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
Mentions
- 1.Author(s): Arunangshu Debnath, Robin SantraPublished in Physical Review Research by American Physical Society (APS) in 202310.1103/physrevresearch.5.023158
- 2.Author(s): Niels Breckwoldt, Sang-Kil Son, Tommaso Mazza, Aljoscha Rörig, Rebecca Boll, Michael Meyer, Aaron C. LaForge, Debadarshini Mishra, Nora Berrah, Robin SantraPublished in Physical Review Research by American Physical Society (APS) in 202310.1103/physrevresearch.5.023114
- 3.Author(s): N. Medvedev, A. E. Volkov, R. Rymzhanov, F. Akhmetov, S. Gorbunov, R. Voronkov, P. BabaevPublished in Journal of Applied Physics by AIP Publishing in 202310.1063/5.0128774
- 4.Author(s): Hao Zhou, Qi Huang, Kai He, GuiLong Gao, Xin Yan, Dong Yao, Tao Wang, Jinshou Tian, RongHao Hu, Meng LvPublished in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences by The Royal Society in 202310.1098/rsta.2022.0213
- 5.Author(s): Zhong Yin, Yi-Ping Chang, Tadas Balčiūnas, Yashoj Shakya, Aleksa Djorović, Geoffrey Gaulier, Giuseppe Fazio, Robin Santra, Ludger Inhester, Jean-Pierre Wolf, Hans Jakob WörnerPublished in Nature by Springer Science and Business Media LLC in 2023, page: 749-75410.1038/s41586-023-06182-6
- 6.Author(s): Beata Ziaja, John Jasper Bekx, Martin Masek, Nikita Medvedev, Vladimir Lipp, Vikrant Saxena, Michal StranskyPublished in Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences by The Royal Society in 202310.1098/rsta.2022.0216
- 7.Author(s): Laura Budewig, Sang-Kil Son, Robin SantraPublished in Physical Review A by American Physical Society (APS) in 202310.1103/physreva.107.013102
- 8.Author(s): Sourav Banerjee, Zoltan Jurek, Malik Muhammad Abdullah, Robin SantraPublished in Structural Dynamics by AIP Publishing in 202210.1063/4.0000166
- 9.Author(s): Nikita Medvedev, Fedor Akhmetov, Ruslan A. Rymzhanov, Roman Voronkov, Alexander E. VolkovPublished in Advanced Theory and Simulations by Wiley in 202210.1002/adts.202200091
- 10.Author(s): Stanislaw Wirok-Stoletow, Rui Jin, Daria Kolbasova, Sang-Kil Son, Andrew Aquila, Robin SantraPublished in Physical Review A by American Physical Society (APS) in 202210.1103/physreva.106.023118
- 11.Author(s): Felix Allum, Valerija Music, Ludger Inhester, Rebecca Boll, Benjamin Erk, Philipp Schmidt, Thomas M. Baumann, Günter Brenner, Michael Burt, Philipp V. Demekhin, Simon Dörner, Arno Ehresmann, Andreas Galler, Patrik Grychtol, David Heathcote, Denis Kargin, Mats Larsson, Jason W. L. Lee, Zheng Li, Bastian Manschwetus, Lutz Marder, Robert Mason, Michael Meyer, Huda Otto, Christopher Passow, Rudolf Pietschnig, Daniel Ramm, Kaja Schubert, Lucas Schwob, Richard D. Thomas, Claire Vallance, Igor Vidanović, Clemens von Korff Schmising, René Wagner, Peter Walter, Vitali Zhaunerchyk, Daniel Rolles, Sadia Bari, Mark Brouard, Markus IlchenPublished in Communications Chemistry by Springer Science and Business Media LLC in 202210.1038/s42004-022-00656-w
- 12.Author(s): Michal Stransky, Zoltan Jurek, Robin Santra, Adrian P. Mancuso, Beata ZiajaPublished in Molecules by MDPI AG in 2022, page: 420610.3390/molecules27134206
- 13.Author(s): Wojciech Błachucki, Anna Wach, Joanna Czapla-Masztafiak, Mickaël Delcey, Christopher Arrell, Rafał Fanselow, Pavle Juranić, Marcus Lundberg, Christopher Milne, Jacinto Sá, Jakub SzlachetkoPublished in Applied Sciences by MDPI AG in 2022, page: 172110.3390/app12031721
- 14.Author(s): Rui Jin, Zoltan Jurek, Robin Santra, Sang-Kil SonPublished in Physical Review E by American Physical Society (APS) in 202210.1103/physreve.106.015206
- 15.Author(s): Rebecca Boll, Julia M. Schäfer, Benoît Richard, Kilian Fehre, Gregor Kastirke, Zoltan Jurek, Markus S. Schöffler, Malik M. Abdullah, Nils Anders, Thomas M. Baumann, Sebastian Eckart, Benjamin Erk, Alberto De Fanis, Reinhard Dörner, Sven Grundmann, Patrik Grychtol, Alexander Hartung, Max Hofmann, Markus Ilchen, Ludger Inhester, Christian Janke, Rui Jin, Max Kircher, Katharina Kubicek, Maksim Kunitski, Xiang Li, Tommaso Mazza, Severin Meister, Niklas Melzer, Jacobo Montano, Valerija Music, Giammarco Nalin, Yevheniy Ovcharenko, Christopher Passow, Andreas Pier, Nils Rennhack, Jonas Rist, Daniel E. Rivas, Daniel Rolles, Ilme Schlichting, Lothar Ph. H. Schmidt, Philipp Schmidt, Juliane Siebert, Nico Strenger, Daniel Trabert, Florian Trinter, Isabel Vela-Perez, Rene Wagner, Peter Walter, Miriam Weller, Pawel Ziolkowski, Sang-Kil Son, Artem Rudenko, Michael Meyer, Robin Santra, Till JahnkePublished in Nature Physics by Springer Science and Business Media LLC in 2022, page: 423-42810.1038/s41567-022-01507-0
- 16.Author(s): Akinobu Niozu, Hironobu Fukuzawa, Toru Hagiya, Akifumi Yamamoto, Daehyun You, Shu Saito, Yudai Ishimura, Tadashi Togashi, Shigeki Owada, Kensuke Tono, Makina Yabashi, Shin-ichi Wada, Kazuhiro Matsuda, Kiyoshi Ueda, Kiyonobu NagayaPublished in Physical Review A by American Physical Society (APS) in 202210.1103/physreva.106.043116
- 17.Author(s): Simone Gargiulo, Ivan Madan, Fabrizio CarbonePublished in Physical Review Letters by American Physical Society (APS) in 202210.1103/physrevlett.128.212502
- 18.Author(s): Laura Budewig, Sang-Kil Son, Robin SantraPublished in Physical Review A by American Physical Society (APS) in 202210.1103/physreva.105.033111
- 19.Author(s): Xiang Li, Ludger Inhester, Timur Osipov, Rebecca Boll, Ryan Coffee, James Cryan, Ave Gatton, Tais Gorkhover, Gregor Hartman, Markus Ilchen, André Knie, Ming-Fu Lin, Michael P. Minitti, Clemens Weninger, Thomas J. A. Wolf, Sang-Kil Son, Robin Santra, Daniel Rolles, Artem Rudenko, Peter WalterPublished in Scientific Reports by Springer Science and Business Media LLC in 202110.1038/s41598-020-79818-6
- 20.Author(s): X. Li, L. Inhester, S. J. Robatjazi, B. Erk, R. Boll, K. Hanasaki, K. Toyota, Y. Hao, C. Bomme, B. Rudek, L. Foucar, S. H. Southworth, C. S. Lehmann, B. Kraessig, T. Marchenko, M. Simon, K. Ueda, K. R. Ferguson, M. Bucher, T. Gorkhover, S. Carron, R. Alonso-Mori, J. E. Koglin, J. Correa, G. J. Williams, S. Boutet, L. Young, C. Bostedt, S.-K. Son, R. Santra, D. Rolles, A. RudenkoPublished in Physical Review Letters by American Physical Society (APS) in 202110.1103/physrevlett.127.093202
- 21.Author(s): Yashoj Shakya, Ludger Inhester, Caroline Arnold, Ralph Welsch, Robin SantraPublished in Structural Dynamics by AIP Publishing in 202110.1063/4.0000076
- 22.Author(s): Beata Ziaja, John Jasper Bekx, Martin Masek, Nikita Medvedev, Przemyslaw Piekarz, Vikrant Saxena, Michal Stransky, Sven ToleikisPublished in The European Physical Journal D by Springer Science and Business Media LLC in 202110.1140/epjd/s10053-021-00235-z
- 23.Author(s): Benoît Richard, Julia M Schäfer, Zoltan Jurek, Robin Santra, Ludger InhesterPublished in Journal of Physics B: Atomic, Molecular and Optical Physics by IOP Publishing in 2021, page: 19400110.1088/1361-6455/ac2f4f
- 24.Author(s): Rui Jin, Malik Muhammad Abdullah, Zoltan Jurek, Robin Santra, Sang-Kil SonPublished in Physical Review E by American Physical Society (APS) in 202110.1103/physreve.103.023203
- 25.Author(s): Phay J. Ho, Adam E. A. Fouda, Kai Li, Gilles Doumy, Linda YoungPublished in Faraday Discussions by Royal Society of Chemistry (RSC) in 2021, page: 139-16010.1039/d0fd00106f
- 26.Author(s): Michael Obermeyer, Ludger Inhester, Robin SantraPublished in Physical Review A by American Physical Society (APS) in 202110.1103/physreva.104.023115
- 27.Author(s): Juncheng E, Michal Stransky, Zoltan Jurek, Carsten Fortmann-Grote, Libor Juha, Robin Santra, Beata Ziaja, Adrian P. MancusoPublished in Scientific Reports by Springer Science and Business Media LLC in 202110.1038/s41598-021-97142-5
- 28.Author(s): Yoshiaki Kumagai, Zoltan Jurek, Weiqing Xu, Vikrant Saxena, Hironobu Fukuzawa, Koji Motomura, Denys Iablonskyi, Kiyonobu Nagaya, Shin-ichi Wada, Yuta Ito, Tsukasa Takanashi, Shuhei Yamada, Yuta Sakakibara, Toshiyuki Nishiyama Hiraki, Takayuki Umemoto, Minna Patanen, John D Bozek, Ioan Dancus, Mihail Cernaianu, Catalin Miron, Tobias Bauer, Melanie Mucke, Edwin Kukk, Shigeki Owada, Tadashi Togashi, Kensuke Tono, Makina Yabashi, Sang-Kil Son, Beata Ziaja, Robin Santra, Kiyoshi UedaPublished in Journal of Physics B: Atomic, Molecular and Optical Physics by IOP Publishing in 2021, page: 04400110.1088/1361-6455/abd878
- 29.Author(s): Aaron C. LaForge, Sang-Kil Son, Debadarshini Mishra, Markus Ilchen, Stephen Duncanson, Eemeli Eronen, Edwin Kukk, Stanislaw Wirok-Stoletow, Daria Kolbasova, Peter Walter, Rebecca Boll, Alberto De Fanis, Michael Meyer, Yevheniy Ovcharenko, Daniel E. Rivas, Philipp Schmidt, Sergey Usenko, Robin Santra, Nora BerrahPublished in Physical Review Letters by American Physical Society (APS) in 202110.1103/physrevlett.127.213202
- 30.Author(s): T. Jahnke, R. Guillemin, L. Inhester, S.-K. Son, G. Kastirke, M. Ilchen, J. Rist, D. Trabert, N. Melzer, N. Anders, T. Mazza, R. Boll, A. De Fanis, V. Music, Th. Weber, M. Weller, S. Eckart, K. Fehre, S. Grundmann, A. Hartung, M. Hofmann, C. Janke, M. Kircher, G. Nalin, A. Pier, J. Siebert, N. Strenger, I. Vela-Perez, T. M. Baumann, P. Grychtol, J. Montano, Y. Ovcharenko, N. Rennhack, D. E. Rivas, R. Wagner, P. Ziolkowski, P. Schmidt, T. Marchenko, O. Travnikova, L. Journel, I. Ismail, E. Kukk, J. Niskanen, F. Trinter, C. Vozzi, M. Devetta, S. Stagira, M. Gisselbrecht, A. L. Jäger, X. Li, Y. Malakar, M. Martins, R. Feifel, L. Ph. H. Schmidt, A. Czasch, G. Sansone, D. Rolles, A. Rudenko, R. Moshammer, R. Dörner, M. Meyer, T. Pfeifer, M. S. Schöffler, R. Santra, M. Simon, M. N. PiancastelliPublished in Physical Review X by American Physical Society (APS) in 202110.1103/physrevx.11.041044
- 31.Author(s): Z.-H. Loh, G. Doumy, C. Arnold, L. Kjellsson, S. H. Southworth, A. Al Haddad, Y. Kumagai, M.-F. Tu, P. J. Ho, A. M. March, R. D. Schaller, M. S. Bin Mohd Yusof, T. Debnath, M. Simon, R. Welsch, L. Inhester, K. Khalili, K. Nanda, A. I. Krylov, S. Moeller, G. Coslovich, J. Koralek, M. P. Minitti, W. F. Schlotter, J.-E. Rubensson, R. Santra, L. YoungPublished in Science by American Association for the Advancement of Science (AAAS) in 2020, page: 179-18210.1126/science.aaz4740
- 32.Author(s): Khadijeh Khalili, Ludger Inhester, Caroline Arnold, Anders S. Gertsen, Jens Wenzel Andreasen, Robin SantraPublished in Structural Dynamics by AIP Publishing in 2020, page: 04410110.1063/4.0000016
- 33.Author(s): Caroline Arnold, Céline Larivière-Loiselle, Khadijeh Khalili, Ludger Inhester, Ralph Welsch, Robin SantraPublished in Journal of Physics B: Atomic, Molecular and Optical Physics by IOP Publishing in 2020, page: 16400610.1088/1361-6455/ab9658
- 34.Author(s): Akinori SaekiPublished in Polymer Journal by Springer Science and Business Media LLC in 2020, page: 1307-132110.1038/s41428-020-00399-2
- 35.Author(s): Alexander Kozlov, Andrew V. Martin, Harry M. QuineyPublished in Crystals by MDPI AG in 2020, page: 47810.3390/cryst10060478
- 36.Author(s): Carl Caleman, Francisco Jares Junior, Oscar Grånäs, Andrew V. MartinPublished in Crystals by MDPI AG in 2020, page: 58510.3390/cryst10070585
- 37.Author(s): Henry I. B. Banks, Antonis Hadjipittas, Agapi EmmanouilidouPublished in The European Physical Journal D by Springer Science and Business Media LLC in 202010.1140/epjd/e2020-100416-6
- 38.Author(s): Hironobu Fukuzawa, Kiyoshi UedaPublished in Advances in Physics: X by Informa UK Limited in 2020, page: 178532710.1080/23746149.2020.1785327
- 39.Author(s): Aliaksei Halavanau, Andrei Benediktovitch, Alberto A. Lutman, Daniel DePonte, Daniele Cocco, Nina Rohringer, Uwe Bergmann, Claudio PellegriniPublished in Proceedings of the National Academy of Sciences by Proceedings of the National Academy of Sciences in 2020, page: 15511-1551610.1073/pnas.2005360117
- 40.Author(s): Phay J. Ho, Benedikt J. Daurer, Max F. Hantke, Johan Bielecki, Andre Al Haddad, Maximilian Bucher, Gilles Doumy, Ken R. Ferguson, Leonie Flückiger, Tais Gorkhover, Bianca Iwan, Christopher Knight, Stefan Moeller, Timur Osipov, Dipanwita Ray, Stephen H. Southworth, Martin Svenda, Nicusor Timneanu, Anatoli Ulmer, Peter Walter, Janos Hajdu, Linda Young, Filipe R. N. C. Maia, Christoph BostedtPublished in Nature Communications by Springer Science and Business Media LLC in 202010.1038/s41467-019-13905-9
- 41.Author(s): Yoshiaki Kumagai, Zoltan Jurek, Weiqing Xu, Hironobu Fukuzawa, Koji Motomura, Denys Iablonskyi, Kiyonobu Nagaya, Shin-ichi Wada, Subhendu Mondal, Tetsuya Tachibana, Yuta Ito, Tsukasa Sakai, Kenji Matsunami, Toshiyuki Nishiyama, Takayuki Umemoto, Christophe Nicolas, Catalin Miron, Tadashi Togashi, Kanade Ogawa, Shigeki Owada, Kensuke Tono, Makina Yabashi, Sang-Kil Son, Beata Ziaja, Robin Santra, Kiyoshi UedaPublished in Physical Review A by American Physical Society (APS) in 202010.1103/physreva.101.023412
- 42.Author(s): Andrei Benediktovitch, Laurent Mercadier, Olivier Peyrusse, Andreas Przystawik, Tim Laarmann, Bruno Langbehn, Cédric Bomme, Benjamin Erk, Jonathan Correa, Caroline Mossé, Daniel Rolles, Sven Toleikis, Maximilian Bucher, Christoph F. O. Bostedt, Alvaro Sanchez-Gonzalez, Stepan Dobrodey, Michael A. Blessenohl, Alexander Nelde, Maria Müller, Daniela Rupp, Thomas Möller, José R. Crespo López-Urrutia, Nina RohringerPublished in Physical Review A by American Physical Society (APS) in 202010.1103/physreva.101.063412
- 43.Author(s): Sang-Kil Son, Rebecca Boll, Robin SantraPublished in Physical Review Research by American Physical Society (APS) in 202010.1103/physrevresearch.2.023053
- 44.Author(s): Karol Nass, Alexander Gorel, Malik M. Abdullah, Andrew V. Martin, Marco Kloos, Agostino Marinelli, Andrew Aquila, Thomas R. M. Barends, Franz-Josef Decker, R. Bruce Doak, Lutz Foucar, Elisabeth Hartmann, Mario Hilpert, Mark S. Hunter, Zoltan Jurek, Jason E. Koglin, Alexander Kozlov, Alberto A. Lutman, Gabriela Nass Kovacs, Christopher M. Roome, Robert L. Shoeman, Robin Santra, Harry M. Quiney, Beata Ziaja, Sébastien Boutet, Ilme SchlichtingPublished in Nature Communications by Springer Science and Business Media LLC in 202010.1038/s41467-020-15610-4
- 45.Author(s): John Jasper Bekx, Sang-Kil Son, Beata Ziaja, Robin SantraPublished in Physical Review Research by American Physical Society (APS) in 202010.1103/physrevresearch.2.033061
- 46.Author(s): Caroline Arnold, Ludger Inhester, Sergio Carbajo, Ralph Welsch, Robin SantraPublished in The Journal of Chemical Physics by AIP Publishing in 201910.1063/1.5054272
- 47.Author(s): Yajiang Hao, Ludger Inhester, Sang-Kil Son, Robin SantraPublished in Physical Review A by American Physical Society (APS) in 201910.1103/physreva.100.013402
- 48.Author(s): Yves Kayser, Chris Milne, Pavle Juranić, Leonardo Sala, Joanna Czapla-Masztafiak, Rolf Follath, Matjaž Kavčič, Gregor Knopp, Jens Rehanek, Wojciech Błachucki, Mickaël G. Delcey, Marcus Lundberg, Krzysztof Tyrała, Diling Zhu, Roberto Alonso-Mori, Rafael Abela, Jacinto Sá, Jakub SzlachetkoPublished in Nature Communications by Springer Science and Business Media LLC in 201910.1038/s41467-019-12717-1
- 49.Author(s): Andrei Benediktovitch, Vinay P. Majety, Nina RohringerPublished in Physical Review A by American Physical Society (APS) in 201910.1103/physreva.99.013839
- 50.Author(s): Sadia Bari, Ludger Inhester, Kaja Schubert, Karolin Mertens, Jan O. Schunck, Simon Dörner, Sascha Deinert, Lucas Schwob, Stefan Schippers, Alfred Müller, Stephan Klumpp, Michael MartinsPublished in Physical Chemistry Chemical Physics by Royal Society of Chemistry (RSC) in 2019, page: 16505-1651410.1039/c9cp02864a