Merge pull request #55 from issp-center-dev/docs

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issp-center-dev · Sep 10, 2023 · da948bc · da948bc
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diff --git a/README.md b/README.md
@@ -74,6 +74,24 @@ and direct problem solvers (`py2dmat` also means this script).
 
 This package is distributed under GNU General Public License version 3 (GPL v3) or later.
 
+We hope that you cite the following references when you publish the results using 2DMAT:
+“Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures”, 
+Y. Motoyama, K. Yoshimi, I. Mochizuki, H. Iwamoto, H. Ichinose, and T. Hoshi, Computer Physics Communications 280, 108465 (2022).
+
+Bibtex:
+
+@article{MOTOYAMA2022108465,
+title = {Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures},
+journal = {Computer Physics Communications},
+volume = {280},
+pages = {108465},
+year = {2022},
+issn = {0010-4655},
+doi = {https://doi.org/10.1016/j.cpc.2022.108465},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465522001849},
+author = {Yuichi Motoyama and Kazuyoshi Yoshimi and Izumi Mochizuki and Harumichi Iwamoto and Hayato Ichinose and Takeo Hoshi}
+}
+
 ## Copyright
 
 © *2020- The University of Tokyo. All rights reserved.*

diff --git a/doc/en/source/introduction.rst b/doc/en/source/introduction.rst
@@ -11,17 +11,17 @@ In the future, we plan to add other direct problem solvers and search algorithms
 
 [1] As a review, see `Y. Fukaya, et al., J. Phys. D: Appl. Phys. 52, 013002 (2019) <https://iopscience.iop.org/article/10.1088/1361-6463/aadf14>`_.
 
-[2] `T. Hanada, Y. Motoyama, K. Yoshimi, and T. Hoshi, arXiv:2110.09477. <https://arxiv.org/abs/2110.09477>`_
+[2] `T. Hanada, Y. Motoyama, K. Yoshimi, and T. Hoshi, Computer Physics Communications 277, 108371 (2022). <https://doi.org/10.1016/j.cpc.2022.108371>`_
 
 [3] W. Voegeli, K. Akimoto, T. Aoyama, K. Sumitani, S. Nakatani, H. Tajiri, T. Takahashi, Y. Hisada, S. Mukainakano, X. Zhang, H. Sugiyama, H. Kawata, Applied Surface Science 252 (2006) 5259.
 
 [4] `M.A. Van Hove, W. Moritz, H. Over, P.J. Rous, A. Wander, A. Barbieri, N. Materer, U. Starke, G.A. Somorjai, Automated determination of complex surface structures by LEED, Surface Science Reports, Volume 19, 191-229 (1993). <https://doi.org/10.1016/0167-5729(93)90011-D>`_
 
 [5] `K. Tanaka, T. Hoshi, I. Mochizuki, T. Hanada, A. Ichimiya, and T. Hyodo, Acta. Phys. Pol. A 137, 188 (2020) <http://przyrbwn.icm.edu.pl/APP/PDF/137/app137z2p25.pdf>`_.
 
-[6] `K. Tanaka, I. Mochizuki, T. Hanada, A. Ichimiya, T. Hyodo, and T. Hoshi, JJAP Conf. Series, in press, arXiv:2002.12165 <https://arxiv.org/abs/2002.12165>`_.
+[6] `K. Tanaka, I. Mochizuki, T. Hanada, A. Ichimiya, T. Hyodo, and T. Hoshi, JJAP Conf. Series, <https://doi.org/10.56646/jjapcp.9.0_011301>`_.
 
-[7] `Y. Motoyama, R. Tamura, K. Yoshimi, K. Terayama, T. Ueno, and K. Tsuda, arXiv:2110.07900 <https://arxiv.org/abs/2110.07900>`_
+[7] `Y. Motoyama, R. Tamura, K. Yoshimi, K. Terayama, T. Ueno, and K. Tsuda,  Computer Physics Communications 278, 108405 (2022) <http://dx.doi.org/10.1016/j.cpc.2022.108405>`_
 
 [8] `K. Hukushima and K. Nemoto, J. Phys. Soc. Japan, 65, 1604 (1996) <https://journals.jps.jp/doi/10.1143/JPSJ.65.1604>`_,  `R. Swendsen and J. Wang, Phys. Rev. Lett. 57, 2607 (1986) <https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.57.2607>`_.
 
@@ -40,7 +40,22 @@ Copyright (c) <2020-> The University of Tokyo. All rights reserved.
 This software was developed with the support of "Project for advancement of software usability in materials science" of The Institute for Solid State Physics, The University of Tokyo.
 We hope that you cite the following reference when you publish the results using 2DMAT:
 
-`Kazuyuki Tanaka, Takeo Hoshi, Izumi Mochizuki, Takashi Hanada, Ayahiko Ichimiya, Toshio Hyodo, Acta. Phys. Pol. A 137(3) 188 - 192 2020 <https://doi.org/10.12693/APhysPolA.137.188>`_
+“Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures”,
+Y. Motoyama, K. Yoshimi, I. Mochizuki, H. Iwamoto, H. Ichinose, and T. Hoshi, Computer Physics Communications 280, 108465 (2022).
+
+Bibtex:
+
+@article{MOTOYAMA2022108465,
+title = {Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures},
+journal = {Computer Physics Communications},
+volume = {280},
+pages = {108465},
+year = {2022},
+issn = {0010-4655},
+doi = {https://doi.org/10.1016/j.cpc.2022.108465},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465522001849},
+author = {Yuichi Motoyama and Kazuyoshi Yoshimi and Izumi Mochizuki and Harumichi Iwamoto and Hayato Ichinose and Takeo Hoshi}
+}
 
 Version Information
 ----------------------

diff --git a/doc/en/source/start.rst b/doc/en/source/start.rst
@@ -43,7 +43,9 @@ Note that among the direct problem solvers used in ``py2dmat``,
 the following solver must be installed separately:
 
 - TRHEPD forward problem solver (``sim-trhepd-rheed``)
-
+- SXRD forward problem solver (``sxrdcalc``)
+- LEED forward problem solver (``satleed``)
+
 Please refer to the tutorials of each solver for installation details.
 
 How to run

diff --git a/doc/ja/source/introduction.rst b/doc/ja/source/introduction.rst
@@ -13,17 +13,17 @@
 [1] レビューとして， `Y．Fukaya, et al., J. Phys. D: Appl. Phys. 52, 013002 (2019) <https://iopscience.iop.org/article/10.1088/1361-6463/aadf14>`_;
 `兵頭俊夫，「全反射高速陽電子回折　(TRHEPD)による表面構造解析」，固体物理 53, 705 (2018) <https://www.agne.co.jp/kotaibutsuri/kota1053.htm>`_.
 
-[2] `T. Hanada, Y. Motoyama, K. Yoshimi, and T. Hoshi, arXiv:2110.09477. <https://arxiv.org/abs/2110.09477>`_
+[2] `T. Hanada, Y. Motoyama, K. Yoshimi, and T. Hoshi, Computer Physics Communications 277, 108371 (2022). <https://doi.org/10.1016/j.cpc.2022.108371>`_
 
 [3] W. Voegeli, K. Akimoto, T. Aoyama, K. Sumitani, S. Nakatani, H. Tajiri, T. Takahashi, Y. Hisada, S. Mukainakano, X. Zhang, H. Sugiyama, H. Kawata, Applied Surface Science 252 (2006) 5259.
 
 [4] `M.A. Van Hove, W. Moritz, H. Over, P.J. Rous, A. Wander, A. Barbieri, N. Materer, U. Starke, G.A. Somorjai, Automated determination of complex surface structures by LEED, Surface Science Reports, Volume 19, 191-229 (1993). <https://doi.org/10.1016/0167-5729(93)90011-D>`_
 
 [5] `K. Tanaka, T. Hoshi, I. Mochizuki, T. Hanada, A. Ichimiya, and T. Hyodo, Acta. Phys. Pol. A 137, 188 (2020) <http://przyrbwn.icm.edu.pl/APP/PDF/137/app137z2p25.pdf>`_.
 
-[6] `K. Tanaka, I. Mochizuki, T. Hanada, A. Ichimiya, T. Hyodo, and T. Hoshi, JJAP Conf. Series, in press, arXiv:2002.12165 <https://arxiv.org/abs/2002.12165>`_.
+[6] `K. Tanaka, I. Mochizuki, T. Hanada, A. Ichimiya, T. Hyodo, and T. Hoshi, JJAP Conf. Series, <https://doi.org/10.56646/jjapcp.9.0_011301>`_.
 
-[7] `Y. Motoyama, R. Tamura, K. Yoshimi, K. Terayama, T. Ueno, and K. Tsuda, arXiv:2110.07900 <https://arxiv.org/abs/2110.07900>`_
+[7] `Y. Motoyama, R. Tamura, K. Yoshimi, K. Terayama, T. Ueno, and K. Tsuda,  Computer Physics Communications 278, 108405 (2022) <http://dx.doi.org/10.1016/j.cpc.2022.108405>`_
 
 [8] `K. Hukushima and K. Nemoto, J. Phys. Soc. Japan, 65, 1604 (1996) <https://journals.jps.jp/doi/10.1143/JPSJ.65.1604>`_,  `R. Swendsen and J. Wang, Phys. Rev. Lett. 57, 2607 (1986) <https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.57.2607>`_.
 
@@ -43,7 +43,22 @@ Copyright (c) <2020-> The University of Tokyo. All rights reserved.
 本ソフトウェアは2020年度 東京大学物性研究所 ソフトウェア高度化プロジェクトの支援を受け開発されました。
 2DMATを引用する際には以下の文献を引用してください。
 
-`Kazuyuki Tanaka, Takeo Hoshi, Izumi Mochizuki, Takashi Hanada, Ayahiko Ichimiya, Toshio Hyodo, Acta. Phys. Pol. A 137(3) 188 - 192 2020 <https://doi.org/10.12693/APhysPolA.137.188>`_
+“Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures”,
+Y. Motoyama, K. Yoshimi, I. Mochizuki, H. Iwamoto, H. Ichinose, and T. Hoshi, Computer Physics Communications 280, 108465 (2022).
+
+Bibtex:
+
+@article{MOTOYAMA2022108465,
+title = {Data-analysis software framework 2DMAT and its application to experimental measurements for two-dimensional material structures},
+journal = {Computer Physics Communications},
+volume = {280},
+pages = {108465},
+year = {2022},
+issn = {0010-4655},
+doi = {https://doi.org/10.1016/j.cpc.2022.108465},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465522001849},
+author = {Yuichi Motoyama and Kazuyoshi Yoshimi and Izumi Mochizuki and Harumichi Iwamoto and Hayato Ichinose and Takeo Hoshi}
+}
 
 
 

diff --git a/doc/ja/source/start.rst b/doc/ja/source/start.rst
@@ -44,6 +44,8 @@ py2dmat のインストール
 なお、 ``py2dmat`` で用いる順問題ソルバーのうち、
 
 - TRHEPD順問題ソルバー (``sim-trhepd-rheed``)
+- SXRD順問題ソルバー (``sxrdcalc``)
+- LEED順問題ソルバー (``satleed``)
 
 については、別途インストールが必要です。
 インストールの詳細については各ソルバーのチュートリアルを参照してください。