides and Related Phonon Calculations
Takayuki MAKINO
Department of Electric and Electronics Engineering,
University of Fukui, Fukui 910-8557, JapanThe natural oxide of Si, amorphous SiO2, isFigure 1 shows temperature dependences of theimportant for the CMOS technology. Due to theband-gap energies. Alloted symbols are open

problem related to its fundamental size limits,

circles for ytterbia and open squares in lutetia,

reduction of the gate-oxide thickness in devices

respectively. We here use Pässler model to fit tois strongly demanded. As one of the expected

the experimental data. the detailed values ofcandidates satisfying these properties, attention

deduced parameters have been given elsewhereis paid on rare-earth metal sesquioxides. Their[1]. We could reduce of the number of running

optical properties are almost far from the fullparameters in the regression analysis which are

understanding. It is expected that such aantemperature-dependent optical study can yield

abovementioned

in several insights not only on electronic or

discussion.

advantage

andsignificance

of

the

phonon-property-related

excitonic properties, but also on phononic
properties. In this activity report, we report theReferences

optical[1] T. Makino et al.: Jpn. J. Appl. Phys. 59

properties

andrelatedphononcalculations of ytterbia (Yb2O3) and lutetia(2020) SCCB13.

(Lu2O3) thin films.

[2] R. Pässler, Phys. Rev. B 66, (2002) 085201.

The phonon properties of the structure are
obtained by a frozen phonon method: The
forces acting on the ions are calculated upon asmall displacement of each ion by using
Quantum ESPRESSO package. The set offorces can be converted into the force constants,
which are required to construct the dynamical
matrix. We used the PHONOPY package togenerate a set of 2×2×2 supercells with

Fig. 1: Temperature dependences of band-gap
Eg in Yb2O3 (circles) and Lu2O3 (squares).

displaced atoms, to compute the phonon
dispersion and density-of-states (DOS) spectra.

149

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles calculation of organic modified metal oxide
nanoparticles
Akira YOKOWPI-Advanced Institute for Materials Research,
Tohoku University, Katahira 2-1-1, Sendai, Miyagi 980-8577
We have studied an interface system ofbasis was set at 500 eV for all the calculations.

organic molecules on metal oxide surface.

Monkhorst–Pack k‐point set of 4 × 4 × 1 wasFrom the experiments, it is known that surface

used for the a slab model. Convergence criteria

stability of metal oxide greatly changes

was set at less than 0.01 eV/Å for the force.
Figure 1 shows the adsorption,

depending on the environment, resulting in the
difference in the properties. For example, CeO2

deprotonation, and dehydration of octanoic acidis ordinary stable with (111) surface, but it turns

on CeO2 (100) surface considered in this study.

to be stable with (100) facet when

From the results, energy stabilization washydrothermally treated with carboxylic acid. As

calculated as -26.63 kJ/mol for adsorption anda result, catalytic activity is greatly enhanced-26.57 kJ/mol for deprotonation. Deprotonation

with (100) facet exposure of CeO2 [1]. In thisdoes not contribute stabilization. Dehydration

year, we studied the interaction betweenof octanoic acid and hydroxide on CeO2 surface,octanoic acid and CeO2 surface using first-

much larger stabilization as -43.20 kJ/mol was

principles simulation.

observed.

Plane-wave basis density functional theory
simulations were conducted with VASP code.
Simulations were The generalized gradientapproximation proposed by Perdew, Burke, andErnzerhof (PBE) represented the exchange‐
correlation energy functional. The DFT+U
method introduced by Dudarev was used totreat electron localization. The parameter U-J

Figure 1 Adsorption, deprotonation, andwas set to 5.0 eV for Ce4f state. The valence

dehydration of octanoic acid on CeO2 (100)configurations of the pseudopotentials wereReferences

5s25p64f15d16s2 for Ce, 2s22p4 for O, and 2s22p2[1] X. Hao, A. Yoko, C. Chen, K. Inoue, M. Saito, G. Seong, S.

for C. The energy cutoff for the plane‐wave

Takami, T. Adschiri, Y. Ikuhara: Small 14 (42), (2018) 1802915

150

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First principles study on leaking current at a
dislocation in doped semiconductors
Yosuke HARASHIMA
Institute of Materials and Systems for Sustainability, Nagoya University
Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601

In the second half fiscal year of 2019, we haverevealed the following results related with theperformance of gallium nitride (GaN) powerdevices [1].
• The threading screw dislocations attract
Mg impurities, and the electronic levels in
the energy gap induced by the threading
dislocations elevate towards the conduction band as the Mg approaches the dislocation line.
This results suggest that the leakage current
which degrade the performance of the devices
is induced by the presence of the Mg and thescrew dislocation complexes.
GaN is one of the most promising compounds for the power devices since it has alarge band gap. For the realization of the device, suppressing the leakage current is an important issue. The leakage current has been
observed at the position of the threading dislocation. Recent experimental study suggeststhat the Mg impurities are condensed aroundthe dislocation. The electronic structure of
the Mg-dislocation complexes should be related with the origin of the leakage current,
and it is important to guarantee the device reliability.
In this study, we systematically perform
first-principles total-energy calculations forpossible 16 core structures of the screw dislocations as shown in Fig. 1. The core structures are expressed as D(n | m) or S(n | m).
The first capital letter denotes the position of
the dislocation line. One is called single core,

Figure 1: The 16 core types of the screw dislocations. A red cross in the top panel denotes
the position of the dislocation line. The left
is for D(n | m) and the right is for S(n | m),where n is the number of removed Ga and mis that of N.
in which the dislocation line is at the centerof the single hexagon; Another is called double core, in which the dislocation line is at the
middle of the bond of hexagon. n and m represent the numbers of Ga and N atoms removed
from the fully filled structures. An example ofD(0 | 0) is shown in Fig. 2
Those first-principles calculations are doneby using the Vienna Ab initio Simulation
Package (VASP) [2] which is based on the
projector augmented-wave (PAW) method.
The exchange-correlation energy is treatedwithin the generalized gradient approxima-

151

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Fictitious hydrogen

Dislocation line
41Å
GaN
49Å

Figure 2: The core structure D(0 | 0). Greenand blue spheres denote Ga and N, respectively. The atoms surrounding the dislocationline are enlarged to emphasize the position.

tion (GGA) with the Perdew-Burke-Ernzerhof
functional. We also use the Heyd-ScuseriaErnzerhof (HSE) hybrid functional to evaluate more accurate electronic levels in the bandgap. The unit cell contains about 800 Ga
and N atoms in total. The GaN pillar issurrounded by the vacuum on the lateral directions perpendicular to the [0001]. We expect that this vacuum relaxes artificial straincaused by rounding the lateral surfaces. The
dangling bonds on the lateral surface of the
GaN pillar are terminated by ≈ 100 fictitioushydrogens. The schematic picture of the unit
cell on the [0001] plane is shown in Fig. 3. The
integration over Brillouin zone is taken with
4 sampling points along the [0001] direction.
The structural optimization is performed foreach core structures.

VacuumFigure 3: A schematic picture of the [0001]
plane of the unit cell. The green region denotes GaN and it is terminated by the fictitioushydrogen atoms. The outermost region is thevacuum. A red cross denotes the position of
the dislocation line.

References[1] T. Nakano, Y. Harashima, K. Chokawa,
K. Shiraishi, A. Oshiyama, Y. Kangawa,S. Usami, N. Mayama, K. Toda, A.
Tanaka, Y. Honda, and H. Amano: arXiv,
2004.06876 (2020).
[2] G. Kresse and J. Furthmuller: Phys. Rev.
B 54, 11169 (1996).

We found that D(0 | 2), S(0 | 3), and S(0 | 6)
are stable. Then we replace one Ga atom inthese three core structures with an Mg atom.
The relative position of the Mg from the dislocation line is sampled. The resultant binding
energy of the Mg shows that Mg is attracted
by the screw dislocation and the electronic levels in the gap elevate towards the conduction
band, as mentioned above.

152

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab Initio Band Structure Calculation of InSb Using VASP
Based on Hybrid Density Functional Theory
Hiroki I. FUJISHIRO, Yoshitaka MATSUMOTO, Takahiro SUZUKI, and Akira ENDOH
Department of Applied Electronics,
Tokyo University of Science, Niijuku, Katsushika, Tokyo 125-8585
Terahertz-wave frequency range (0.1 to 10

of unstrained and compressively strained InSb

THz) will be the major resources in futureusing Vienna Ab initio Simulation Package

communication and sensing systems. InSb

(VASP) based on the method in the local density

channel high electron mobility transistors

approximation to obtain band parameters [3].

(HEMTs) are one of the most promising devices

We obtained nonzero bandgap energy Eg values

that can operate in the terahertz band. Although

by using PBE0 (Perdew-Burke-Ernzerhof 0) as

InSb has the lightest electron effective mass ina functional. In this work, we investigated

III-V semiconductors, the lattice constant offunctionals used for band structure calculation in

InSb is the largest. Therefore, compressive strain

order to obtain the Eg values close to theis always applied to the InSb channel.

literature ones.

In our previous work [1], we carried out

We studied the hybrid coefficient of theMonte Carlo (MC) simulations of InSb channel

density functional [4]. The hybrid functional

HEMTs to predict device performance. We used

used in this work was a modification of PBE0.

the band parameters calculated by the empirical

The functional is constructed by the mixing of apseudopotential method [2]. However, the band

fraction 𝛼 of the Fock exchange with a fraction

structure obtained from the first-principles

1

calculation seems to be preferable. In 2018, we

correlation energy 𝐸

carried out ab initio band structure calculations

following equation:

𝛼 of the PBE exchange. The exchangecan be expressed by the2Bandgap energy [eV]

1.8
1.6
1.4
1.2
1
0.8
0.6
0.4
0.2
0
0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

Mixing coefficient, Fig. 1 Calculated bandgap energy as a function of mixing coefficient, .

153

0.5

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

𝐸

𝛼𝐸

(1)

However, the increase in the value of m* for theis the PBE-1.32% compressively strained InSb also

is the PBE correlation [4].

appears to be small. Furthermore, there is room

1

𝛼 𝐸

𝐸

where 𝐸 is the Fock exchange, 𝐸
exchange, and 𝐸

In PBE0, the mixing coefficient 𝛼

0.25 . In

for reconsideration of the energy difference

our previous work [3], we obtained the bandgap
energyEgvaluesofunstrained

between  and L valleys, 𝐸

andvalleys, 𝐸

compressively strained InSb. However, the Eg
values are too large when using 𝛼

and  and X.

Regarding the mixing coefficient of the

0.25

density functional, further work is necessary(PBE0). We calculated the bandgap energy

considering the correspondence with various

values as a function of 𝛼 . Figure 1 shows theliterature and experimental values.

calculation results of bandgap energy. We
obtained the closest bandgap energy Eg to theReferences

previous work [5, 6] with 𝛼[1] T. Takahashi, S. Hatsushiba, S. Fujikawa,

0.21.

and H. I. Fujishiro: Phys. Status Solidi A 214

Table 1 summarizes the band parameters of
InSb in Refs. [3, 5, 6] and in this work. In our(2017) 1600599.

previous work [3], we obtained the bandgap[2] H. Nishino, I. Kawahira, F. Machida, S. Hara,

energy Eg of 0.34 and 0.48 eV for unstrainedand H. I. Fujishiro: Proc. 22nd Int. Conf. on(0%) and compressively strained (-1.32%) InSb,

IPRM (2010) p. 156.

respectively. The Eg value for unstrained InSb in[3] H. I. Fujishiro, Activity Report 2018,[3] is much larger than that in [5, 6]. In the

Supercomputer Center, Institute for Solid State

present work, the Eg value was relatively

Physics, The University of Tokyo, p. 137.

reasonable because the mixing coefficient 𝛼 was[4] T. Garwood, N. A. Modine, and S. Krishna:

set to match the “general” bandgap value of InSb

Infrared Physics & Technology, 2017.

[5, 6]. On the other hand, the increase in Eg when

[5] M. Levinshtein, S. Rumyantsey, and M.

compressive strain is applied seems to be small

Shur: Handbook Series on Semiconductor

for 𝛼

0.21. The electron effective mass in the

Parameters in 2 Volumes, World Scientific, 1996.

 valley m* of unstrained InSb is almost same

[6] H. Rodilla, T. González, D. Pardo, and J.

as the values in the previous results [3, 5, 6].

Mateos: J. Appl. Phys. 105 (2009) 113705.

Table 1 Main band parameters of InSb.
0%[5, 6]
𝐸 eV)
𝑚∗
𝐸
eV)
𝐸
eV)

0.18
0.014
0.76
0.46

0%
(VASP)
[3]
0.34
0.015
1.04
2.64

-1.32%(VASP)
[3]
0.48
0.022
1.06
2.69

154

0%
(VASP)[This work]
0.151
0.012
1.05
2.64

-1.32％(VASP)[This work]
0.154
0.013
1.05
2.64

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles investigation of electronic propertiesof carbon nanotubes and graphene
Yoshitaka FUJIMOTO
Depertment of Physics, Tokyo Institute of Technology
Ohokayama, Meguro, Tokyo 152-8551

Graphene and carbon nanotubes (CNTs)
show high charge mobility at room temperature, and therefore they are expected to be a
promising device material to be used in nanoelectronics such as field-eﬀect transistors. Substitutional doping is one of the eﬀective ways
to tune the electronic properties of graphene
and CNTs, and is also shown to improve thechemical reactivity to adsorbates. Therefore
dope graphene and doped CNTs are a goodcandidate for future sensor device materials.
We here present the adsorption propertiesof toxic NO and NO2 molecules on the borondoped graphene and (8,0) CNT using a firstprinciples density-functional calculation [1, 2,
3]. It is found that the NO and NO2 molecules
can be adsorbed strongly with short distancesand large adsorption energies on the B-dopedmonolayer graphene [2]. For the AB-stacked
bilayer graphene, NO and NO2 molecules canbe also strongly adsorbed [1, 3]. It is also
found that the adsorption energies of NO andNO2 molecules on the B-doped (8,0) CNTs aremuch larger than those of monolayer and bilayer graphenes.
Table 1 lists the adsorption energies and the

distances between the B atom in the doped
graphene layer and the adsorbed molecules for
NO and NO2 molecules on the B-doped monolayer and AB-stacked bilayer graphenes. The
NO and NO2 molecules are found to be adsorbed strongly with short distances and large
adsorption energies on the B-doped monolayer
graphene. For the case of the AB-stacked bilayer graphene, it is interesting that the adsorption energies as well as the binding distances for the adsorptions of the NO and NO2
molecules are comparable to those of the Bdoped monolayer graphene.

Table 1: Adsorption energy Ea (eV) and distance d (Å) between adsorbed molecule andB atom for molecules adsorbed on B-dopedmonolayer and AB-stacked bilayer graphenes.

In summary, we have studied the adsorption properties of the toxic NO and NO2
molecules on the B-doped graphene and Bdoped (8,0) CNT, based on first-principles
density-functional calculations. The NO andNO2 molecules strongly bind on the B-dopedmonolayer and bilayer graphenes. The adsorption energies of NO and NO2 molecules on the
B-doped (8,0) CNTs are larger than those on
the B-doped graphene layers.

NO
NO2

Monolayer
Ea
-1.23
-1.16

d
2.15
1.59

Bilayer
Ea
-1.19
-1.13

d
2.14
1.60

155

We also study the adsorption energies
and the binding distances of NO and NO2
molecules on the B-doped (8,0) carbon nanotubes (CNTs).
Like monolayer and bilayer graphenes, the NO and NO2 molecules
are found to strongly bind on the B-doped(8,0) CNTs with the large adsorption energies and the short binding distances. Furthermore, the adsorption energies for NO andNO2 molecules on the B-doped (8,0) CNTs
are considerably larger than those on the Bdoped monolayer as well as the B-doped bilayer graphenes due to the curvature eﬀects.

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

References[1] Y. Fujimoto and S. Saito, Chem. Phys.
478, 55 (2016).
[2] Y. Fujimoto and S. Saito, Jpn. J. Appl.
Phys. 58, 015005 (2019).
[3] Y. Fujimoto and S. Saito, to be published.

156

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Study of appearance of ferromagnetism by electric field
application to Pt thin film
Tatsuru Yamada1, Hiroyuki Kageshima2, and Tetsuya Sato1
1Department of Applied Physics and Physico-Informatics, Keio University, 3-14-1 Hiyoshi,
Kohoku-ku, Yokohama 223-0061, Japan
2Graduate School of Natural Science and Technology, Shimane University, 1060
Nishikawatsu-cho, Matsue 690-8504, Japan
Recently, It was reported that ferromagnetism

that

the

ferromagnetism

appearedinappears in an oscillatory manner in the Pt(100)oscillatory manner with a period of 6 ML only

thin films depending on the film thickness[1][2].

when spin-orbit interaction (SOI) was not

This property suggests that magnetism inincluded (Fig.1). This oscillatory behavior

Pt(100) thin film can be controlled by electricagrees with the experiment[2]. These results

field. In order to clarify the magnetism changesuggest that magnetism in Pt(100) thin film iswith application of electric field, we performed

intrinsically unrelated to SOI. For the next

first-principles calculation using the PHASE/ 0

step, we calculate magnetism in Pt(100) thinprogram.

film under application of electric field.

The first-principles calculation based on the
DFT within the GGA was performed, where
Vanderbilt type pseudopotential and a planewave basis set were used to evaluate electric
structure and magnetization of Pt(100) thinfilm. We used 88×88×1 k points (based on
Monkhorst-Pack) and a cutoff energy of 36
Rydberg.

Fig. 1: Thickness-dependent magnetic

We calculated lattice constant that minimizes

moment per Pt atom.

the energy. Using the obtained lattice constant,
we calculated the Pt layer thickness dependence

Referencesof the magnetic moment of Pt slab. Calculations[1] A. M. N. Niklasson et al.: Phys. Rev. B 75,

of electronic structure for the free-standing

172402 (2007).

Pt(100) thin films from 2 monolayers(ML) up[2] K. Ochiai et al.: JPS2019, Gifu, 10aPS27

to 17 ML were performed and it was clarified(2019).

157

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Ab Initio Calculation of High-Rate Deposition of Copper
Film by Low-Pressure Chemical Vapor Deposition with CuI
on Ru Substrate
Tatsuya JOUTSUKA
Institute of Quantum Beam Science,
Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511 Ibaraki,Japan
We have studied low-pressure chemical

integration metallization.

vapor deposition of Cu on Ru substrate using

Based on this study, we are now extending

CuI [1] using VASP program package (MPI

our calculations to analyze the dynamicalparallelization with multiple threads). This year,

properties in more detail. In addition, new sets

we focused on the molecular mechanism ofof precursor and substrate are explored for ultra

adsorption, migration and desorption. This is alarge scale integration metallization together

collaborative work with the experimentalist [2]with experiment.

(Prof. Satoshi Yamauchi at Ibaraki University),
who conducted the LPCVD experiment.
In this study, we elucidated the molecularmechanism of Cu deposition using copper(I)iodide (CuI) on Ru substrate by low-pressurechemical vapor deposition through electronic
structure calculations. Using density functional
theorycalculations,molecules

adsorb

we

show
and

that

CuI

decompose

exothermically due to a strong adsorption ofFig. 1: Molecular mechanism of LPCVD of Cu.

iodine atoms onto the Ru(001) surface. The
rate-limiting step of the Cu deposition is found

References

to be the desorption of iodine molecules from

[1] T. Joutsuka, S. Yamauchi: Chem. Phys. Lett.

the Cu(111) surface, suggesting that the741 (2020) 137108.

removal of iodine species is necessary to[2] T. Nishikawa, K. Horiuchi, T. Joutsuka andachieve the high-rate deposition of highly-

S. Yamauchi: submitted.

conductive copper films for ultra large scale

158

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical Analysis of Photocatalytic Reaction Mechanism atTitanium Dioxide Interfaces
Tatsuya JOUTSUKA
Institute of Quantum Beam Science,
Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511 Ibaraki,Japan
We have studied photocatalytic reaction

adsorption and the photogenerated hole can bemechanism at anatase TiO2 surfaces [1] using

trapped not on the neat surface but on the

cp2k program packagehydroxylated surface better at the (112) and(MPI parallelization

with multiple threads). This year, we focused(001)

surfaces.

The

experimental

andon the energetics and structure during the holetheoretical findings elucidate that the (112)

migration. This is a collaborative work with thefacet shows the larger stabilization of absorbed

experimentalist [2] (Prof. Satoshi Yamauchi atwater and trapped holes than other facets by

Ibaraki University), who conducted the LPCVD

larger structural relaxation at the surface.

experiment.
Anatase TiO2 shows a high photocatalytic
activity to decompose organic compounds andplays a crucial role in chemistry and physics.
To enhance the photocatalytic activity, proper
control of surface properties is crucial and themolecular-level mechanism can offer valuable
insight. We herein clarify the facet dependenceof hole trapping at the anatase TiO2 surface bydensity functional theory (DFT) calculations

Fig. 1: Molecular mechanism of hole migration.

using the constrained DFT method with thehybrid functionals. The photocatalytic activity

References

by UV irradiation around 365 nm in methylene[1] T. Joutsuka, H. Yoshinari, K. Yamamoto

blue aqueous solution is significantly high,and S. Yamauchi: in preparation for submission.

which is two-order larger than that on the[2] S. Yamauchi, K. Yamamoto, and S.

multi-oriented TiO2. The DFT calculations

Hatakeyama: J. Chem. Eng., 3 (2015) 28–38.

show the (112) surface can stabilize water

159

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Search and realization of novel electronic properties ofsolid surfaces and interfaces and of small particles
Takeshi INAOKA

Department of Physics and Earth Sciences, Faculty of Science,
University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213(1) Application of the tight-binding method
to a novel single-layer structure of carbon
atoms [4]The above-stated electron pocket andthe hole pocket are formed by-orbital-derived bands around the Fermi
level EF. Therefore, we can expect that thetight-binding method in terms of pz orbitalsof C atoms is effective for this system.
Figure 2 exhibits the band dispersion on
the  - M line for the hybrid density-functional method (Hyb) and the tightbinding method (TB). The transfer integral
for a diagonal nearest-neighbor pz pair and160

that for a lateral nearest-neighbor pz pair
were chosen to be -2.9 eV and -3.2 eV,
respectively. In view of band dispersions onother symmetric dispersion lines as well,
we found that the tight-binding method
can reproduce adequately the band
dispersions around EF, and consequently
the electron and hole pockets. The
tight-binding method provides a useful toolfor evaluating electronic properties of thissystem arising from -orbital-derived
bands.

Fig. 1 Carbon monolayer structure
considered here

E(k)-EF (eV)We mention two subjects which we
addressed this year.
Graphene is a very popular single-layer
structure of carbon (C) atoms arranged ina hexagonal lattice. However, we explore
different monolayer structures of C atoms.
Previously, we showed that the monolayer
structure in Fig. 1 is stable, and that theelectron system is a semi-metal which ischaracterized by the electron pocket
around the M point and the hole pocket
around the  point. We applied thetight-binding method to this system andclarified its utility and limitation for thissystem.
In scanning tunneling microscopy (STM)
light emission spectra of Ni(110)-(2x1)-O
surface emerge stepwise structures dueto oxygen (O) atom vibration parallel tothe surface [1]. These structures are
considered to arise from the change in thelocal density of states (LDOS) below the
STM tip owing to the vibration [1]. Using
first-principles calculations, we examinedthe variation in LDOS due to adiabaticin-plane displacement of an adsorbed O
atom.
We employed the program package‘Vienna Ab initio Simulation Package’(VASP) [2,3] on systems B and C.

5

0

TB
Hyb

-5

-10



M

Fig. 2 Band dispersions on the  - Mline for the hybrid density-functional method (Hyb) and thetight- binding method (TB).

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

161

Fig. 3 Optimized slab structure of Op(2x1) Ni(110) surface. The slab iscomposed of 21 Ni atom layers and anadsorbed O atom at each surface.

0.15

O atompy-projectedEF

Majority spin

0.3Å disp.

0.1

opDOS

(2) Electronic structure of Ni(110)-(2x1) O
surface [5]Last year, by means of the generalized
gradient approximation, we investigated
the ground state of a proposed promising
structure, namely, the missing-row
reconstructed O p(2x1)/Ni(110) surface.
We optimized a slab composed of 11 Ni
atom layers and an O atom adsorbed ateach surface. This year, for a 21 Ni atom-layer slab, we treated phonon vibration
adiabatically, and examined the change inthe orbital-projected DOS (op-DOS) at
each atom when O atoms are displaced inthesurface-parallel
direction.
We
optimized the structure when the distance
between the O atom and the Ni atom
numbered 40 (see Fig. 3) in the y direction
is reduced by a certain length and fixed.
The height of the O atom measured fromthe No.40 Ni atom is 0.29Å in the groundstate. As the O atom gets closer to theNo.40 Ni atom by 0.3Å, this height rises
to 0.71Å. We pay attention to p orbitals of
the O atom and d orbitals of Ni atoms. We
analyzed the variation in the op-DOS ateach atom due to O-atom displacement.
Here, we present a part of our results for
majorityspin
originatingfromferromagnetic Ni. Figure 4 exhibits thepy-projected DOS at the O atom which isquite important in the STM experimentwith the tip placed right above the O atom.
The broken curve marked ‘GS’ and thefull curve labelled as ‘0.3Ådisp’ display
the results for the ground state and for 0.3Å displacement in the y direction,
respectively. The peak around the Fermi
level EF shifts to the higher energy side,and the peak intensity increases with
O-atom displacement. The peak position
reaches EF at 0.3Ådisplacement. The peakin the py-projected DOS for minority spin
also shows a similar shift to the higher
energy side. Our analysis including
d-orbital-projected DOS at Ni atoms
indicated that approach of the O atom to
the No.40 Ni atom leads to stronger
hybridization between the py orbital of the
O atom and the dyz orbital of the Ni atom.
The above peak shift implies that thephonon vibration affects the STM lightemission through the change in opDOS.

GS

0.05

0
-3

-2

-1

0

1

2

3

E (eV)
Fig. 4 py-orbital-projected density ofstates at the adsorbed O atom for the
ground state and for O-atom
displacement by 0.3Å.
References[1] Y. Uehara, T. Inaoka, T. Nishio, and
S. Katano: J. Appl. Phys. 123 (2018) 224302(8 pages).
[2] G. Kresse and J. Hafner: Phys. Rev. B 47
(1993) 558-561.
[3] G. Kresse and J. Furthmüller: Comput. Mat.
Sci. 6 (1996) 15-50.
[4] T. Inaoka and M. Furugen: unpublished.
[5] T. Inaoka and Y. Uehara: to be prepared.

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Atomic and electronic structures of intermetallic
compound catalysts
Kazuki NOZAWA
Department of Physics and Astronomy, Kagoshima University
1-21-35, Korimoto, Kagoshima 890-0065

In this fiscal year we have studied theinitial stage of oxidation of Ni3 Al(210) and
PdZn(111) surfaces. All calculations are caried
out using VASP with the PAW method and the
PBE exchange-correlation functional.
It was reported that Ni3 Al is highly active
for hydrogen production from methanol andmethane, and its catalytic performance is considered to be attributed to the selective oxidation and hydroxylation of Al and the formation of metallic Ni particles at low oxygen
partial pressures[1]. An X-ray photoelectron
spectroscopy study shows Al oxide is formed
preferentially in the beginning of the oxidation process, and Ni oxides start to form at
1.6 ML oxygen coverage[2]. We first searched
for the stable adsorption sites at 0.25 and 0.5
ML. In both cases, it turned out that the moststable adsorption site is a pseud-threefold sitesurrounded by two Al atom at the top layer
and one Ni atom at the second layer. The adsorption geometry is similar to the result reported for NiAl(110)[3], but this structure isnot consistent with the XPS experiment showing no sign of Ni oxides formation at this coverage. Inspired by the previous study[3], we introduced some antisite defects in the oxidized
surface, and it is found that antisite defect stabilizes the surface when they form a specificstructure. According to the simulated STM
images using the Tersoﬀ-Hamann approximation, this structure shows a unique image easily
distinguished from other structures with diﬀerent antisite arrangement or without the defect.

Although pure Pd is not active for methanol
steam reforming (MSR), PdZn exhibits comparable catalytic activity and selectivity to theconventional Cu catalyst in MSR. Recently,
some groups reported that ZnO formed during
the reaction is essential for the catalytic performance of PdZn. However, this is not straightforward because Zn has no d-state around the
Fermi level implying the chemical inactivity of
ZnO. We first determined the stable adsorption
structure of oxygen on PdZn(111), and investigated the electronic structure of this system.
We previously reported that bulk PdZn has asimilar electronic structure to Cu[5], but thePd 4d-band of PdZn is broadened when oxygen is adsorbed. It was also found that Zn-dstates appear below the Fermi level when oxygen adsorbs on the most stable site.

References[1] D. H. Chun et al., J. Catal. 243 (2006)99,
Y. Xu et al., J. Phys. Chem. C 114(2010))6047.
[2] Y. Xu et al., Appl. Surf. Sci., 39 (2017)18.
[3] A. Y. Lozovoi et al., Phys. Rev. Lett., 85(2000)610.
[4] K.
Yamaguchi,
Master(Kagoshima University, 2020).

Thesis[5] A. P. Tsai et al., Acc. Chem. Res. 50(2017)2879.

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Switching of magnetism via modifying phase shift ofquantum-well states by tailoring the interface
electronic structure
Shunsuke SAKURAGI
Institute for Solid State Physics, University of Tokyo
Kashiwa-no-ha, Kashiwa, Chiba 277-8581

In this project, we expanded Phase modelfor the Quantum-well states (QWs), and suggested the method to control the QW induced
ferromagnetism in Pd(100) by changing scattering phase shift. Then, we verified this theory using density functional theoretical (DFT)
calculation [1].
The following Phase model, describing the
QWs, indicates the conditions under which astanding wave can exist:

electrons, phase shift Φ of the QWs might depend on kx , ky , and ϵ. Thus, it is necessary to
expand the phase model to include kx and ky(i.e. the wave number of the in-plane directionk∥ ) dependencies.
First, kz (n) = (2πn − Φ) /2d is defined fromeq. (1). Then, the n-th energy level of()
Pd(100) film quantum well ϵQW n, k∥ can beobtained from the Pd bulk energy band structure ϵ(kz , k∥ ) as

2kz d + Φ = 2πn,()()ϵQW n, k∥ = ϵ kz (n), k∥ ,(1)where kz is the confined wave number, d is thefilm thickness, Φ is the scattering phase shift at
surface and interface, and n is an integer quantum number. Previous experiments and DFT
calculations showed that the period of oscillation by modification of magnetic properties
via QWs is expressed as p = 1/kF z , where pis the period of oscillation (where thickness ofthe film is d) and kF z is the vertical Fermi wave
number i.e. the Fermi wave number of the confined band. This and eq. (1) indicate that theconfined wave number kz reaches Fermi energy
periodically depending on the film thickness dand the phase shift Φ is unrelated to the periodof oscillation.
Previous DFT calculations and experiments
predicted that dxz,yz electrons are confined at
the QWs of Pd(100) films, and this induces ferromagnetism in Pd(100) ultrathin films. These
orbital characters express one dimensional dispersion in the in-plane direction. For these

163

(2)

where k∥ = (kx , ky ) is the in-plane wave vector
because the band dispersion of the QWs is a
projection of the specific bulk band. Then, thebinding energy of the quantum-well state ϵQW
in Pd(100) can be described by expanding ϵQWaround the Fermi energy as
(
)
)
∂ϵ (
ϵQW n, k∥ ∼ ϵF + [kz (n) − kFz ]kFz , kF∥
∂kz
)
∂ϵ (
+ ∆k∥ ·
kFz , kF∥ ,∂k∥(3)
where kF∥ is the in-plane Fermi wave vector,()∆k∥ = k∥ − kF∥ , and ϵF = ϵ kFz , kF∥ .
Considering Pd bulk band dispersion, dispersion of dxz,yz has a flat shape around Γpoint and zone edges. Therefore, in Pd(100)film, the following relation is satisfied:)∂ϵ (kFz , kF∥ ∼ 0.
∂k∥

(4)

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

According to eq. (5), this means that()ϵQW n, k∥ almost coincides with the Fermi
energy ϵF being independent of k∥ , if kz (n)matches kFz . Then the density of states at the
Fermi energy D(ϵF ) diverges and induces ferromagnetism from the standpoint of the Stonercriterion. The condition kz (n) = kFz leads tooscillatory appearance of ferromagnetism withthe periodicity p depending on the film thickness d.
Now we extend the theory above as shallbe discussed later, the phase shift Φ generally depends on k∥ . If we permit such k∥ dependence for Φ, kz (n) also depends on k∥ .
()
Since kz (n, k∥ ) = 2πn − Φ(k∥ ) /2d eq. (5)must be modified into()ϵQW n, k∥ ∼ ϵF[] ∂ϵ ()+ kz (n, kF∥ ) − kFz
kFz , kF∥
∂kz
(
)
∂ϵ
(5)
kFz , kF∥
+ ∆k∥ ·
∂k∥
)
∂kz
∂ϵ (
+ ∆k∥ ·
kFz , kF∥ ,(n, kF∥ )∂k∥∂kztransition metals on Pd(100) films. In addition, if the d-electron band of a stacking layer
appears near the Fermi energy at S-point, magnetic change via modifying phase shift might
be clearly observed, as indicated in eq. (5).
The present DFT calculation using Phase/0
code [2] well verified the above theory [1]. The
electronic states of Au stacked Pd film weremodified by changing the Au-Pd layer distance, and the QW induced ferromagnetism
was controlled. Contrastingly, we observedthat stacking of Al, which contains only selectrons around Fermi energy, cannot modify the shape of the band dispersion of delectron QWs because there is no hybridization between the s- and d-electrons. We see
above behaviour from the calculated band dispersion and the shape of wave function. Ourfindings suggest a mechanism for controllingmagnetism using modification of interface electronic states in metal-nano structures.

Because of the fourth term on the right hand()
side of eq. (7), ϵQW n, k∥ is no longer theconstant for k∥ and the divergence of D(ϵF )does not occur often, even when kz (n, kF∥ )matches kFz and eq. (6) is satisfied. Furthermore, the divergence of D(ϵF ) can be promoted
if we appropriately modify the k∥ -dependenceof Φ even when kz (n, kF∥ ) does not match kFz
or eq. (6) is not satisfied. Thus, we can expect that a fine control of the k∥ -dependenceof phase shift Φ can reduce the magnetism in asimilar way to induce the magnetism for nonmagnetic materials.
In the case of quantum confinement of Pd
dxz,yz electrons, which we discussed in this paper, the hybridization between the d-electron
wave function of the stacking layer and Pd atthe zone edge (S-point) is intrinsically important for producing a flat band. Because typical 3, 4, 5d transition metals forming fcc structure have d-electron bands around the S-point,
this eﬀect generally occurs by stacking of these[1] Shunsuke Sakuragi, Hiroyuki Kageshima,
and Tetsuya Sato : Phys. Rev. B. 101(2020) 014410.

164

References[2] https://azuma.nims.go.jp/software/phaseActivity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Stability of vacancy cluster and interaction with impurities intungsten lattice
Kazuhito Ohsawa
Institute for Applied Mechanics,
Kyushu University, Kasuga-koen, Kasuga, Fukuoka 816-8580

Introduction

Simulation method

The study of lattice defects in tungsten (W)The binding energies of the vacancy clusters

are important issue in the field of fusion reactor

were calculated in terms of first-principle

because W is one of the plausible plasma facing

calculations based on density functional theory.

materials (PFMs). Usually, hydrogen (H) and H

We used the Vienna ab-initio simulation package

isotopes seldom dissolve in W. However, H(VASP). A large simulation cell, composed of

atoms are trapped in the vacancy-type lattice

6x6x6 bcc lattice (432 atoms), were used in

defects (vacancy clusters etc.) created in theorder to reduce the effects of periodic boundary

irradiation circumstance. In particular, tritium

condition imposed on the simulation cell. The(T) retention in the PFM is one of the serious

cut-off energy of plane wave was 520eV.

problem associated with fusion reactor because

The

T is radioisotope whose half-life is 12 years. So,

composed of n mono-vacancies Vn was defined

the stability and binding energy of the vacancy

Eb(Vn)=nE[V]-{E[Vn]+(n-1)E[P]},clusters in the bulk W were investigated bywhere E is cohesive energy of the supercell andsimulations and experiments.

P indicates perfect lattice of W. Positive binding

bindingenergyofvacancycluster

Small vacancy clusters in the W lattice has

energy corresponds to attractive interaction.

been reported to be unstable by the first-

Similarly, the binding energy of vacancy cluster

principle calculations. On the other hand, suchcontaining an oxygen VnO issmall clusters and their growth to larger clusters

Eb(VnO)=

were observed in positron annihilation lifetime

E[VO]+(n-1)E[V]-{E[VnO]+(n-1)E[P]}.

measurements. In the present work, we

Results

investigate the reason why the small vacancy
clusters exist in the W lattice. The vacancy

We investigated the most stable structure ofclusters are stabilized by impurities. In particular,

vacancy clusters composed of n mono-vacancies

they are greatly stabilized by the presence of

without and with an oxygen ( n ≤ 6 ). We

oxygen.

examined di-vacancy V2 in the first (1nn),

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Discussion

second (2nn), and third (3nn) nearest neighborconfigurations. The di-vacancy in the 1nn

Growth of vacancy cluster in W lattice wasconfiguration is the most stable among them.

observed in the positron annihilation lifetime

However, small vacancy clusters, V2 and V3, aremeasurements but the vacancy clusters wereenergetically unstable compared with isolated

expected to be energetically unstable in the first-

mono-vacancies, as shown in Fig. 1. On theprinciple

other hand, larger vacancy clusters, Vn ( n ≥ 4 ),stabilization effects by impurities contained inare stable. Therefore, if V4 were nucleated in thethe W specimen. Even if high purity metalbulk W, the vacancy cluster growth would

specimen were prepared, some kinds ofspontaneously occur.

impurities would be inevitably contained.

calculations.

We

examinedtheThe presence of impurities in W lattice

Carbon, nitrogen, and oxygen are the typicalcontributes to the stabilization of vacancy

inevitable impurities in the actual metals.

clusters. Fig. 2 shows the most stable structure

Actually, vacancy clusters are greatly stabilizedof vacancy clusters with an oxygen VnO. The

by the presence of such impurities. Besides, themost stable structure of V2O is the 2nn

diffusivity and binding energy to a mono-configuration, which is different from thatvacancy of oxygen in the W lattice arewithout an oxygen V2. According to Fig. 1, allremarkably

vacancy clusters trapping an oxygen are stable

impurities. The presence of oxygen is the mostand the binding energy increases as a function ofplausible candidate to explain the vacancy

the number of vacancies composed of thecluster growth observed in the positron

vacancy clusters.

annihilation lifetime measurements.

larger,compared

with

other

Fig. 2: Schematic view of the most stable structure of
Fig. 1: Binding energies of vacancy

vacancy clusters trapping an oxygen (VnO). The doted

clusters without and with an oxygen,circles indicate positions of mono-vacancies in bcc W(Vn and VnO).

lattice.

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First principles study on static structure of glass materials
Akihide KOURA
Student Affairs Department,
Kumamoto University, Kurokami, Kumamoto, Kumamoto 860-8555
Cu2GeTe3 (CGT) is one of fast phaseof number of ring to that from the experimenttransition materials. This material changes[1] was obtained [3]. This result shows that the

between crystalline and amorphous phases

distribution of six-membered ring is higher thanquickly like Ge2Sb2Te5. In order to clarify thethat by Chen et al. [2]. The coexistence of 3+5

phase

many

and distorted 6 membered rings would enhance

experimental and theoretical studies were

the fast phase transition between crystal andcarried out so far. From results of anomalous x-

amorphous phases.

transition

mechanism,ray scattering and extended x-ray absorption
fine structure experiments, the local andReferencesintermediate range structures of glass were

[1] J. R. Stellhorn, B. Paulus, S. Hosokawa, W.-

preserved structural motifs of the crystal [1].

C. Pilgrim, N. Boudet, N. Blanc, and Y. Sutou:

However, the ring structure from theoreticalarxiv:1908.07297v1 [cond-mat.mtrl-sci] (2019).

study [2] was different from the experimental[2] N.-K. Chen, X.-B. Li, X.-P. Wang, M.-J.

result [1]. In order to clarify the structure of

Xia, S.-Y. Xie, H.-Y. Wang, Z. Song, S. Zhanga,

amorphous CGT, we have performed ab initio

H.-B. Suna: Acta Matter. 90 (2015) 88.

molecular dynamics simulations.

[3] A. Koura and F. Shimojo: J. Phys.: Condens.
Matter 32 (2020) 244001.

In this study, we made two amorphousstates, which were called a1 and a2 amorphousstates. Figures 1 shows the distribution of
number of M-membered ring 𝑃𝑃(𝑀𝑀) [3]. In the
crystalline state, there are only six-memberedrings. In the amorphous state, some sixmembered rings are distorted from 6 to 3+5rings, and distorted six-membered rings also
remain in the amorphous state [1]. Using ring

Fig. 1 The distribution of number of M-memberedanalysis method for our ab initio molecularring 𝑃𝑃(𝑀𝑀) [3].

dynamics simulations, the similar distribution

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Graphene-based Symmetric and Non-Symmetric
Magnetoresistive Junctions
Arqum Hashmi
Center for Computational Sciences,
University of Tsukuba, Tsukuba, Ibaraki 305–8577, Japan
We have studied the structural, magnetic, andspectraspin-dependent transport properties of Graphene

indicating

lowcontact resistanceirrespective of the electrode material.

based MTJs using massive parallel computer
simulations. Gr layer is sandwiched between
ferromagnetic

electrodes.

Typical Dirac cone feature of Gr is not preserved
upon the formation of MTJ and Gr derived 𝜋Furthermore, the influence of different

states near the Fermi level was strongly

stacking of electrode layers on transport

hybridized with the 𝑑𝑧 2 orbital of the Ni and Co

properties is also checked although not muchsurfaces. APC was found to be stable in the Gr-

difference is observed in conductance spectra.

based ML junctions and distinct hybridization ofBoth symmetric and non-symmetric junctions

the Gr 𝜋 states are observed with symmetric andexhibit distinctive selection rules due to thenon-symmetric junctions. Spin filtering is quite

incompatibility of wave functions of electrodes.

sensitive to the electrode materials. The

Our comparative study reveals the effect ofsymmetric junction has higher TMR ratio

various electrode materials on spin transportcompared to non-symmetric junction.

property that can help to develop Gr-based highThe

highest TMR ratio

observed in

TMR ratio devices.

symmetric junction is 13.60%, while it is 8.26%

Referencesin non-symmetric Gr based junction. Gr based[1] A. Hashmi, K. Nakanishi, T. Ono: J. Phys.

junctions displayed the higher transmission

Soc. Jpn. 89, 034708 (2020).

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Local physical quantities analysis based on thequantum field theory in material surface
Masahiro FUKUDA
Institute for Solid State Physics, University of Tokyo
Kashiwa-no-ha, Kashiwa, Chiba 277-8581

region between the surface and the Si tip are
positive (tensile stress) and the eigenvectors
form the spindle structure [1], which visualizes
a covalent bonding. In the future work, moredetail analysis will give a deep understandingof chemical bond formation between a material
surface and a molecular cluster.
14

0.001

13

0

12
−0.00111y (Å)

The local physical quantities, which is defined in the framework of quantum field theory (energy-momentum tensor density, current
density, chiral current density, and so on), aresignificant to understand the fundamental aspect of nature of materials. In particular, since
surface materials and two dimensional materials may have physical or chemical properties
which cannot be explained by bulk feature insolids, it is important not only to evaluate theenergy of the whole system and band structures but also to investigate the local physicalproperties.

10−0.0029−0.0038

In the previous work, the local physicalquantities in molecular systems have been investigated by using a post-process calculationfrom wave packets obtained by molecular orbital method [1].
In this project, we developed a program code
which enables us to calculate local physicalquantities as a post-process calculation from
OpenMX [2] (DFT calculation program code)in order to evaluate the local physical quantities in large periodic systems. It supports
OpenMP/MPI parallelization to handle large
system calculations.
The physical and chemical nature around√√the interaction region between a 7 × 7
Si(111) surface and a Si cluster (a model ofatomic force microscopy tip), were investigatedas a demonstration. The system is a periodic
system including 402 atoms in a unit cell. The
Fig. 1 shows that the maximum eigenvalues ofthe electronic stress tensor density around the7−0.0046−0.005
0

2

4

6

8
x (Å)

10

12

14

Figure 1: Distribution of maximum eigenvalues and eigenvectors of the electronic stresstensor density and zero surface of the electronic kinetic energy density in the region be√√
tween Si tip and 7 × 7 Si(111) surface.

References[1] A. Tachibana, Journal of Chemical
Physics, 115, 3497 (2001); A. Tachibana,“New Aspects of Quantum Electrodynamics”, Springer (2017); M. Fukuda,
K. Soga, M. Senami, and A. Tachibana,Int. J. Quant. Chem., 116, 920 (2016).
[2] OpenMX, http://www.openmx-square.org/.

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First principle simulation on reactions and electronic
structures of new material synthesizedfrom organic molecules
Toshihiro SHIMADA, Wei LIU, Ichiro YAMANE, Taro NAGAHAMA, Takashi YANASE
Division of Applied Chemistry, Faculty of Engineering
Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8628
We have experimentally synthesized newi]phenazine (DDQP) under pressure[4].

Itcarbon materials by applying high temperatureshows Diels-Alder type intermolecular reaction.

and / or high pressure to organic molecules.

The electronic band structures showed three-

Using this ISSP supercomputer time, we havedimensional dispersion (Fig.3).

studied the reactions and electronic structuresof these materials[1-3]. We present some of theexamples.
Figure 1 shows optimized structure of
Fig. 2: Pressure-induced bond formation
reaction of DDQP revealed by calculation.

graphitic carbon nitride (g-C3N4) and a nitrogenmolecule.
based

We developed a liquid nitrogenquenchingprocesstopreparephotocatalyst materials with atomic layer
separated. This process greatly improved thephotocaltalytic activity of the material. This
calculation supports N2 molecule can beintercalated to g-C3N4, which assists exfoliationof the layers.
Fig.3 Band dispersion of pressure-polymerized
DDQP.
References[1] W. Liu, T. Shimada et al.: Journal of Colloid& Interface Science 567 (2020) 369.
[2] W. Liu, T. Shimada et al.: International J. of
Hydrogen Enegry 44 (2020) 8444.
[3] W. Liu, T. Shimada et al.: Applied Surface
Science499(2020)
143901.

Fig. 1: Optimized crystal structure of twolayered g-C3N4 and N2-inserted interlayer of gC3N4.
Figure 2 shows optimized structure ofdibenzo[a,c]dibenzo[5,6:7,8]quinoxalino[2,3-170Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Developments of a derivation method of a low-energy
models in ﬁrst-principles
Hirofumi Sakakibara
Department of Applied Mathematics and Physics, Tottori university, Tottori 680-8552, JapanFirst principles calculation is useful method
to determine the electronic structure. Most of
the ﬁrst-principles assumes local density approximation(LDA) in density functional theory, however, LDA usually underestimatesband gaps of semiconductor. This underestimation is overcome by the consideration of theeﬀect of particle excitation. The quasiparticle
self-consistent GW method (QSGW) is a ﬁrstprinciples method to determine the one-body
Hamiltonian H0 taking into such excitation effects account.
However, even QSGW improves the size ofband gaps compared to LDA, there still havesome errors. For example, QSGW systematically overestimates the size of band gaps [1].
This overestimation is investigated from theviewpoint of vertex correction on the proper
polarization P by Shishkin et al.. Their work
has shown that such vertex corrections improve the dielectric constant very well. However, their method is somewhat ambiguous andconsuming for computing resource.
To solve this problem, we introduced amethod to numerically estimate the vertex
correction[3]. Our method is to determine thevertex correction by a self-consistent calculation applying static electric ﬁelds to obtainthe linear response of electronic density. On
this purpose, we implemented the combination of QSGW and eﬀective screening medium
method (ESM, Ref. [4]). Namely, we calculate a slab model applying an external electrostatic potential varying along z axis. Fig. 1 isa schematic picture of ESM method applied to

MgO slab. Then, it is better that slabs are as
thick as possible because we intend to estimate
the vertex correction of bulk materials.
To access the eﬀectiveness of our method, we
calculate optical dielectric constant ϵ∞ , where
ϵ∞ is measured by the slope of the electrostatic potential. In Tab.1, we compare ϵ∞ ofbulk calculation in the random phase approximation (RPA) and the QSGW+ESM method.
Here we applied generalized gradient approximation(GGA) instead of LDA. We have chosen ﬁve simple ionic materials LF, KF, NaCl,
MgO, and CaO for the examination system.
We can ﬁnd that QSGW+ESM is in an extremely good agreement with experiments. It
is interesting that LDA(GGA)+ESM method
does not necessarily improve the value of ϵ∞ .
This may because that the exchange eﬀect
taken in the exchange correlation functional of
GGA is not accurate.
In Tab.1, the underestimation of ϵ∞ of bulk
system corresponds to the overestimation ofband gaps. It is also found that the material
dependence of the vertex corrections is not solarge. From this result, some hybrid methods
between QSGW and GGA may be applicable
instead of present QSGW+ESM method as acompromise. In the previous work by Deguchi
et al., a hybrid method named QSGW80 (hybridization between QSGW and GGA at theratio 8:2) has shown good agreements with experiments. Therefore, the systematic overestimation of QSGW may be improved by considering vertex corrections, which are eﬀectively
taken into account in QSGW80.

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Table 1: Calculated optical dielectric constant
ϵ∞ . ‘RPA’ are in bulk calculations. ‘Slab’ arecalculated from the slab models in the settingof Fig.1.
RPA Slab Experiments
GGA
1.95 2.01
LiF
1.96
QSGW 1.67 1.94
GGA
1.96 1.94
KF
1.85
QSGW 1.68 1.86
GGA
2.33 2.42
NaCl
2.34
QSGW 1.92 2.31
GGA
2.96 3.09
MgO
2.96
QSGW 2.50 2.37
2.91
GGA
3.59 3.68
CaO
3.33
QSGW 2.88 2.68
3.31

References[1] D. Deguchi, K. Sato, H. Kino, and T.
Kotani, Jpn. J. Appl. Phys. 55, 051201(2016).
Figure 1: Schematic picture of ESM method.
The upper panel shows the electrostatic potential when the diﬀerence bias voltages at
z = 30, −30 are 0.0 Ry and 0.2, respectively.
The lower panel shows the diﬀerence between
the potentials among these to cases. The optical dielectric constant ϵ∞ is measured from theratio of the slope between vacuum and slab region, as indicated in the lower panel.

[2] M. Shishkin, M. Marsman, and G. Kresse,
Phys. Rev. Lett. 99, 246403 (2007).
[3] H. Sakakibara, T. Kotani, M. Obata. andT. Oda, Phys. Rev. B (2020)(in press).
[4] M. Otani and O. Sugino, Phys. Rev. B 73,
115407 (2006).

To summarize,
we have developed
QSGW+ESM method to determine thevertex correction in QSGW. Our method
can calculate dielectric function in a good
agreement with experimental observation.
The future problem is to derive a low-energy
model Hamiltonian based on the one-body
Hamiltonian H0 derived from QSGW or
QSGW80.

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles calculation of
the higher-order phonon-phonon scattering strength
Haruhiko DEKURA
Geodynamics Research Center
Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan
Phonon-phonon interaction is a key parameter that describes thermal transport properties insolids [e.g., 1]. First-principles calculation of lifetimes of phonon quasiparticles owing to theinteraction is computationally demanding for precise determination of phonon thermal conductivity.
From the theoretical point of view for the many-body interacting systems, the phonon-phonon
scattering rate is approximately inversely proportional to the imaginary part of the phonon selfenergy [1]. Most density-functional theoretic calculations for determining phonon thermal
conductivity is limited to the lowest order phonon-phonon interaction. The higher-orderanharmonicity is likely to contribute to the conductivity particularly at temperatures higher than the
Debye temperature as would be seen in the deep Earth’s interior [2]. The primary purpose of thisproject in this period is to try to establish a roadmap as a first step for the accurate determination ofphonon thermal conductivity at high temperature considering the effect of higher-order phononphonon scattering. Silicon was selected for this purpose for its simplicity.
We have performed the density-functional theoretic calculations based on the plane-wave basis
pseudopotential method within the local density approximation. In order to extract harmonic andanharmonic force constants (AFC), the higher-order derivatives of the adiabatic potential surface
were determined by the self-consistent field calculations for the structures in which some atoms areslightly shifted from the equilibrium positions. The 3×3×3 cubic supercell containing 216 atoms in
total was primarily adopted in this study to capture the anharmonic interaction.
During this period, by the use of supercomputer (system B) in ISSP, we have launched test
calculations to check the computational conditions regarding the size dependency in the AFC,
convergency in the with respect to the simulation cell size of the mesh to sample the phonon wave
number vectors. Also, the self-consistent field calculations to extract AFC using the optimum
condition have been almost finished. In parallel, post-processors to calculate the total phononphonon scattering rate including up to the fourth-order anharmonicity and thermal conductivity
based on the Boltzmann transport equation have been almost developed. Using the complete data set

173

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyoobtained in this study, we will make a thorough examination of the effect of the higher-orderscattering on the lattice thermal conductivity at high temperatures. After the establishment of theprocedure to compute the thermal conductivity, we plan the application of the developed technique
to Earth’s minerals under very high-temperature conditions [2].

References[1] G. K. Horton, A.A. Maradudin, eds., Dynamical Properties of Solids: Crystalline solids,
fundamentals (North-Holland, Amsterdam), (1974).
[2] 出倉春彦, 高圧力の科学と技術, (2020), in press.

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Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical Study on the Aggregation-Induced Emission
Norifumi YAMAMOTO
Department of Applied Chemistry,
Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016
In this study, the mechanism of aggregation-states are degenerated at a conformation withinduced emission (AIE) of diphenyldibenzo-

the twist angle of 90° around its ethylenic C=C

fulvene (DPDBF) was studied theoretically.

bond,

The DPDBF has been known to exhibit

which

can

lead

the

fluorescencequenching of DPDBF molecule in dilute

the AIE, which is non-emissive in dilute

solutions.

solutions but becomes highly emissive in solid

The free-energy profile of the photoor aggregates [1]. In this study, the AIE of

isomerization of DPDBF in condensed phase

DPDBF was investigated by using ab initio

was computed using MD simulations based onelectronic structure calculations, together with

an empirical force field representation. All MD

molecular dynamics (MD) simulations.

simulations of DPDBF presented herein wereIn order to elucidate the characteristics ofthepotential

for

the

The results of MD simulations revealed

DPDBF,

thethat DPDBF tends to assemble in close contact,

minimum energy paths for the photo relaxation

where the ethylenic C=C bond rotation isprocess of DPDBF in an isolated phase weremarkedly restricted in aggregates, preventing

investigated using ab initio electronic structure

the fluorescence quenching via the S0/S1

calculations. The spin-flip approach within theconical intersection; DPDBF in acetonitrile

time-dependent density functional theory (SF-solution, however, proceeds a barrierless non-

TDDFT) method was used to compute theradiative transition. These results gave a clear

potential energies and analytical gradients for

picture of the AIE of DPDBF, which is agree

the electronic ground (S0) and first excited (S1)with that of a cyanostilbene derivative [2].

photochemicalenergyprofilesprocessesofcarried out using the GROMACS program.

states of the molecule. All electronic structure
calculations of DPDBF presented herein wereReferences

performed using the GAMESS program.

[1] Tong, H, et al., J. Phys. Chem. C, Vol. 111,

The results of SF-TDDFT calculations

pp. 2287−2294 (2007).

showed that the potential energies of DPDBF[2] Yamamoto, N., J. Phys. Chem. C, Vol. 122,for electronic ground (S0) and first excited (S1)

pp. 12434−12440 (2018).

175

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Benchmark of density functional theory forsuperconductors in elemental materials
Mitsuaki Kawamura
Institute for Solid State Physics, University of Tokyo
Kashiwa-no-ha, Kashiwa, Chiba 277-8581

1

introduction

The first-principles calculation of the superconducting properties, such as the transition
temperature (Tc ) and the gap function, isof great interest to explore new materials aswell as to understand the physical mechanism of known superconductors. Density functional theory for superconductors (SCDFT)
is one of the frameworks for such calculations; this method enables us to perform fully
non-empirical simulations in the superconducting phases at a reasonable computationalcost. In SCDFT, we can treat the electronphonon interaction, the electron-electron repulsion, the spin-orbit interaction (SOI) [1],and the spin-fluctuation (SF)-mediated interaction in a first-principles manner.
However, the accuracy of the current approximated functional of SCDFT and the effects of SOI and SF have not been verified
systematically, although such verification ishighly desirable before applying this method
to a wide range of materials. Such a highthroughput calculation was performed, forexample, in the exploration of low-thermalconductivity compounds using first-principles
calculations together with the materials informatics. A benchmark is also a useful tool used
to find a guideline for improving the theory andapproximations of the superconducting density
functional. For this purpose, in this project,
we are presenting the benchmark calculationsof SCDFT [2]. As benchmark targets, we havechosen the simplest superconducting, and non-superconducting materials, i.e., elemental materials; each material in this group comprises asingle element. The particular computational
cost is relatively low because most materials
in this group contain only one or two atoms in
the unit cell. Moreover, we can see the eﬀects
of the chemical diﬀerence and the strength of
the SOI of each element.

2

methodWithin SCDFT, Tc is obtained as a temperature where the following Kohn-Sham superconducting gap ∆nk becomes zero at all theband n and wavenumber k:
1 ∑ Knkn′ k′ (ξnk , ξn′ k′ )2 ′ ′ 1 + Znk (ξnk )
nk
√

2
2
ξ
+
∆
′
′
′
′
′
′
∆n k
nk
nk
,
×√
tanh 
2T
ξ 2 + ∆2

∆nk = −n′ k′

n ′ k′(1)
where ξnk is the Kohn-Sham eigenvalue measured from the Fermi level (εF ) at the band index n and wave-number k. ξnk is obtained bysolving the spinor Kohn-Sham equation. The
integration kernel Knkn′ k′ (ξ, ξ ′ ) indicates thesuperconducting-pair breaking and creating interaction and comprises the following threeterms:
ep′ee′Knkn′ k′ (ξ, ξ ′ ) ≡ Knkn
′ k′ (ξ, ξ ) + Knkn′ k′ (ξ, ξ )sf′+ Knkn′ k′ (ξ, ξ ),

176

(2)

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

namely, the electron-phonon, Coulomb repulsion, and spin-fluctuation kernel, respectively.
However, the renormalization factor Znk (ξnk )comprises only the electron-phonon and spinfluctuation terms as follows.
epsf
Znk (ξ) ≡ Znk(ξ) + Znk
(ξ),

(3)

because the Coulomb-repulsion contribution tothis factor is already included in the KohnSham eigenvalue ξnk .

3

Result and Discussion

We have plotted the computed- andexperimental-Tc in Fig. 1 to visualize theeﬀect by SOI and SF; we can detect thefollowing trends by inspecting this graph: SF
always reduces Tc s for the elemental systems.
This reduction becomes significant for thetransition metals and is crucial to reproduce
the experimental Tc quantitatively. In thetransition metals, the eﬀect of SF weakens
with the increasing of the period numberin the periodic table. The eﬀect of SOI issmall in most cases, excepting Tc, Sn, Re,
Tl, Pb. In these elements, the Fröhlich’s
parameter λ changes drastically by turning on
the SOI. We can reproduce the absence of thesuperconductivity in alkaline, alkaline earth,and noble metals, excepting Pt and Au with
SOI and SF; we have observed small finite Tc
for these two elements; we can reproduce thenon-superconductivity also in Sc by including
SF while we observe Tc = 2.711 K by ignoring
SF. Since Sc has highly localized 3d electrons,
the SF largely reduces Tc . For the group 12
elements (Zn and Cd), Tc s are overestimatedeven if we include SF. For these materials, theSF eﬀect is small because the d orbitals are
fully occupied.

0

1

2 Be
1 Na
2 Mg
13 Al
1K
2 Ca
3 Sc
4 Ti
5V
11 Cu
12 Zn
13 Ga
1 Rb
2 Sr
3Y
4 Zr
5 Nb
6 Mo
7 Tc
8 Ru
9 Rh
10 Pd
11 Ag
12 Cd
13 In
14 Sn
1 Cs
2 Ba
3 La
4 Hf
5 Ta
6W
7 Re
8 Os
9 Ir
10 Pt
11 Au
12 Hg
13 Tl
14 Pb
2
0

3rd row
4th row
SOI+SF :SOI :SF :no SOI/SF :Exp. :

5th row

6th row2

4 6
Tc [K]

8 10 12 14 20 22

Figure 1: Theoretical and experimental Tc s [2].
The vertical axis is the atomic symbol together
with the group of the periodic table. Downward (upward) triangles indicate the Tc s computed with (without) SF. Filled (empty) triangles indicate the Tc s computed with (without)
SOI. “+” indicates the experimental value of
Tc . The plot which ranges from zero to two
Kelvin in the upper panel is magnified into thebottom panel.

M. Kriener, Y. Taguchi, and Y. Tokura,Phys. Rev. B 101, (2020) 014505.
[2] M. Kawamura, Y. Hizume, and T. Ozaki,
Phys. Rev. B 101, (2020) 134511.

References[1] T. Nomoto, M. Kawamura, T. Koretsune, R. Arita, T. Machida, T. Hanaguri,

177

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Simulation of scanning tunneling microscopy
images of graphene ribbons with edges
Junhuan LI, Kenta ARIMA
Graduate School of Engineering, Osaka University, Yamadaoka, Suita, Osaka 565-0871
We are aiming at elucidating local electronic

STATE is based on the density functional

structures of finite-size graphene sheets and their

theory. The exchange and correlation potential is

impact on scanning tunneling microscopy (STM)

described

images. For this purpose, we have started first-

approximation

principles calculations of single-layer graphene(GGA-PBE). We also used both a plane-wave

ribbons possessing either zigzag or armchairbasis set and pseudopotentials. When runningedges by the use of a simulation package named

STATE, we first defined the atomic structure of

STATE (Simulation Tool for Atom TEchnology).

a finite-size graphene. This model as well as

by

the
by

generalized

gradient

Perdew-Burke-Ernzerhof

other parameters were placed as an input file ona supercomputer. The self-consistent field
method was employed, which is an iterative
method that involves selecting a Hamiltonian,solving the Kohn-Sham equation to obtain amore accurate set of orbitals, constructing thepotential for each wave function, and solving the
Fig. 1(a) Structure of single-layer graphene

Kohn-Sham equation again with these until the
results converge. In order to draw a map of local
density of states, an electron density was
integrated over an energy window of 0.05 eV
below the HOMO (Highest Occupied MolecularOrbital). At each (x, y) coordinate, a z-height
possessing the same electron density (1×10-4

Fig. 1(b) Simulated STM image of single-layer/Bohr3) was investigated and its contour map

graphene

was depicted, which is regarded as a simulated
STM image at the sample bias of -0.05 V. We

178

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

used the module (intel/18.0.5.274) for theimage of the surface in Fig. 1(a) at the sample

compilers and mpt/2.16 for MPI library. The set

bias of -0.05V. A brighter area in Fig.1(b)of calculation was usually executed on F4cpu orindicates a higher corrugation, which is caused

F36cpu with suitable nodes in ISSP.

by a higher density of the occupied states. It is

To check both the validity of our parameters

apparent that a hexagonal pattern is formed inin the input file for STATE calculations and thewhich the position of a bright dot coincides withperformance of STATE itself, we first modeledthat of a carbon atom comprising the graphene

an infinite, single-layer graphene. The creatednetwork. Figure 1 insists that the combination ofmodel is shown in Fig.1(a). The cutoff energies

our modeling and parameters with the STATE

were

Ry

software works well. In the next fiscal year, we(GMAXP=20) for the wave functions and theare going to characterize the distribution of local

augmentation charge, respectively. Then we

charge densities near the edges of a graphene

conducted first-principles calculations withinribbon and to unveil its relationship with an

STATE to get the electronic structure of the

STM image around the Fermi level.

36

Ry(GMAX=6)and

400model. Figure 1(b) shows a simulated STM

179

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

An open source code for QUANTUM ESPRESSO to compute
irreducible representations of Bloch wave functions
Seishiro ONO
Institute for Solid State Physics,
The University of Tokyo, Kashiwa-no-ha, Kashiwa, Chiba 277-8581
indicators has been extended to magnetic spacegroups and superconductors [2].
As seen in the preceding paragraphs, it is
helpful to compute irreducible representations
by using DFT. Although the authors of Refs.
[3,4] implemented programs for WIEN2k and
VASP to calculate irreducible representations,these packages need paid licenses. In contrast,
QUANTUM ESPRESSO, a free package for abinitio calculations, can obtain irreducible
representations only for symmorphic spacegroups.
In this work, we developed an open-sourcecode for QUANTUM ESPRESSO to getirreducible representations for all space groups.
In addition to this function, we implemented afunction to automatically compute the ℤ" index
that can diagnose various topological phasessuch as higher-order topological insulators.
Furthermore, we also apply our program toabout 40 magnetic materials. Then, we used thefacilities of the Supercomputer Center to get
wave functions for these materials. We are stillsearching for new topological materials byusing our program and DFT calculations.

Since the remarkable discovery of ℤ!
topological insulators, topological materials
have attracted researchers around the world.
Topological materials host robust surface statesand exhibit unique bulk responses, which could
be leveraged for new low-power devices.
Therefore, discovering various topologicalmaterials is one of the important tasks forengineering.
Given a symmetry setting, establishing
topological invariants that characterize all
possible topological phases is a pending
problem. Furthermore, it is sometimes difficult
to compute topological invariants even when
we know the mathematical definition of
topological invariants. However, when spatial
symmetries exist, it is effortless to diagnose
topological phases by using information of
spatial symmetries. A prototypical example ofthis relation is the Fu-Kane formula, which canevaluate the topological invariant of insulatorsfrom eigenvalues of the inversion symmetry. In
recent years, this idea has been generalized to
all combinations of crystalline symmetries byusing irreducible representations of wave
functions instead of eigenvalues, and thegeneralized theory is called symmetry
indicators [1]. While it does not bring thecomplete classification, this theory is suitable
to discover realistic topological materials. In
fact, this method is a basis of recent
comprehensive surveys of topological materials
among existing databases of inorganic
substances. As a result, thousands of candidatesof topological (crystalline) insulators andsemimetals have been discovered. In addition
to these developments, the theory of symmetry

References[1] H. C. Po, A. Vishwanath, and H. Watanabe,Nat. Commun. 8, 50 (2017).
[2] S. Ono, H. C. Po, and H. Watanabe, Sci.
Adv. 6, eaaz8367 (2020).
[3] F. Tang, et al., Nature, 566, 486-489 (2019).
[4] M. G. Vergoniry, et al., Nature, 566, 480485 (2019).

180

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First Principles Calculation of 2-Dimensional Silicides
Formed on Nickel Surfaces
Tsuneo FUKUDA1 and Ippei KISHIDA2*
1

Department of Physical Electronics and Informatics, Graduate School of Engineering,Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka 558-8585
2
Department of Mechanical and Physical Engineering, Graduate School of Engineering,Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka 558-8585
Metal silicides are indispensable materials
foradvanced

microelectronics.

We

have

recently proposed a new route to form a robust
two-dimensional (2-D) silicide [1,2]. Unlike
conventional thin film silicide formed by

1 nm

depositing metal on the silicon surface, Si was
deposited on a clean metal surface to form

Fig. 1 Typical STM image for a 0.39 ML Si deposited
surface. White square corresponds to the 1×1 unit cell.

silicide. Our recent studies show that robust 2-

top layer. Since the STM image is reflected by

D silicides are formed on Ni(110) and Ni(100)the surface local density of states (LDOS) nearsurfaces due to the large diffusion asymmetry

EF, the embedded Si reduces the tunnelingbetween Si in bulk metal and metals in bulk Si

current without the large LDOS due to Ni 3d[1,2]. However, the lack of theoretical support

bands, making it a dark site. Therefore, theclearly undermines the significance of ourdiscrimination between individual Si and Ni is

research findings.

fairly straightforward, but the relationshipbetween Si and Ni is unsolved.

First-principles calculation code VASP wasexperimentally

Therefore, the first principle calculation was

obtained 2-D atomic structure with theoretical

performed in this system. The calculation

simulations. A typical scanning tunnelingparameters are shown in Table 1. Before

microscope (STM) image of a Si-deposited

performing

Ni(100) surface is shown in Fig. 1 [2]. The

evaluated the ground state energies of Ni and Si

initial clean surface was essentially a 1×1

atoms, and bulk Ni and Si, respectively.

structure, but many dark sites were formed after

Because of the slow convergence of self-

Si deposition. These dark sites are not due toconsistent electronic states in the surface

structural defects, but Si replaced by Ni in the

structure, we adjusted the mixing parameters as

adoptedtocomparethe181

surfaceslab calculations,weActivity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Table 1 Parameters for present calculation

shown in Table 1 (so-called linear mixing, see

VASP Version
slab geometry

VASP manual). First, all atoms except for the
middle layer has been completely relaxed. Thenvacuum region
k-points
potential
cut off energy
Fermi level smearing

0-8 surface Ni atoms in the top layer were
replaced by Si, and the top 5 layers were fully
optimized. A total of 36 different surface

convergent condition
ion cordinationelectronic states
mixing parameters

configurations were evaluated for 0-1 ML Si
coverage.
In order to compare the formation energy
for different numbers of surface species, we

5.3.5
Ni(100) 2×4 unit
11 layers
2.12 nm16×8×1
PBE [3]350.39 eV
Methfessel & Paxton
σ = 0.12 eV0.01 eV/Ang.
10-5 eVspin-resolved
AMI = 0.02
BMIX = 0.0001
AMIX_MAG = 0.08
BMIX_MAG = 0.0001

evaluated chemical potential as,
𝐸𝑡𝑜𝑡𝑎𝑙 = 𝐸𝑠𝑙𝑎𝑏 − 𝑛𝑁𝑖 𝐸𝑏𝑁𝑖 − 𝑛𝑆𝑖 𝐸𝑏𝑆𝑖 ,N
S

where 𝐸𝑠𝑙𝑎𝑏 is a total energy of a particular slab
structure, 𝑛𝑁𝑖 and 𝑛𝑆𝑖 are respectively numbersof Ni and Si atoms in the slab, and 𝐸𝑏𝑁𝑖 and 𝐸𝑏𝑆𝑖
are respectively bulk cohesive energies for Ni
and Si.
As shown in Fig. 2, the relative energies ofFig. 2 Relative formation energies of Si-embedded
Ni(100) surfaces with various configurations of Si
coverage between 0-1 ML. Inset: The most stableconfigurations with Si coverage of 0.125, 0.25, 0.375,
and 0.5 ML.

various configurations referenced from that for
the Ni(100) surface are plotted as a function of
Si coverage. Negative formation energy meansthat energies of Si embedded structures are

results. As a future study, the displacement

lower than that of the Ni(100). There is aprocess, so-called depressive adsorption, should

negative slope for Si coverage from 0 to 0.5

beML, indicating that Si substitution with Ni issimulations.

revealedbymolecular

dynamics*present address: Nagamori Institute of Actuators,
Kyoto University of Advanced Science, 18
Yamanouchi, Gotanda-Cho, Ukyo-Ku, Kyoto 6158577, Japanenergetically favorable. On the other hand, apositive slope above 0.5 ML means that Si will
be ejected from the structure, which is in good

References

agreement with experimental observations.

[1] T. Fukuda, I. Kishida, and K. Umezawa,
Surf. Sci. 659 (2017) 1.
[2] T. Fukuda, I. Kishida, and K. Umezawa,
Jpn. J. Appl. Phys. in press.
[3] J. P. Perdew, K. Burke, and M. Ernzerhof,
Phys. Rev. Lett. 77, (1996) 3865.

In conclusion, the first-principles study of
two-dimensional Ni silicide formed on Ni (100)is in good agreement with the experimental

182

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles Study of Defects of Magnesium Alloys
Daisuke Matsunaka
Department of Mechanical Systems Engineering,
Shinshu University, 4-17-1 Wakasato, Nagano 380-8553
interatomic potentials.

Magnesium (Mg) has been of increasingly
viewpoint,

One way for improving the limited ductility

because of its low density and relatively highof Mg at room temperature is to activate non-

specific strength. Despite intensive researchbasal slips. In particular, Mg-Y alloy has shown

efforts, there remain various problems to bea significantly enhanced ductility. It has been

overcome; low ductility and low toughness atsuggested that the improvement of ductility wasroom

activeattributed to the reduction of the intrinsic I1

deformation mode under an applied load, thestacking fault (SF) energy by Y addition. We

Schmid factor and the critical resolved shear

investigated defect nucleation in the vicinity ofstress (CRSS) for each deformation mode areahelpful. However, several studies showed thatsimulations. While formation of (11-21) twin

the activated deformation mode under various

was observed under shear stress on (0001)

uniaxial loadings deviated the Schmid’s law

along [11-20], <c+a> partial dislocations were

and their CRSSs were not uniquely determined.

generated with SFs for higher resolved shear

In order to investigate influences of non-glide

stress for pyramidal slips. The dissociationstress on deformation modes, we carried out

reactions of the dislocations at the side ends ofmolecular dynamics (MD) simulations for slips

the I1 SF were energetically evaluated, and itwith <a> Burgers vector under several normal

was implied that nucleation of the <c+a>stress conditions. For basal slip, extended

dislocations on the first-pyramidal planes isdislocations were generated and glided on the

more favorable than on the second-pyramidal

basal planes, irrespective of the applied normal

planes.

stress conditions. In MD simulations of shear

References

deformation for first-pyramidal slip, distinct[1] S. Yoshikawa and D. Matsunaka: Mater.

dislocation gliding was not observed andTrans. 61 (2020) 127.

alternatively (10-11) twin was generated. For[2] S. Yoshikawa and D. Matsunaka: Comp.

prismatic slip, deformation behavior depended

Mater. Sci. 179 (2020) 109

interest

from

the

temperature.

engineeringTo

understandon the applied normal stress as well as

183

pre-existing

intrinsic

I1

SF

by

MD

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles study of magnetoresistance ratios and magnetic anisotropy
in magnetic tunnel junctions
Keisuke MASUDA, Tsuyoshi SUZUKI, and Kenji NAWA
Research Center for Magnetic and Spintronic Materials,
National Institute for Materials Science, Sengen, Tsukuba, Ibaraki 305-0047
Magnetic tunnel junctions (MTJs), where an

barrier is around 10 Å, which is consistent withinsulating tunnel barrier is sandwiched between

experiments. We found that the low RA is

two ferromagnetic electrodes, are the mostattributed to a small band gap in the MGO

practical spintronic devices. The MTJs havebarrier. In addition, our detailed analysis of thevariousnonvolatileelectronic structure clarified that the obtained

magnetic random access memories (MRAMs)

high MR ratio can be understood from theand many types of magnetic sensors includinginterfacial resonance effect [2].

read heads of hard-disk drives. For these

As a second topic, we tried the calculation of

applications, we have several requirements in

MR ratios in unconventional (111)-oriented

the physical properties of MTJs. In the present

MTJs, which have not been examined well sowork, we studied such properties using thefar owing to the successful history in the (001)-

first-principles calculations.

oriented MTJs. By using the first-principles

The spinel oxides AB2O4 can be hopeful

approach mentioned above, we calculated ainsulating tunnel barriers in MTJs. Among

MR ratio of Co/MgO/Co(111) and obtained athem, MgGa2O4 (MGO) has recently attracted

quite high value (>2000%). We found that suchattention because the MGO-based MTJs havea high MR ratio also comes from the interfacial

low resistance-area products (RA) and highresonance effect [3].

applications

such

as

magnetoresistance (MR) ratios [1], both ofwhich are necessary for MRAM and read-head

References

applications. To understand the mechanism of[1] H. Sukegawa et al., Appl. Phys. Lett. 110,such properties, we calculated RA and MR(2017) 122404.

ratiosby[2] K. Nawa, K. Masuda, and Y. Miura, 第 24

combining the density-functional theory (DFT)

回半導体スピン工学の基礎と応用, 東北大学,

and the Landauer formula. As a result, a low

2019 年 12 月.

RA (~0.5 Ωμm2) and a high MR ratio (~200%)[3] K. Masuda, H. Itoh, and Y. Miura, Phys.

were obtained when the thickness of the MGO

Rev. B 101, (2020) 144404.

in

the

Fe/MGO/Fe(001)

MTJ

184

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Study on Carrier Dynamics in Nano Scale Semiconductor
Devices with Machine Learning
Masakazu Muraguchi
Faculty of Engineering, Hokkaido University of Science,
Maeda, Teine, Sapporo 006-8585
We have studied a Machine Learning(ML) approach to make a model of electrontransport process in nanostructures. The
transmission coefficients and timedevelopment of electron density in thenanostructures are computed by timedependent schrödinger equation to provide
training and test datasets to the machinelearning [1,2]. Calculations are performedon the motion of electron wave packets ofdifferent energies in a two-dimensional
nanostructure under random impurity
distribution.
We work on the creation of two
types of predictive models; thetransmission probability of electron
wave packet from the impurity
distribution; the impurity distribution
from the image sequence of electron
density
distributioninthetransmission process. By combining
these predictive models, we expect toachieve a more efficient device design
methodwithtime-dependentcalculation than ever before.
As the ML methods, a Random
Forest (RF) and a Neural Network(NN) are employed for modeling therelationship between the impurity
distributions and the transmission
coefficients of electron. The mean
absolute error is compared to eachmodel. In both methods, it is foundthat the approach of capturing theimpurity distribution as an image
could build a better model than using
simple impurity coordinates as input.
In addition, we investigate thepredictive model for the impurity
distribution from the image sequenceof the time evolution of electron
density as shown in Fig.1. Modelingby convolutional NN is performed,
and the accuracy is compared when
the image sequence is individually
inputted, when the mean of the image
sequence is inputted, and when theimage sequence is inputted with arecurrent network.
x

Propagation Direction
Propagation Directionyxy

Impurity
Potential

Modeling

Electron Density

Impurity Distribution

Fig.1
Modeling
theimpurity
distribution from the image sequence ofthe time evolution of electron density.

References[1] N. Watanabe and M. Tsukada: Phys. Rev.
B 62 (2000) 2914.

[2]. T. Okunishi, Y. Ohtsuka, M. Muraguchi, K.
Takeda, Phys. Rev. B, 75, 24 (2007), 2453141~245314-15.

185

Wavelength selection for the photocleavage of coumarin-caged Dluciferin via quantum chemical calculation
Junko Usukura a,†, Miyabi Hiyama b, Maki Kurata a, Yuji Hazama a,c, Xing-Ping Qiu d,Francoise M. Winnik e,f, Hidefumi Akiyama a,c, Nobuaki Koga gaInstitute for Solid State Physics, University of Tokyo, Kashiwa, Chiba, Japanb

Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japanc

AIST-UTokyo OPERANDO-OIL, Kashiwa, Chiba, JapandDépartement de Chimie, Université de Montréal, Montréal, CanadaeDepartment of Chemistry, University of Helsinki, Helsinki, FinlandfInternational Center for Materials Nanoarchitectonics (MANA), National Institute for Materials
Science (NIMS), Tsukuba, Ibaraki,Activity
Japan
Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyog

Graduate School of Informatics, Nagoya University, Nagoya, Japan†

usukura@issp.u-tokyo.ac.jp

Keywords: firefly, bioluminescence,quantum chemical
calculation, absorption
spectrum
Analysisof absorption
spectrafor caged compounds

in aqueous solution
The firefly luciferin-luciferase system has been widely used as a bioluminescence-imaging probe.
MiyabiHIYAMAandrelease D-luciferins, are needed to
Photolabile caged D-luciferins, which cleave by light trigger
Graduate
Schoolof
ScienceandTechnology,
Gunma
control the initiation and the position of bioluminescent reaction. Recently,
we University,
synthesized a new
Tenjin-cho,
Kiryu,
Gunma
376-8515
photolabile caged D-luciferin, (7-diethylaminocoumarin-4-yl)methyl caged D-luciferin (DEACM-caged
D-luciferin), aiming at rapid photolytic cleavage1. Fig. 1 shows
the chemical structure of DEACM-caged D-luciferin. Its
Coumarin caged-luciferins, which can
genWe found that the peak near 384 nm of theoquantum yield (QY) after irradiation
by a 70 mWcm-2 higherate firefly luciferin (’luciferin’ in this ar- retical absorption spectrum corresponds to thenm) was only 6%, a value
pressure mercury lump (254-600
ticle) by UV photolytic reaction, would be absorption from the ground electronic statemuch lower than that of D-luciferin (41%). Higher QY may be
to understand the firefly biolumines- (S0 ) to the first excited state (S1 ) and that the
wavelengthis selected.
obtained if light of suitableusefulcence. We synthesized the new caged-luciferin(coumarin caged-luciferin) and obtained theabsorption spectra for this caged-luciferin itIn the present work, we studied
theoretically the equilibrium
self and irradiated caged-luciferin[1]. When we
structures and optical properties of DEACM-caged D-luciferin
use this caged-luciferin for spectroscopic studin neutral aqueous solution in order to predict the wavelengthies, we need the detail of electronic states ofof the irradiation light suitable for the photocleavage of DEACMthis molecule in aqueous solutions. In thiscaged D-luciferin2. 40 conformers were identified by scanning
year, we performed the density functional thethe potential energy surface. The conformers are similar inory (DFT) calculations for coumarin cagedterms of energies, oscillator
strengths and assignments of theluciferin .

lowest three excitations although their structures are different.
The theoretical absorption spectrum, which is the Boltzmann
The polarized
continuum
was usedin agreement
weighted average of the oscillator
strengths,
was model
1
for the description
solute inmolecules.
as shown
Fig. 2.
with the experimental absorption
spectrumof water
All calculations
usingbandthe
The theoretical analysis showedthat thewere
firstperformed
absorption
GAUSSIAN09[2]
programonsystemB
andat 384 nm is attributed to the S1 state, corresponding to the
C of caged
Super Computerin ISSP.
The
group Centerand thesecondelectronic excitation of thestates forto40
is attributed
theequilibrium
S2 and Sstructures
absorption band at 339 nmground3 states,forcoumarin
caged-lucifein
inaqueoussolucorresponding to the electronic excitations of the luciferin
tion
were
obtained.
The
time
dependent
moiety.

peak near 339 nm corresponds to the absorptions from S0 to the second (S2 ) and third (S3 )excited state[3]. We also found that the characteristics of 339 nm peak in the theoretical absorption spectrum of coumarin caged luciferin
is similar to that of the peak in the absorption
Fig. 1 Chemical structure of DEACM-caged Dspectrum
luciferin of luciferin.

Fig. 2 Absorption spectra of DEACM-caged D-

DFT (TDDFT) calculations for these strucluciferin and D-luciferin1
tures were poerformed to obtain the theoret- Figure 1: Absorption spectra for coumarin
ical absorption
spectra. T. Ito, Y. Hayamizu, X.-P.
caged
and luciferin[3].
solid[1] M. Kurata, M. Hiyama, T. Narimatsu,
Y. Hazama,
Qiu,luciferin
F.M. Winnik,
H. Akiyama,Black
Synthesis
line : Experimentalof
Photobiol. absorption
B (2018) spectrum
189:81-86.
and quantitative characterization of coumarin-caged D-luciferin, J. Photochem.
DOI:10.1016/j.jphotobiol.2018.10.002
Figure 1 shows the experimental and theo- coumarin caged luciferin, Red solid line: Theoabsorption
spectrumof coumarin
caged
Y. Hazama,
X.-P. of
Qiu,
F.M. Winnik,
Akiyama,
N. Koga,
Theoretical
study ofthe[2] J. Usukura, M. Hiyama, M. Kurata,
retical absorption
spectracoumarin
caged- H. reticalluciferin,Blackdashedline:
Experimental
abwavelength selection for the photocleavageof coumarin-caged
D-luciferin,
luciferin. The
experimental absorption
spec-Photochem. Photobiol. DOI:10.1111/php.13212
trum of luciferin is also shown in Figure 1. The sorption spectrum of luciferin, Orange dashedshape of the theoretical absorption spectrum line: the component of absorption from S0 toof coumarin caged-luciferin is quite similar to S1 , Green dashed line: the components of absorptions from S0 to S2 and S3 .
that of experimental spectrum.

186

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

References[1] Kurata et al. , J. Photochem. Photobiol.
B, 189 (2018) 81.
[2] Gaussian 09, Revision D.01, M. J. Frischet al.
[3] Usukura et al. Photochem. Photobiol.
(2020) in press

187

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Calculation of multication oxide surface properties forcatalyst informatics
Yoyo HINUMA
Center for Frontier Science
Chiba University, 1-33 Yayoicho, Inage, Chiba, Chiba 263-8522
Surface point defects of metal oxides, for[1,2] was expanded to allow automatic

instance O vacancies, have a dominant effectderivation of models where the topmost andon heterogeneous catalysis. The Mars-Van

bottommost surfaces need to be reconstructed,

Krevelen mechanism is one of the mostwhich is the case in the normal spinel surfaces

frequently encountered catalytic process. In one

in this study [3]. The surface energy was

example, O vacancies on a metal oxide catalyst

smallest in the (100) surface in all systems, andsurface act as reaction sites. The energy

EOvac was largest in the (100) surface in all

minimum required to remove O from a surface,systems except ZnCo2O4. The reactivity of awhich is denoted as the surface O vacancy

site is expected to be high if the site is unstable.

formation energy (EOvac), can be used to

In other words, a site with low EOvac is expectedrationalize and predict catalytic performance into have a higher reactivity and therefore cansuch a catalytic process. Calculation of EOvac

open up new capabilities in, for example,

requireswithcatalysis. The importance of finding unstablesufficient spacing between O vacancies, hence

sites, which roughly translates to having asome estimation of EOvac from less costly

lower EOvac for surface O sites, that arecalculations, such as slab-and-vacuum model

expected to have lower surface energy wascalculations with minimum cell size and even

identified in this study. Needless to say, thebulk calculations, will be effective in screening

surface must be proven to be experimentallymaterials for a given purpose.

accessible, which is a very important issue thataslab-and-vacuum

model

The EOvac of ZnM2O4, where M is one of Al,

need to be worked on.

Ga, In, V, Cr, Mn, Fe, or Co, was calculated.

References

These compounds take the normal spinel[1] Y. Hinuma et al.: Comp. Mater. Sci. 113

structure, and the (100), (110), and (111)(2016) 221.

surfaces[2] Y. Hinuma et al.: Phys. Rev. Mater. 2 (2018)

were

evaluated.

The

automated

nonstoichiometric and nonpolar slab-and-model

124603.

generation algorithm already by Hinuma et al.

[3] Y. Hinuma et al.: Mater. Trans. 61 (2020) 78.

188

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Study on physical properties of structural elementary
excitations of semiconductor surfaces and interfaces
Hiroyuki KAGESHIMA
Graduate School of Natural Science and Technology, Shimane University
1060 Nishi-Kawatsucho, Matsue, Shimane 690-8504

Our project has been focused on physicalproperties of structural elementary excitationsof semiconductor surface and interfaces. We
have performed three topics in this year. One
is the physical properties of SiO interstitials in
SiO2 at interface with Si [1, 2]. The second
is the physical properties of oxygen vacancies(VO ) in SiO2 at interface with Si. And thethird is the physical properties of vacancies ina two-dimensional material MoSe2 . The calculations were performed based on the ﬁrstprinciples calculation. Program package VASP
was employed for the ﬁrst and the third topics,
while program package PHASE0 was employed
for the second topic.
In the ﬁrst topic, we focus on the role of SiO
interstitials for the selfdiﬀusions in SiO2 undercompressive pressure. It is known that SiO interstitials are injected into the oxide when Si
is thermally oxidized. In addition, for Si pillar
oxidation, it is known that a large compressive
pressure as high as 5 GPa is induced in the oxide. We have calculated the pressure eﬀect for
temperatures 3000, 4000, 5000, and 6000 K,
and derived activation volumes as well as activation energies. We found that the SiO reallyacts as a unit for the diﬀusion mechanism. As
the result, the pressure dependence of Si diffusion is largely aﬀected by the SiO incorporation, while that of O diﬀusion is not muchaﬀected. [1, 2]
In the second topic, we focus on the strain
eﬀect on VO diﬀusion in SiO2 . As described
before, for the Si pillar oxidation, a large com-189

pressive pressure is accumulated in SiO2 . We
have calculated activation barriers as the function of modulated lattice constants. We havealso checked crystal polymorph dependence forQuartz, Cristobalite, or Tridymite. As theresults, we found that the barrier height increases with the Si density almost being independent of the polymorph type. The reason
comes from the fact that the initial Si-Si distance at VO controls the barrier height.
In the third topic, we focus on the supporting eﬀect on vacancy formation in monolayer
MoSe2 . The results are similar to our previous study on MoS2 . We found that the supporting eﬀect makes the charging more diﬃcult because the reduced quantum conﬁnement
shrinks the band gap. The hetero-stacking also
makes the charging more diﬃcult because thetype II band alignment also shrinks the bandgap. These lead to the reduction of charging
eﬀect on the vacancy formation.

References[1] H. Kageshima, Y. Yajima, K. Shiraishi,
and T. Endoh, Jpn. J. Appl. Phys. 58(2019) 111004 (11pages).
[2] Y. Yajima, H. Kageshima, K. Shiraishi,
and T. Endoh, 2019 International Workshop on Dielectric Thin Films for FutureElectron Devices – Science and Technology – (2019 IWDTF), Tokyo, Japan, p-7(Nov. 18, 2019).

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Theoretical Study on Electronic Properties
in New Nanoscale Surfaces and Interfaces
Katsuyoshi KOBAYASHI, Yoko TANAKA
Department of Physics, Ochanomizu University
2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610

In 2019 we theoretically studied electron transport properties through higher-order
topological insulators. Higher-order topological insulators were recently proposed theoretically [1]. Higher-order topological insulators
are materials that have topologically protectedstates in two or more lower spatial dimensions.
There are several reports that higher-order
topological insulators are experimentally observed [2, 3]. We calculated electrical conduction properties through topological edge statesin a three dimensional crystal.
We used a tight-binding model of higherorder topological insulators given by Langbehn
et al. [4]. This model is a three dimensional
insulator and has one dimensional edge states
protected by mirror symmetry. Transmission
properties through the edge states are investigated. We consider a cubic structure of higherorder topological insulator. Two electrodes areattached to two corners of the cube. The electrodes are normal conductors. We solve scattering states of the Hamiltonian of the open
system. Electrical conductance is calculatedusing the Landauer formalism.
We consider several diﬀerent conditions ofcontact between the high-order topologicalinsulator and electrodes.
Calculated conductance depends strongly on contact conditions. Conductance increases with increasing
the strength of the contact for weak strengthof contact. But, it turns to decrease with further increase of the contact strength. There isa peak in conductance as a function of the contact strength. This result is due to a following
reason.
The incident electrons are transmitted to another electrode or reﬂected to the incident elec-

190

trode with conserved or inverted spin. The
reﬂection with conserved spin is dominant in
the region of weak contact strength. The spinconserved reﬂection decreases with increasing
the contact strength. The transmission to theother electrode increases in place of the decrease of conserved reﬂection. However, withfurther increase of the contact strength, thereﬂection with inverted spin increases and it
becomes dominant. Accordingly, the transmission turns to decrease. This result means that
there is moderate contact strength for highttransmission.
In addition to the study of electron transmission properties through the high-order topological insulators, we also developed the calculation method of spin and angle resolved
photoelectron spectroscopy. We extended themethod for obtaining time-reversed LEED
states from the results of repeated-slab calculations. It became possible to treat general cases
containing any number of bulk Bloch states byusing the singular value decomposition.

References[1] F. Schindler et al.:eaat0346.

Sci. Adv. 4 (2018)[2] F. Schindler et al.: Nat. Phys. 14 (2018) 918.
[3] S. N. Kempkes et al.: Nat. Mater. 18 (2019)1292.
[4] J. Langbehn et al.: Phys. Rev. Lett. 119(2017) 246401.

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development of First-principles calculations methodof Seebeck coeﬃcient in the framework of linear
response theory
Sonju KOU
Department of Materials Science and Engineering, Tokyo Institute of Technology J1-3,
KNagatsuta-cho 4259, Midori-ku, Yokohama 226-8502, Japanµ    

The study combines three approaches:
phonon density of state calculations, the CPA
method for static phonons, and linear response
theory in the framework of the KKR method.
The electrical conductivity and Seebeck coefficients at finite temperature were calculated
by using this method. Concretely, we first
calculate the phonon density of states assuming harmonic oscillations by the direct method
using the first-principles packages VASP[1] orQuantum-ESPRESSO[2] and ALAMODE[3] .
Next, the average displacement of the atoms ateach temperature is obtained from the phonon

density of states, and the eﬀect is incorporated
into the Green function in AkaiKKR, which
extends the CPA method to handle the effect of displacement. Finally, the Green function is substituted into the Kubo-Greenwood
equation[4] of the KKR-CPA method by Butlar to calculate the temperature-dependent
electrical conductivity, and the Seebeck coefficient is obtained from Mahan’s equation[5].
In the transition metal system, which is considered to be diﬃcult to calculate using theBoltzmann equation and the relaxation time
approximation, we calculate the Seebeck coefficients for the simplest single transition metals
using the above method, and confirm that thecoeﬃcients reproduce the experimental values
well[6].

 

The simulation of the Seebeck coeﬃcient ismainly calculated by using the relaxation time
approximation to the Boltzmann equation, but
this approximation is correct only if the relaxation time is constant, and it is not a good approximation method for transition metal systems where the band structure on the Fermi
surface is very complex. As a method to solve
this problem and calculate the Seebeck coeﬃcient in a non-semi-classical quantum mechanical way, a method to calculate the Seebeck
coeﬃcient from the energy dependence of electrical conductivity near the Fermi energy using
linear response theory has been proposed. In
this study, we deal with the temperature dependence of the phonon density of states andanharmonic oscillations, which are not considered in the method for obtaining Seebeck coefficients from electrical conductivities using linear response theory in previous studies.



 

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  

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Figure 1: (Color online) Calculated (closed
symbol) and experimental[7] (open symbol)
Seebeck coeﬃcients S of pure Cu, Mo, and W
as functions of temperature.

191

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

References[1] G. Kresse and D. Joubert, Phys. Rev. B
59, 1758 (1999)µ)K/V ( tneiciffeoc kcebeeS

0

-50
Ag

exp.

Au

exp.

Pt

exp.

Pd

exp.

[2] Paolo Giannozzi et al., Phys. Condens.
Matter 21 395502 (2009)

-100
0

500

1000

1500

2000

Tmeperature (K)[3] T Tadano et al., Phys. Condens. Matter 26,
225402 (2014)[4] W. H. Butler, Phys. Rev. B 31 3260 (1985)

Figure 2: (Color online) Calculated (closed
symbol) and experimental[7] (open symbol)
Seebeck coeﬃcients S of pure Ag, Au, Pt, and
Pd as functions of temperature.

[5] M. Jonson and G. D. Mahan, Phys. Rev. B
21, 4223 (1980)[6] S. Kou and H. Akai Solid State Communications 276 1-4 (2018)[7] N. Cusack and P. Kendall, Proc. Phys. Soc.
72, 898 (1958)

192

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

First-principles calculation of spin-density wave statein chromium metals
Yohei KOTA
National Institute of Technology, Fukushima College
Iwaki, Fukushima 970-8034

Chromium metal ﬁlms are one of practicalmaterials for strain gauge sensor due to showing the high-sensitive response of the electrical resistivity by strain eﬀect. [1] Though themechanism of the high sensitivity is still unclear, we consider a possibility that the electrical resistivity of chromium metal is greatly
inﬂuenced by lattice strain, through the modulation of the spin-density wave state. To
verify this possibility in the theoretical view
point, we analyze the strain eﬀect on the electronic structure in the spin-density wave stateof chromium metals by ﬁrst-principles calculations. For the calculation of the incommensurate spin-density wave state in chromium metals, large unit cells including more than 40
atoms were adopted, with reference to the previous works by Hirai and Hafner et al. [2, 3]
The Vienna ab-initio simulation package [4]was used for the calculations, where the exchange correlation functional was describedwithin the general gradient approximation.
Figure 1 shows the calculation result of thetotal energy in the nonmagnetic (NM) state,
the commensurate spin-density wave (CSDW)
state, and the incommensurate spin-density
wave (ISDW) state as a function of the lattice
constant a. Note that the wave-number in the
ISDW state was set to q = 0.95 · 2π/a [Å−1 ].
The equilibrium lattice constant in the ISDW
state is aeq = 2.845 [Å], which is approximately 1% smaller than the experimental value
aexp = 2.884 [Å]. We should mention here thatthe ground state is not the ISDW state but

Figure 1: Total energy per atom in NM (red),
CSDW (blue), and ISDW (green) states as afunction of the lattice constant a.
the CSDW state in the calculation, however,the similar result was obtained in the previous
works [2, 3]. On the other hand, it is remarkable that the magnetism of chromium metal
disappears for a ≤ 2.78 [Å]; this feature is qualitatively consistent with an experiment that
the Néel temperature of metallic chromium becomes zero for applying 15 GPa of hydrostaticpressure. [5] This result implies that the magnetism of chromium metal is sensitively variable by lattice strain, corresponding to the factthat the magnetovolume eﬀect is observed signiﬁcantly in chromium metal.

References[1] E. Niwa and Y. Sasaki, IEEJ Trans. SM
134, 385 (2014).

193

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo[2] K. Hirai, J. Phys. Soc. Jpn. 66, 560(1997).
[3] R. Hafner et al., Phys. Rev. B 65, 184432(2002).
[4] G. Kresse et al., Phys. Rev. B 47, 558(1993); Phys. Rev. B 54, 11169 (1996).
[5] K. Shimizu et al., Physica B 378-380, 632(2006)

194

Activity Report 2019 / Supercomputer Center, Institute for Solid State Physics, The University of Tokyo

Development and application of the first-principles approach
Hiroaki IKEDA
Department of Physics,
Ritsumeikan University, Kusatsu, Shiga 525-8577
We have investigated unconventional super-model. In general, the conventional LDA /conductors in the strongly correlated electron

GGA calculations describe the overall featuresystems (SCES). The main theme is to developof the band structure. However, the size and

the

well

curvature of the Fermi surface and thedescribe the electronic structure of SCES. This

composed orbital characters are significantly

year, using a Class B, we have studied two

deviated from the experimental observations.

topics; superconducting gap anisotropy of thelayered Bismuth chalcogenide superconductors

This has a sizable effect on the gap structure. In(BiCh2) and the electron correlation effect ofgap structure. Emergence of propeller-type

the gap structure in iron-based superconductors.
The layered BiCh2 superconductors possess

Fermi pockets is well consistent with thenon-symmorphic structure. Locally inversion

orbital characters turns the gap structure fromsymmetry breaking and the strong spin-orbit

horizontal nodes to octet node structure. This

coupling (SOC) on a Bismuth site can lead tostudy was reported in MRM2019 [3].

first-principles

calculations

andFig. 1, we indicates the Fermi surface and theexperimental data. Furthermore, the change ofthe parity mixing between spin singlet andtriplet pairing. In addition, the observed charge/ orbital fluctuations potentially yield the gap
anisotropy even without strong repulsive
interactions. First, we performed the DFT band
structure calculations using Qunatum espresso[1] in Sekirei system, and made an effective
four-orbital models with the SOC using the
maximum localized Wannier functions. We

Fig. 1 Gap structure on the Fermi surface in
KFe2As2 obtained by GGA (left) and QSGW(right).

have solved the superconducting gap equationin multi-orbital attractive Hubbard model. In
the obtained phase diagram, we have found a
possibility of topological superconductivity.

References

This study was reported in the JPS autumn
meeting 2019 [2].

[1] P. Giannozzi et al., J.Phys.:Condens.Matter
21, 395502 (2009)

Next, in the iron-based superconductors, we[2] K. Suzuki, JPS Autumn meeting 10pB17-4

have applied the quasi-particle self-consistent
GW (QSGW) method to KFe2As2 and studied[3] K. Suzuki, MRM2019 D3-13(1)-l13

the gap structure in the effective Hubbard

195