Research on data acquisition and 3D atomic image reconstruction algorithm

2017 Fiscal Year Annual Research Report

• Project Area: 3D Active-Site Science
• Project/Area Number: 26105013
• Research Institution: Japan Synchrotron Radiation Research Institute
• Principal Investigator: 松下 智裕 公益財団法人高輝度光科学研究センター, 情報処理推進室, 室長 (10373523)
• Co-Investigator(Kenkyū-buntansha): 八方 直久 広島市立大学, 情報科学研究科, 准教授 (30285431) ; 窪田 昌史 広島市立大学, 情報科学研究科, 助教 (60305787)
• Project Period (FY): 2014-07-10 – 2019-03-31
• Keywords: アルゴリズム / 計算物理 / 物性理論 / 原子配列解析

Outline of Annual Research Achievements

研究開始当初、研究課題として3つの項目を挙げてスタートし、さらに1つの研究課題を追加して研究を進めてきた。
【課題1】共通3D解析プラットフォームとして、中核となるソフトウエア「3D-AIR-IMAGE」の開発をすすめ、この1年で約20回程度のリリースを行った。原子分解能ホログラムから3D原子像を再生するアルゴリズムSPEA-L1については、さらに研究が進み収束速度や再生像が向上した。このプラットフォームの他研究班による利用が進み、Si中のAsドーパント、Bi2Te3のMnドーパンなどの原子構造解析に応用された。さらに他研究班からのフィードバックを受けて、様々な点でプラットフォームの改良を施した。
【課題2】高精度低ノイズ計測系開発として、阻止電位型電子アナライザーの高度化と電源制御の開発が進んた。また蛍光X線ホログラフィー測定系の開発を行い、ノーマルモード測定系開発や、蛋白結晶などの放射線ダメージを受けるサンプルに対応する測定系開発、微小サンプルに対応できる測定系の開発を行った。
【課題3】4D空間の高解像度再生は像再生計算にかかる時間の短縮を目的とする開発を進めた。96コアのCPUを持つ大型計算機と、GPU計算機(3584 CUDAコア)の両方のソフト開発を行い、その実行速度を比較した。その結果GPUを利用した方が2.73倍も短時間で計算できることが分かった。
【課題4】ホログラムのデータ処理技術として、蛍光X線ホログラフィーのバックグラウンド作成のアルゴリズムを共通解析プラットフォームに追加した。また、ホログラムの方位決めの為の角度探索の機能も追加している。
以上のように、本研究は順調に進展している。

Current Status of Research Progress

1: Research has progressed more than it was originally planned.

Reason

【課題1】共通3D解析プラットフォームが利用可能レベルまで完成し、他研究班での利用が進んだ。SPEA-L1アルゴリズムなどにさらなる改良を加えている。
【課題2】蛍光X線ホログラフィーの計測系開発については、計画当初に想定されていなかったノーマルモード計測や、放射線ダメージ対応、微小サンプル計測対応が可能な計測系開発が進んだ。
【課題3】大型計算機よりもGPUの方が高速に処理できることが分かり、GPUを搭載したノートパソコンでも十分な速度が得られる可能性があることが判った。

Strategy for Future Research Activity

多くのデータ処理をするための【課題3】におけるデータ処理の高速化の研究を進める。大型計算機よりもGPUの方が高速に処理できることが分かり、GPU計算機の導入とGPU計算機用コード開発を進める。
【課題1,2,4】については、利用レベルに達しているが、さらなる改良を加える。【課題1】のプラットフォームとなるソフトウエア3D-AIR-IMAGEは本研究メンバーに継続して改良版を提供する。また、共通3D解析プラットフォームに【課題3】の成果を取り込み解析速度の向上を図る。【課題2】3D-AIR-IMAGEと連動する計測ソフトウエアの改良を進める。【課題4】のデータ処理技術も利用者からのフィードバックを元に改良を加えていく。【課題1～4】の成果物を他研究班に提供して密に連携し、成果を創出する。

Research Products

• [Journal Article] Principle and Reconstruction Algorithm for Atomic-Resolution Holography (2018)
  • Author(s): T. Matsushita、T. Muro、F. Matsui、N. Happo、S. Hosokawa、K. Ohoyama、A. Sato-Tomita、Y. C. Sasaki、K. Hayashi
  • Journal Title: J. Phys. Soc. Jpn. Volume: 87 Pages: 061002-1-11
  • DOI: 10.7566/JPSJ.87.061002
  • Peer Reviewed / Open Access
• [Journal Article] Local structure analysis of Cu(In,Ga)Se2 by x-ray fluorescence holography (2017)
  • Author(s): S. Shirakata, Y. Kitamura, N. Happo, S. Hosokawa, and K. Hayashi
  • Journal Title: Physica Status Solidi C Volume: 14 Pages: 1600171-1-4
  • DOI: 10.1002/pssc.201600171
  • Peer Reviewed
• [Journal Article] In-plane disordering of Zn-Y clusters in single crystal Mg85Zn6Y9 alloy studied by X-ray fluorescence holography (2017)
  • Author(s): K. Kimura, K. Hayashi, K. Hagihara, H. Izuno, N. Happo, S. Hosokawa, M. Suzuki, and H. Tajiri
  • Journal Title: Materials Transaction Volume: 58 Pages: 539-542
  • DOI: 10.2320/matertrans.M2016459
  • Peer Reviewed / Open Access
• [Journal Article] Multiple-wavelength neutron holography with pulsed neutrons (2017)
  • Author(s): K. Hayashi, K. Ohoyama, N. Happo, T. Matsushita, S. Hosokawa, M. Harada, Y. Inamura, H. Nitani, T. Shishido, and K. Yubuta
  • Journal Title: Science Advances Volume: 3 Pages: e1700294-1-7
  • DOI: 10.1126/sciadv.1700294
  • Peer Reviewed / Open Access
• [Journal Article] A valence-selective x-ray fluorescence holography study of an yttrium oxide thin film (2017)
  • Author(s): J. R. Stellhorn, S. Hosokawa, N. Happo, H. Tajiri, T. Matsushita, K. Kaminaga, T. Fukumura, T. Hasegawa, and K. Hayashi
  • Journal Title: Journal of Applied Crystallography Volume: 50 Pages: 1583-1589
  • DOI: 10.1107/S1600576717012821
  • Peer Reviewed
• [Journal Article] Impurity position and lattice distortion in a Mn doped Bi2Te3 topological insulator investigated by x-ray fluorescence holography and x-ray absorption fine structure (2017)
  • Author(s): S. Hosokawa, J. R. Stellhorn, T. Matsushita, N. Happo, K. Kimura, K. Hayashi, Y. Ebisu, T. Ozaki, H. Ikemoto, H. Setoyama, T. Okajima, Y. Yoda, H. Ishii, Y.-F. Liao, M. Kitaura, and M. Sasaki
  • Journal Title: Physical Review B Volume: 96 Pages: 214207-1-12
  • DOI: 10.1103/PhysRevB.96.214207
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Wide-angle display-type retarding field analyzer with high energy and angular resolutions (2017)
  • Author(s): T. Muro, T. Ohkouchi, Y. Kato, Y. Izumi, S. Fukami, H. Fujiwara, T. Matsushita
  • Journal Title: Rev. Sci. Instrum. Volume: 88 Pages: 23106
  • DOI: 10.1063/1.4990769
  • Peer Reviewed
• [Journal Article] Individual Atomic Imaging of Multiple Dopant Sites in As-Doped Si Using Spectro-Photoelectron Holography (2017)
  • Author(s): K. Tsutsui, T. Matsushita, K. Natori, T. Muro, Y. Morikawa, T. Hoshii, K. Kakushima, H. Wakabayashi, K. Hayashi, F. Matsui, T. Kinoshita
  • Journal Title: Nano Lett. Volume: 17 Pages: 7533-7538
  • DOI: 10.1021/acs.nanolett.7b03467
  • Peer Reviewed / Open Access
• [Presentation] 原子分解能ホログラフィーの原理とドーパントの立体構造の観測 (2018)
  • Author(s): 松下智裕
  • Organizer: 日本物理学会
  • Invited
• [Presentation] 蛍光X線ホログラフィーを用いたCuIn3Se5単結晶の構造解析 (2018)
  • Author(s): 白方祥、八方直久、他3名
  • Organizer: 第65回応用物理学会春季学術講演会
• [Presentation] 蛍光X線ホログラフィーによる青色発光ダイオードInGaNの局所構造解析 (2018)
  • Author(s): 林好一、八方直久、他4名
  • Organizer: 第31回日本放射光学会年会・放射光科学合同シンポジウム
• [Presentation] 蛍光X線ホログラフィーによるBi2Te3:Mnトポロジカル絶縁体の不純物位置の同定 (2018)
  • Author(s): 細川伸也、松下智裕、八方直久、他3名
  • Organizer: 第31回日本放射光学会年会・放射光科学合同シンポジウム
• [Presentation] 蛍光X線ホログラフィによる長周期積層秩序構造Mg75Zn10Y15合金の局所構造解析 (2018)
  • Author(s): 木村耕治、八方直久、他7名
  • Organizer: 蛍光X線ホログラフィによる長周期積層秩序構造Mg75Zn10Y15合金の局所構造解析
• [Presentation] Novel usage of neutrons white neutron holography for investigations of local atomic structures (2018)
  • Author(s): K. Ohoyama, Y. Fukumoto, S. Uechi, Y. Kanazawa, K. Hayashi, N. Happo, K. Kimura, S. Hosokawa, T. Hada, B. Paulus, J. Stellhorn, M. Lederer, M. Harada, Y. Inamura, K. Oikawa, W. Matsuura, F. Iga, K. Tsutsui, and P. Wellmann
  • Organizer: ISSP - J-PARC Joint Workshop on Science Frontier by Neutron Scattering
  • Int'l Joint Research
• [Presentation] Investigations of Local Structures by White Neutron Atomic Resolution Holography with γ-ray Energy Analysis (2018)
  • Author(s): Y. Fukumoto, S. Uechi, T. Kanazawa, K. Ohoyama, K. Hayashi, N. Happo, T. Hada, K. Kimura, S. Hosokawa, M. Harada, K. Oikawa, Y. Inamura, K. Tsutsui, B. Paulus, M. Lederer, P. Wellmann
  • Organizer: ISSP - J-PARC Joint Workshop on Science Frontier by Neutron Scattering
  • Int'l Joint Research
• [Presentation] Local structure observation of Sm doped LaB6 by white neutron atomic resolution holography (2018)
  • Author(s): S. Uechi, Y. Kanazawa, Y. Fukumoto, B. Paulus, K. Ohoyama, N. Happo, K. Hayashi, K. Kimura, S. Hosokawa, T. Hada, M. Harada, K. Oikawa, Y. Inamura, W. Matsuura, F. Iga
  • Organizer: ISSP - J-PARC Joint Workshop on Science Frontier by Neutron Scattering
  • Int'l Joint Research
• [Presentation] Local structure investigations of B doped Si by neutron atomic-resolution holography (2018)
  • Author(s): Y. Kanazawa, Y. Fukumoto, S. Uechi, K. Ohoyama, M. Lederer, N. Happo, K. Hayashi, K. Kimura, S. Hosokawa, T. Hada, M. Harada, K. Oikawa, Y. Inamura, K. Tsutsui
  • Organizer: ISSP - J-PARC Joint Workshop on Science Frontier by Neutron Scattering
  • Int'l Joint Research
• [Presentation] Principle of holography and reconstruction theory (2017)
  • Author(s): T. Matsushita
  • Organizer: Swedish-Japanese Workshop on Nano-Structure Science by Novel Light Sources
  • Int'l Joint Research / Invited
• [Presentation] 3D atomic image reconstruction algorithm for photoelectron holography and x- ray fluorescence holography (2017)
  • Author(s): T. Matsushita
  • Organizer: 3rd International Symposium on Kumamoto Synchrotron Radiation (ISKSR3)
  • Int'l Joint Research / Invited
• [Presentation] Principles of Atomic Resolution Holography and New Atomic Image Reconstruction Algorithm (2017)
  • Author(s): T. Matsushita
  • Organizer: 11th Atomic level Characterizations for New Materials and Devices
  • Int'l Joint Research / Invited
• [Presentation] スパースモデリングによる原子分解能ホログラフィーの立体原子像再生 (2017)
  • Author(s): 松下智裕
  • Organizer: ポスト「京」重点課題(7) 「次世代の産業を支える新機能デバイス・高性能材料の創成」サブ課題G第6回「共通基盤シミュレーション手法」連続研究会
  • Invited
• [Presentation] An x-ray fluorescence holographic study on a Fe-based high-temperature superconductor FeSe0.4Te0.6 (2017)
  • Author(s): J. R. Stellhorn, S. Hosokawa, N. Happo, K. Kimura, K. Hayashi, H. Okazaki, A. Yamashita, and Y. Takano
  • Organizer: 30th International Symposium on Superconductivity
  • Int'l Joint Research
• [Presentation] X-ray fluorescence holography of Ca1-xPrxFe2As2 (2017)
  • Author(s): K. Kudo, S. Ioka, N. Happo, H. Ota, Y. Ebisu, K. Kimura, T. Hada, T. Kimura, H. Tajiri, S. Hosokawa, K. Hayashi, M. Nohara
  • Organizer: 30th International Symposium on Superconductivity
  • Int'l Joint Research
• [Presentation] Local structure investigations of B doped Si by neutron atomic-resolution holography (2017)
  • Author(s): Y. Kanazawa, Y. Fukumoto, S. Uechi, K. Ohoyama, M. Lederer, N. Happo, K. Hayashi, K. Kimura, S. Hosokawa, T. Hada, M. Harada, K. Oikawa, Y. Inamura, and K. Tsutsui
  • Organizer: 2nd International Symposium of Quantum Beam Science at Ibaraki University
  • Int'l Joint Research
• [Presentation] Investigations of Local Structures by White Neutron Atomic Resolution Holography with γ-ray energy analysis (2017)
  • Author(s): Y. Fukumoto, S. Uechi, T. Kanazawa, K. Ohoyama, K. Hayashi, N. Happo, T. Hada, K. Kimura, S. Hosokawa, M. Harada, K. Oikawa, Y. Inamura, K. Tsutsui, B. Paulus, M. Lederer, and P. Wellmann
  • Organizer: 2nd International Symposium of Quantum Beam Science at Ibaraki University
  • Int'l Joint Research
• [Presentation] Local structure observation of Sm doped LaB6 by white neutron atomic resolution holography (2017)
  • Author(s): S. Uechi, Y. Kanazawa, Y. Fukumoto, B. Paulus, K. Ohoyama, N. Happo, K. Hayashi, K. Kimura, S. Hosokawa, T. Hada, M. Harada, K. Oikawa, Y. Inamura, W. Matsuura, and F. Iga
  • Organizer: 2nd International Symposium of Quantum Beam Science at Ibaraki University
  • Int'l Joint Research
• [Presentation] A valence selective x-ray fluorescence holography study of an yttrium oxide thin film (2017)
  • Author(s): J. R. Stellhorn, S. Hosokawa, N. Happo, H. Tajiri, T. Matsushita, K. Kaminaga, T. Fukumura, T. Hasegawa, and K. Hayashi
  • Organizer: 11th International Symposium on Atomic Level Characterizations for New Materials and Devices '17
  • Int'l Joint Research
• [Presentation] Temperature dependent local atomic structures in the traditional Fe65Ni35 Invar alloy by x-ray fluorescence holography (2017)
  • Author(s): Y. Ideguchi, J. R. Stellhorn, S. Hosokawa, N. Happo, T. Matsushita, K. Yubuta, K. Kimura, and K. Hayashi
  • Organizer: 11th International Symposium on Atomic Level Characterizations for New Materials and Devices '17
  • Int'l Joint Research
• [Presentation] In plane local atomic configuration of Mg-Zn-Y long period stacking ordered alloys studied by X-ray fluorescence holography (2017)
  • Author(s): K. Kimura, T. Nishioka, K. Hayashi, K. Hagihara, H. Izuno, N. Happo, Y. Yamamoto, E. Abe, S. Hosokawa, and M. Suzuki
  • Organizer: 11th International Symposium on Atomic Level Characterizations for New Materials and Devices '17
  • Int'l Joint Research
• [Presentation] Impurity positions and lattice distortions in a Mn doped Bi2Te3 topological insulator studied by x-ray fluorescence holography (2017)
  • Author(s): S. Hosokawa, J. R. Stellhorn, T. Matsushita, N. Happo, K. Kimura, K. Hayashi, M. Kitaura, and M. Sasaki
  • Organizer: 11th International Symposium on Atomic Level Characterizations for New Materials and Devices '17
  • Int'l Joint Research
• [Presentation] Local structural analysis of In doped Bi2Se3 topological insulator using X-ray fluorescence holography (2017)
  • Author(s): K. Kimura, K. Hayashi, L. V. Yashina, N. Happo, Y. Ebisu, T. Nishioka, Y. Yamamoto, T. Ozaki, S. Hosokawa, and H. Tajiri
  • Organizer: 11th International Symposium on Atomic Level Characterizations for New Materials and Devices '17
  • Int'l Joint Research
• [Presentation] An x-ray fluorescence holographic study on a Fe-based high-temperature superconductor FeSe0.4Te0.6 (2017)
  • Author(s): S. Hosokawa, Y. Ideguchi, J. R. Stellhorn, N. Happo, K. Kimura, K. Hayashi, H. Okazaki, A. Yamashita, and Y. Takano
  • Organizer: International Symposium on Novel Energy Nanomaterials
  • Int'l Joint Research
• [Presentation] Atomic imaging around Pr atoms in Ca1-xPrxFe2As2 by x-ray fluorescence holography (2017)
  • Author(s): K. Kudo, S. Ioka, N. Happo, H. Ota, Y. Ebisu, K. Kimura, T. Hada, T. Kimura, H. Tajiri, S. Hosokawa, K. Hayashi, and M. Nohara
  • Organizer: J-Physics 2017: International Workshop on Multipole Physics and Related Phenomena
  • Int'l Joint Research
• [Presentation] Analysis of x-ray fluorescence holography data using sparse modeling on Mn-doped Bi2Te3 topological insulator (2017)
  • Author(s): S. Hosokawa, J. R. Stellhorn, T. Matsushita, N. Happo, K. Kimura, K. Hayashi, M. Kitaura, and M. Sasaki
  • Organizer: International Meeting on High-Dimensional Data-Driven Science
  • Int'l Joint Research
• [Presentation] Analysis of x-ray fluorescence holography data using sparse modeling on the traditional Fe65Ni35 Invar alloy (2017)
  • Author(s): Y. Ideguchi, J. R. Stellhorn, S. Hosokawa, T. Matsushita, N. Happo, K. Yubuta, K. Kimura, and K. Hayashi
  • Organizer: International Meeting on High-Dimensional Data-Driven Science
  • Int'l Joint Research
• [Presentation] X-ray fluorescence holography of Pr-doped CaFe2As2 (2017)
  • Author(s): K. Kudo, S. Ioka, N. Happo, H. Ota, Y. Ebisu, K. Kimura, T. Hada, T. Kimura, H. Tajiri, S. Hosokawa, K. Hayashi, and M. Nohara
  • Organizer: 28th International Conference on Low Temperature Physics
  • Int'l Joint Research
• [Presentation] Local structure characterization of CuIn3Se5 single crystal by x-ray fluorescence holography (2017)
  • Author(s): S. Shirakata, N. Happo, S. Hosokawa, and K. Hayashi
  • Organizer: 29th International Conference on Defects in Semiconductors
  • Int'l Joint Research
• [Presentation] An x-ray fluorescence holographic study on Bi2Te3:Mn topological insulator (2017)
  • Author(s): S. Hosokawa, Y. Ideguchi, K. Kamimura, N. Happo, K. Kimura, K. Hayashi, Y. Ebisu, T. Ozaki, Y. Yoda, H. Ishii, M. Kitaura, and M. Sasaki
  • Organizer: 8th International Conference on Amorphous and Nanostructured Chalcogenides
  • Int'l Joint Research
• [Presentation] An x-ray fluorescence holographic study on high-temperature superconductor FeSe0.4Te0.6 (2017)
  • Author(s): Y. Ideguchi, J. R. Stellhorn, S. Hosokawa, N. Happo, K. Kimura, K. Hayashi, H. Okazaki, A. Yamashita, and Y. Takano
  • Organizer: 8th International Conference on Amorphous and Nanostructured Chalcogenides
  • Int'l Joint Research
• [Presentation] 蛍光X線ホログラムからの3次元原子像再生のGPUによる高速化 (2017)
  • Author(s): 原智裕，窪田昌史，松下智裕，八方直久，弘中哲夫
  • Organizer: 第6回電子デバイス・回路・照明・システム関連教育・研究ワークショップ
• [Remarks] 3D活性サイト科学
  • URL: http://www.3d-activesite.jp/