XRAYPAC
A software package for modeling x-ray-induced dynamics of matter
Description
Rapid development of x-ray free-electron laser (XFEL) science has taken place in recent years due to the consecutive launch of large-scale XFEL facilities such as LCLS in the U.S., SACLA in Japan, European XFEL in Germany. Research areas such as ultrafast chemical dynamics, warm dense matter physics or coherent x-ray imaging take advantage of the unprecedentedly high intensities of XFELs, opening up new opportunities to observe, predict, and manipulate matter at the atomic spatial and temporal scales. A single XFEL pulse can induce very complex dynamics within matter initiated by core-hole photoionization and subsequent relaxation processes. Owing to the multifaceted nature of these phenomena, the development and employment of suitable theoretical models becomes imperative in elucidating the complexities.
In our endeavor to achieve this goal, we have successfully engineered a sophisticated software package named XRAYPAC, within the CFEL-DESY Theory Division. XRAYPAC consists of the following computer codes:
- XATOM
- XMOLECULE
- XMDYN
XATOM is an integrated toolkit to describe ab initio electronic structure and dynamics of atoms interacting with x-rays. XMOLECULE is for ab initio molecular electronic structure calculations for modeling ultrafast x-ray experiments. XMDYN is developed for modeling dynamics of matter induced by high-intensity x-rays, which utilizes atomic data calculated using XATOM, and is particularly designed for large polyatomic systems. These codes operate collectively as well as separately based on the nature of the problem and have already demonstrated their potential in many applications targeting the modeling of experiments at XFELs. The toolkit has been instrumental in predicting and facilitating comparisons across a broad spectrum of experiments, ranging from Coulomb explosion to x-ray molecular imaging.

Artist's impression of a buckyball in an X-ray laser flash. Credit: Greg Stewart/SLAC
Participating organisations
Reference papers
- 1.Author(s): Zoltan Jurek, Sang-Kil Son, Beata Ziaja, Robin SantraPublished in Journal of Applied Crystallography by International Union of Crystallography (IUCr) in 2016, page: 1048-105610.1107/s1600576716006014
- 2.Author(s): Ludger Inhester, Kota Hanasaki, Yajiang Hao, Sang-Kil Son, Robin SantraPublished in Physical Review A by American Physical Society (APS) in 201610.1103/physreva.94.023422
- 3.Author(s): Yajiang Hao, Ludger Inhester, Kota Hanasaki, Sang-Kil Son, Robin SantraPublished in Structural Dynamics by AIP Publishing in 201510.1063/1.4919794
- 4.Author(s): B. F. Murphy, T. Osipov, Z. Jurek, L. Fang, S.-K. Son, M. Mucke, J.H.D. Eland, V. Zhaunerchyk, R. Feifel, L. Avaldi, P. Bolognesi, C. Bostedt, J. D. Bozek, J. Grilj, M. Guehr, L. J. Frasinski, J. Glownia, D. T. Ha, K. Hoffmann, E. Kukk, B. K. McFarland, C. Miron, E. Sistrunk, R. J. Squibb, K. Ueda, R. Santra, N. BerrahPublished in Nature Communications by Springer Science and Business Media LLC in 201410.1038/ncomms5281
- 5.Author(s): Sang-Kil Son, Linda Young, Robin SantraPublished in Physical Review A by American Physical Society (APS) in 201110.1103/physreva.83.033402
Mentions
- 1.Author(s): Hideaki TakabePublished in Springer Series in Plasma Science and Technology, The Physics of Laser Plasmas and Applications - Volume 2 by Springer International Publishing in 2024, page: 197-28410.1007/978-3-031-45473-8_5
- 2.Author(s): Alessandro Colombo, Daniela RuppPublished in Structural Dynamics with X-ray and Electron Scattering by Royal Society of Chemistry in 2023, page: 172-23210.1039/bk9781837671564-00172
- 3.Author(s): Phay J. Ho, Gilles Doumy, Linda YoungPublished in ACS Symposium Series, Emerging Trends in Chemical Applications of Lasers by American Chemical Society in 2021, page: 15-4810.1021/bk-2021-1398.ch002
- 4.Author(s): Robin Santra, Linda YoungPublished in Synchrotron Light Sources and Free-Electron Lasers by Springer International Publishing in 2020, page: 1435-146210.1007/978-3-030-23201-6_25
- 5.Author(s): Christoph Bostedt, Tais Gorkhover, Daniela Rupp, Thomas MöllerPublished in Synchrotron Light Sources and Free-Electron Lasers by Springer International Publishing in 2020, page: 1525-157310.1007/978-3-030-23201-6_39
- 6.Author(s): Christoph Bostedt, Tais Gorkhover, Daniela Rupp, Thomas MöllerPublished in Synchrotron Light Sources and Free-Electron Lasers by Springer International Publishing in 2019, page: 1-4910.1007/978-3-319-04507-8_39-2
- 7.Author(s): Nora BerrahPublished in Fullerenes and Relative Materials - Properties and Applications by InTech in 201810.5772/intechopen.70769
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- 9.Author(s): Henry N. ChapmanPublished in Methods in Molecular Biology, Protein Crystallography by Springer New York in 2017, page: 295-32410.1007/978-1-4939-7000-1_12
- 10.Author(s): Robin Santra, Linda YoungPublished in Synchrotron Light Sources and Free-Electron Lasers by Springer International Publishing in 2016, page: 1233-126010.1007/978-3-319-14394-1_25
- 11.Author(s): Christoph Bostedt, Tais Gorkhover, Daniela Rupp, Thomas MöllerPublished in Synchrotron Light Sources and Free-Electron Lasers by Springer International Publishing in 2016, page: 1323-136410.1007/978-3-319-14394-1_39
- 12.Author(s): Daniela RuppPublished in Springer Theses, Ionization and Plasma Dynamics of Single Large Xenon Clusters in Superintense XUV Pulses by Springer International Publishing in 2016, page: 1-5610.1007/978-3-319-28649-5_1
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- 14.Author(s): Robin Santra, Linda YoungPublished in Synchrotron Light Sources and Free-Electron Lasers by Springer International Publishing in 2015, page: 1-2410.1007/978-3-319-04507-8_25-1
- 15.Author(s): Andrei Benediktovitch, Ilya Feranchuk, Alexander UlyanenkovPublished in Springer Series in Materials Science, Theoretical Concepts of X-Ray Nanoscale Analysis by Springer Berlin Heidelberg in 2013, page: 53-6910.1007/978-3-642-38177-5_2
- 1.Author(s): Kai Sdeo, Bastian Rieck, Filip SadloPublished in 2018 IEEE Pacific Visualization Symposium (PacificVis) by IEEE in 2018, page: 111-11510.1109/pacificvis.2018.00022
- 2.Author(s): C. Fortmann-Grote, A. A. Andreev, K. Appel, J. Branco, R. Briggs, M. Bussmann, A. Buzmakov, M. Garten, A. Grund, A. Huebl, Z. Jurek, N. D. Loh, M. Nakatsutsumi, L. Samoylova, R. Santra, E. A. Schneidmiller, A. Sharma, K. Steiniger, S. Yakubov, C. H. Yoon, M. V. Yurkov, U. Zastrau, B. Ziaja-Motyka, A. P. MancusoPublished in SPIE Proceedings, Advances in X-ray Free-Electron Lasers Instrumentation IV by SPIE in 2017, page: 102370S10.1117/12.2270552
- 3.Author(s): H.-K. Chung, B. I. Cho, O. Ciricosta, S. M. Vinko, J. S. Wark, R. W. LeePublished in AIP Conference Proceedings by Author(s) in 2017, page: 02000110.1063/1.4975712
- 4.Author(s): Zoltan Jurek, Beata Ziaja-Motyka, Robin Santra, Adrian P. Mancuso, Johan Bielecki, Carsten Fortmann-GrotePublished in Advances in Computational Methods for X-Ray Optics IV by SPIE in 2017, page: 2210.1117/12.2275274
- 5.Author(s): F. X. KärtnerPublished in High-Brightness Sources and Light-Driven Interactions by OSA in 2016, page: ES3A.110.1364/euvxray.2016.es3a.1
- 6.Author(s): Kenji TamasakuPublished in International Conference on Ultrafast Phenomena by OSA in 2016, page: UF1A.110.1364/up.2016.uf1a.1
- 7.Author(s): Lorenzo Galli, Peter Metcalf, Henry N. ChapmanPublished in SPIE Proceedings, Damage to VUV, EUV, and X-ray Optics V by SPIE in 2015, page: 95110H10.1117/12.2182654
- 8.Author(s): Aleksandr Leonov, Dmitriy Ksenzov, Andrei Benediktovitch, Ilya Feranchuk, Ullrich PietschPublished in SPIE Proceedings, Damage to VUV, EUV, and X-ray Optics IV; and EUV and X-ray Optics: Synergy between Laboratory and Space III by SPIE in 2013, page: 87770E10.1117/12.2017453
- 9.Author(s): Siddharth Bhardwaj, Sang-Kil Son, Robin Santra, Franz X KärtnerPublished in Conference on Lasers and Electro-Optics 2012 by OSA in 2012, page: JW4A.1810.1364/cleo_at.2012.jw4a.18
- 1.Author(s): Baoning Sun, Hao Zhou, Yang Du, Meiyi Wu, Kuisong Huang, Siyuan Tan, Zhongmin Xu, Qinming Li, Weiqing ZhangPublished in International Journal of Thermal Sciences by Elsevier BV in 2026, page: 11060310.1016/j.ijthermalsci.2025.110603
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- 4.Author(s): Ludger Inhester, Arturo Sopena Moros, Sam Macé, Caroline Arnold, Robin SantraPublished in The Journal of Chemical Physics by AIP Publishing in 202510.1063/5.0258328
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- 9.Author(s): Markus Ilchen, Enrico Allaria, Primož Rebernik Ribič, Heinz-Dieter Nuhn, Alberto Lutman, Evgeny Schneidmiller, Markus Tischer, Mikail Yurkov, Marco Calvi, Eduard Prat, Sven Reiche, Thomas Schmidt, Gianluca Aldo Geloni, Suren Karabekyan, Jiawei Yan, Svitozar Serkez, Zhangfeng Gao, Bangjie Deng, Chao Feng, Haixiao Deng, Wolfram Helml, Lars Funke, Mats Larsson, Vitali Zhaunerchyk, Michael Meyer, Tommaso Mazza, Till Jahnke, Reinhard Dörner, Francesca Calegari, Olga Smirnova, Caterina Vozzi, Giovanni De Ninno, Jonas Wätzel, Jamal Berakdar, Sadia Bari, Lucas Schwob, Jérémy R. Rouxel, Shaul Mukamel, Klaus Bartschat, Kathryn Hamilton, Luca Argenti, Nicolas Douguet, Nikolay M. Novikovskiy, Philipp V. Demekhin, Peter WalterPublished in Physical Review Research by American Physical Society (APS) in 202510.1103/physrevresearch.7.011001
- 10.Author(s): Adam E. A. Fouda, Bhavnesh Jangid, Eetu Pelimanni, Stephen H. Southworth, Phay J. Ho, Laura Gagliardi, Linda YoungPublished in The Journal of Physical Chemistry A by American Chemical Society (ACS) in 2025, page: 8419-843110.1021/acs.jpca.5c01789
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- 13.Author(s): Nora Berrah, James Cryan, River Robles, Taran Driver, Agostino Marinelli, Philip BucksbaumPublished in Advances in Optics and Photonics by Optica Publishing Group in 2025, page: 62310.1364/aop.540527
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- 16.Author(s): Mei Bai, Robin Santra, Sang-Kil Son, Henning Kirchberg, Michael ThorwartPublished in The Journal of Physical Chemistry B by American Chemical Society (ACS) in 2025, page: 374-38310.1021/acs.jpcb.5c06230
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- 32.Author(s): Xu Zhou, Chuan Wang, Rong-Hao Hu, Zhi-Hao Tao, Xiao-Liang Deng, Yi-Han Liang, Xiao-Ya Li, Meng Lü, Wen-Jun Zhu, College of Physics, Sichuan University, Chengdu 610064, China, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Chengdu 610065, China, Key Laboratory of Radiation Physics and Technology, Ministry of Education, Chengdu 610065, China, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621000, ChinaPublished in Acta Physica Sinica by Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences in 2024, page: 10310410.7498/aps.73.20240213
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- 37.Author(s): Zhe Lin, Junzi Liu, Chaoqun Zhang, Xuechen Zheng, Lan ChengPublished in The Journal of Physical Chemistry A by American Chemical Society (ACS) in 2024, page: 8373-838310.1021/acs.jpca.4c04089
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- 40.Author(s): Arturo Sopena Moros, Shuai Li, Kai Li, Gilles Doumy, Stephen H. Southworth, Christopher Otolski, Richard D. Schaller, Yoshiaki Kumagai, Jan-Erik Rubensson, Marc Simon, Georgi Dakovski, Kristjan Kunnus, Joseph S. Robinson, Christina Y. Hampton, David J. Hoffman, Jake Koralek, Zhi-Heng Loh, Robin Santra, Ludger Inhester, Linda YoungPublished in Journal of the American Chemical Society by American Chemical Society (ACS) in 2024, page: 3262-326910.1021/jacs.3c11857
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- 42.Author(s): Laura Budewig, Sang-Kil Son, Zoltan Jurek, Malik Muhammad Abdullah, Marina Tropmann-Frick, Robin SantraPublished in Physical Review Research by American Physical Society (APS) in 202410.1103/physrevresearch.6.013265
- 43.Author(s): Stasis Chuchurka, Andrei Benediktovitch, Špela Krušič, Aliaksei Halavanau, Nina RohringerPublished in Physical Review A by American Physical Society (APS) in 202410.1103/physreva.109.033725
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