Citing sisl

sisl is an open-source software package intended for the scientific community. It is released under the MPL-2 license.

You are encouraged to cite sisl when you use it to produce scientific contributions.

The sisl citation can be found through Zenodo: zenodo

By citing sisl you are encouraging development and exposing the software package.

Citing basic usage

If you are only using sisl as a post-processing tool and/or tight-binding calculations you should cite this (Zenodo DOI):

@software{zerothi_sisl,
  author       = {Papior, Nick},
  title        = {sisl: v<fill-version>},
  year         = {2024},
  doi          = {10.5281/zenodo.597181},
  url          = {https://doi.org/10.5281/zenodo.597181}
}

The sgeom, sgrid or sdata commands all print-out the above information in a suitable format:

sgeom --cite
sgrid --cite
sdata --cite

which fill in the version for you, all yield the same output.

Citing transport backend

When using sisl as tight-binding setup for Hamiltonians and/or dynamical matrices for TBtrans and/or PHtrans you should cite these two DOI’s:

@software{zerothi_sisl,
  author       = {Papior, Nick},
  title        = {sisl: v<fill-version>},
  year         = {2024},
  doi          = {10.5281/zenodo.597181},
  url          = {https://doi.org/10.5281/zenodo.597181}
}

@article{Papior2017,
  author = {Papior, Nick and Lorente, Nicol{\'{a}}s and Frederiksen, Thomas and Garc{\'{i}}a, Alberto and Brandbyge, Mads},
  doi = {10.1016/j.cpc.2016.09.022},
  issn = {00104655},
  journal = {Computer Physics Communications},
  month = {mar},
  number = {July},
  pages = {8--24},
  title = {{Improvements on non-equilibrium and transport Green function techniques: The next-generation transiesta}},
  volume = {212},
  year = {2017}
}

If using real-space self-energies one should additionally cite:

@article{papior2019,
  author = {Papior, Nick and Calogero, Gaetano and Leitherer, Susanne and Brandbyge, Mads},
  doi = {10.1103/physrevb.100.195417},
  number = {19},
  source = {Crossref},
  url = {https://doi.org/10.1103/physrevb.100.195417},
  volume = {100},
  journal = {Phys. Rev. B},
  publisher = {American Physical Society (APS)},
  title = {Removing all periodic boundary conditions: {Efficient} nonequilibrium Green's function calculations},
  issn = {2469-9950, 2469-9969},
  year = {2019},
  month = nov,
}

Publications using sisl

The sisl tool-suite has been used one way or the other in the listed publications below.

Please help maintaining the list complete via a pull request or by writing an email to nickpapior AT gmail.com.

  1. Sanghita Sengupta, Thomas Frederiksen, and Geza Giedke. Hyperfine interactions in open-shell planar $sp^2$-carbon nanostructures. Phys. Rev. B, 107:224433, Jun 2023. URL: https://link.aps.org/doi/10.1103/PhysRevB.107.224433, doi:10.1103/PhysRevB.107.224433.

  2. César Moreno, Xabier Diaz de Cerio, Manuel Vilas-Varela, Maria Tenorio, Ane Sarasola, Mads Brandbyge, Diego Peña, Aran Garcia-Lekue, and Aitor Mugarza. Molecular bridge engineering for tuning quantum electronic transport and anisotropy in nanoporous graphene. Journal of the American Chemical Society, 145(16):8988–8995, 2023. PMID: 36988648. URL: https://doi.org/10.1021/jacs.3c00173, arXiv:https://doi.org/10.1021/jacs.3c00173, doi:10.1021/jacs.3c00173.

  3. Jakob Kjærulff Svaneborg, Aleksander Bach Lorentzen, Fei Gao, Antti-Pekka Jauho, and Mads Brandbyge. Manipulation of magnetization and spin transport in hydrogenated graphene with thz pulses. Frontiers in Physics, 2023. URL: https://www.frontiersin.org/articles/10.3389/fphy.2023.1237383, doi:10.3389/fphy.2023.1237383.

  4. Yuefei Huang, Tariq Altalhi, Boris I. Yakobson, and Evgeni S. Penev. Nucleobase-bonded graphene nanoribbon junctions: Electron transport from first principles. ACS Nano, 16(10):16736–16743, October 2022. URL: https://doi.org/10.1021/acsnano.2c06274, doi:10.1021/acsnano.2c06274.

  5. Calin-Andrei Pantis-Simut, Amanda Teodora Preda, Nicolae Filipoiu, Alaa Allosh, and George Alexandru Nemnes. Electric-field control in phosphorene-based heterostructures. Nanomaterials, 12(20):3650, October 2022. URL: https://doi.org/10.3390/nano12203650, doi:10.3390/nano12203650.

  6. N. Papior, S. Leitherer, and M. Brandbyge. Simple approach to current-induced bond weakening in ballistic conductors. Phys. Rev. B, October 2022. URL: https://doi.org/10.1103/physrevb.106.155401, doi:10.1103/physrevb.106.155401.

  7. Joel G Fallaque, Sandra Rodríguez-González, Fernando Martín, and Cristina Díaz. Self-energy corrected DFT-NEGF for conductance in molecular junctions: An accurate and efficient implementation for TRANSIESTA package applied to au electrodes. J. Phys. Condens. Matter, 34(43):435901, August 2022. URL: https://doi.org/10.1088/1361-648x/ac89c4, doi:10.1088/1361-648x/ac89c4.

  8. Dongzhe Li, Yongfeng Tong, Kaushik Bairagi, Massine Kelai, Yannick J. Dappe, Jérôme Lagoute, Yann Girard, Sylvie Rousset, Vincent Repain, Cyrille Barreteau, Mads Brandbyge, Alexander Smogunov, and Amandine Bellec. Negative differential resistance in spin-crossover molecular devices. The Journal of Physical Chemistry Letters, 13(32):7514–7520, August 2022. URL: https://doi.org/10.1021/acs.jpclett.2c01934, doi:10.1021/acs.jpclett.2c01934.

  9. Maria Tenorio, Cesar Moreno, Pol Febrer, Jesús Castro-Esteban, Pablo Ordejón, Diego Peña, Miguel Pruneda, and Aitor Mugarza. Atomically sharp lateral superlattice heterojunctions Built-In Nitrogen-Doped nanoporous graphene. Adv. Mater., 34(20):2110099, April 2022. URL: https://doi.org/10.1002/adma.202110099, doi:10.1002/adma.202110099.

  10. Guodong Yu, Yunhua Wang, Mikhail I. Katsnelson, Hai-Qing Lin, and Shengjun Yuan. Interlayer hybridization in graphene quasicrystal and other bilayer graphene systems. Phys. Rev. B, March 2022. URL: https://doi.org/10.1103/physrevb.105.125403, doi:10.1103/physrevb.105.125403.

  11. Nils Wittemeier, Matthieu J. Verstraete, Pablo Ordejón, and Zeila Zanolli. Interference effects in one-dimensional moiré crystals. Carbon, 186:416–422, January 2022. URL: https://doi.org/10.1016/j.carbon.2021.10.028, doi:10.1016/j.carbon.2021.10.028.

  12. Tao Wang, Sofia Sanz, Jesús Castro-Esteban, James Lawrence, Alejandro Berdonces-Layunta, Mohammed S. G. Mohammed, Manuel Vilas-Varela, Martina Corso, Diego Peña, Thomas Frederiksen, and Dimas G. de Oteyza. Magnetic interactions between radical pairs in chiral graphene nanoribbons. Nano Lett., 22(1):164–171, December 2021. URL: https://doi.org/10.1021/acs.nanolett.1c03578, doi:10.1021/acs.nanolett.1c03578.

  13. Isaac Alcón, Nick Papior, Gaetano Calogero, Francesc Viñes, Pablo Gamallo, and Mads Brandbyge. Acetylene-mediated electron transport in nanostructured graphene and hexagonal boron nitride. The Journal of Physical Chemistry Letters, 12(45):11220–11227, November 2021. URL: https://doi.org/10.1021/acs.jpclett.1c03166, doi:10.1021/acs.jpclett.1c03166.

  14. El-Abed Haidar, Sherif Abdulkader Tawfik, and Catherine Stampfl. Twist-dependent electron charge transfer and transport in Phosphorene–Graphene heterobilayers. The Journal of Physical Chemistry C, 125(46):25886–25897, November 2021. URL: https://doi.org/10.1021/acs.jpcc.1c08282, doi:10.1021/acs.jpcc.1c08282.

  15. Armando Pezo, Zeila Zanolli, Nils Wittemeier, Pablo Ordejón, Adalberto Fazzio, Stephan Roche, and Jose H Garcia. Manipulation of spin transport in graphene/transition metal dichalcogenide heterobilayers upon twisting. 2D Mater., 9(1):015008, November 2021. URL: https://doi.org/10.1088/2053-1583/ac3378, doi:10.1088/2053-1583/ac3378.

  16. Jeremy Hieulle, Silvia Castro, Niklas Friedrich, Alessio Vegliante, Francisco Romero Lara, Sofía Sanz, Dulce Rey, Martina Corso, Thomas Frederiksen, Jose Ignacio Pascual, and Diego Peña. On-Surface synthesis and collective spin excitations of a Triangulene-Based nanostar. Angew. Chem. Int. Ed., 60(48):25224–25229, October 2021. URL: https://doi.org/10.1002/anie.202108301, doi:10.1002/anie.202108301.

  17. Junwei Tong, Yanzhao Wu, Liuxia Ruan, Bo Yang, Guangming Xie, Gaowu Qin, Fubo Tian, and Xianmin Zhang. Breaking the symmetry of spin-sublattices in antiferromagnet by interfacial tailoring in the \ensuremath <i\ensuremath >L\ensuremath </i\ensuremath >1\ensuremath <sub\ensuremath >0\ensuremath </sub\ensuremath >-MnPt/NaCl/Fe junction. Appl. Phys. Lett., 119(17):172401, October 2021. URL: https://doi.org/10.1063/5.0064931, doi:10.1063/5.0064931.

  18. Jingcheng Li, Sofia Sanz, Nestor Merino-Díez, Manuel Vilas-Varela, Aran Garcia-Lekue, Martina Corso, Dimas G. de Oteyza, Thomas Frederiksen, Diego Peña, and Jose Ignacio Pascual. Topological phase transition in chiral graphene nanoribbons: From edge bands to end states. Nat. Commun., September 2021. URL: https://doi.org/10.1038/s41467-021-25688-z, doi:10.1038/s41467-021-25688-z.

  19. Michael Mohr, Alexander Weismann, Dongzhe Li, Mads Brandbyge, and Richard Berndt. Current shot noise in atomic contacts: Fe and FeH2 between au electrodes. Phys. Rev. B, September 2021. URL: https://doi.org/10.1103/physrevb.104.115431, doi:10.1103/physrevb.104.115431.

  20. Juan M. Marmolejo-Tejada and Andres Jaramillo-Botero. Four-terminal graphene nanoribbon sensor devices: In-silico design and characterization. Nato. Sc. S. Ss. Iii. C. S., 196:110506, August 2021. URL: https://doi.org/10.1016/j.commatsci.2021.110506, doi:10.1016/j.commatsci.2021.110506.

  21. Jie Zhang and Eric P. Fahrenthold. Spin current distribution in antiferromagnetic zigzag graphene nanoribbons under transverse electric fields. Scientific Reports, August 2021. URL: https://doi.org/10.1038/s41598-021-96636-6, doi:10.1038/s41598-021-96636-6.

  22. Isaac Alcón, Gaetano Calogero, Nick Papior, and Mads Brandbyge. Electrochemical control of charge current flow in nanoporous graphene. Adv. Funct. Mater., 31(40):2104031, July 2021. URL: https://doi.org/10.1002/adfm.202104031, doi:10.1002/adfm.202104031.

  23. Dongzhe Li, Jonas L. Bertelsen, Nick Papior, Alexander Smogunov, and Mads Brandbyge. Surface states and related quantum interference in ab initio electron transport. Phys. Rev. Research, July 2021. URL: https://doi.org/10.1103/physrevresearch.3.033017, doi:10.1103/physrevresearch.3.033017.

  24. Fei Gao, Yu Zhang, Lin He, Shiwu Gao, and Mads Brandbyge. Control of the local magnetic states in graphene with voltage and gating. Phys. Rev. B, June 2021. URL: https://doi.org/10.1103/physrevb.103.l241402, doi:10.1103/physrevb.103.l241402.

  25. S.A. Sozykin. GUI4dft — a SIESTA oriented GUI. Comput. Phys. Commun., 262:107843, May 2021. URL: https://doi.org/10.1016/j.cpc.2021.107843, doi:10.1016/j.cpc.2021.107843.

  26. Bruno Focassio, Gabriel R Schleder, Marcio Costa, Adalberto Fazzio, and Caio Lewenkopf. Structural and electronic properties of realistic two-dimensional amorphous topological insulators. 2D Mater., 8(2):025032, February 2021. URL: https://doi.org/10.1088/2053-1583/abdb97, doi:10.1088/2053-1583/abdb97.

  27. Delwin Perera and Jochen Rohrer. Semi-analytical approach to transport gaps in polycrystalline graphene. Nanoscale, 13(16):7709–7713, 2021. URL: https://doi.org/10.1039/d1nr00186h, doi:10.1039/d1nr00186h.

  28. Junwei Tong, Feifei Luo, Liuxia Ruan, Gaowu Qin, Lianqun Zhou, Fubo Tian, and Xianmin Zhang. High and reversible spin polarization in a collinear antiferromagnet. Appl. Phys. Rev., 7(3):031405, September 2020. URL: https://doi.org/10.1063/5.0004564, doi:10.1063/5.0004564.

  29. Sofia Sanz, Pedro Brandimarte, Géza Giedke, Daniel Sánchez-Portal, and Thomas Frederiksen. Crossed graphene nanoribbons as beam splitters and mirrors for electron quantum optics. Phys. Rev. B, July 2020. URL: https://doi.org/10.1103/physrevb.102.035436, doi:10.1103/physrevb.102.035436.

  30. Alberto García, Nick Papior, Arsalan Akhtar, Emilio Artacho, Volker Blum, Emanuele Bosoni, Pedro Brandimarte, Mads Brandbyge, J. I. Cerdá, Fabiano Corsetti, Ramón Cuadrado, Vladimir Dikan, Jaime Ferrer, Julian Gale, Pablo García-Fernández, V. M. García-Suárez, Sandra García, Georg Huhs, Sergio Illera, Richard Korytár, Peter Koval, Irina Lebedeva, Lin Lin, Pablo López-Tarifa, Sara G. Mayo, Stephan Mohr, Pablo Ordejón, Andrei Postnikov, Yann Pouillon, Miguel Pruneda, Roberto Robles, Daniel Sánchez-Portal, Jose M. Soler, Rafi Ullah, Victor Wen-zhe Yu, and Javier Junquera. Siesta: Recent developments and applications. J. Chem. Phys., 152(20):204108, May 2020. URL: https://doi.org/10.1063/5.0005077, doi:10.1063/5.0005077.

  31. Jingcheng Li, Sofia Sanz, Jesus Castro-Esteban, Manuel Vilas-Varela, Niklas Friedrich, Thomas Frederiksen, Diego Peña, and Jose Ignacio Pascual. Uncovering the triplet ground state of triangular graphene nanoflakes engineered with atomic precision on a metal surface. Phys. Rev. Lett., April 2020. URL: https://doi.org/10.1103/physrevlett.124.177201, doi:10.1103/physrevlett.124.177201.

  32. Tanja Schmitt, Sean Bourelle, Nathaniel Tye, Giancarlo Soavi, Andrew D. Bond, Sascha Feldmann, Boubacar Traore, Claudine Katan, Jacky Even, Siân E. Dutton, and Felix Deschler. Control of crystal symmetry breaking with halogen-substituted benzylammonium in layered hybrid metal-halide perovskites. JACS, 142(11):5060–5067, February 2020. URL: https://doi.org/10.1021/jacs.9b11809, doi:10.1021/jacs.9b11809.

  33. Nick Papior, Gaetano Calogero, Susanne Leitherer, and Mads Brandbyge. Removing all periodic boundary conditions: Efficient nonequilibrium green's function calculations. Phys. Rev. B, November 2019. URL: https://doi.org/10.1103/physrevb.100.195417, doi:10.1103/physrevb.100.195417.

  34. Frank Schindler, Marta Brzezińska, Wladimir A. Benalcazar, Mikel Iraola, Adrien Bouhon, Stepan S. Tsirkin, Maia G. Vergniory, and Titus Neupert. Fractional corner charges in spin-orbit coupled crystals. Phys. Rev. Research, November 2019. URL: https://doi.org/10.1103/physrevresearch.1.033074, doi:10.1103/physrevresearch.1.033074.

  35. Jonathan Brand, Susanne Leitherer, Nick R. Papior, Nicolas Néel, Yong Lei, Mads Brandbyge, and Jörg Kröger. Nonequilibrium bond forces in single-molecule junctions. Nano Lett., 19(11):7845–7851, September 2019. URL: https://doi.org/10.1021/acs.nanolett.9b02845, doi:10.1021/acs.nanolett.9b02845.

  36. Gaetano Calogero, Isaac Alcón, Nick Papior, Antti-Pekka Jauho, and Mads Brandbyge. Quantum interference engineering of nanoporous graphene for carbon nanocircuitry. JACS, 141(33):13081–13088, July 2019. URL: https://doi.org/10.1021/jacs.9b04649, doi:10.1021/jacs.9b04649.

  37. S. Leitherer, N. Papior, and M. Brandbyge. Current-induced atomic forces in gated graphene nanoconstrictions. Phys. Rev. B, July 2019. URL: https://doi.org/10.1103/physrevb.100.035415, doi:10.1103/physrevb.100.035415.

  38. László Oroszlány, Jaime Ferrer, András Deák, László Udvardi, and László Szunyogh. Exchange interactions from a nonorthogonal basis set: From bulk ferromagnets to the magnetism in low-dimensional graphene systems. Phys. Rev. B, June 2019. URL: https://doi.org/10.1103/physrevb.99.224412, doi:10.1103/physrevb.99.224412.

  39. Gurvinder Singh, Krishan Kumar, and R.K. Moudgil. On topology-tuned thermoelectric properties of noble metal atomic wires. Physica E, 109:114–132, May 2019. URL: https://doi.org/10.1016/j.physe.2019.01.007, doi:10.1016/j.physe.2019.01.007.

  40. Jingcheng Li, Sofia Sanz, Martina Corso, Deung Jang Choi, Diego Peña, Thomas Frederiksen, and Jose Ignacio Pascual. Single spin localization and manipulation in graphene open-shell nanostructures. Nat. Commun., January 2019. URL: https://doi.org/10.1038/s41467-018-08060-6, doi:10.1038/s41467-018-08060-6.

  41. Gaetano Calogero, Nick Papior, Mohammad Koleini, Matthew Helmi Leth Larsen, and Mads Brandbyge. Multi-scale approach to first-principles electron transport beyond 100 nm. Nanoscale, 11(13):6153–6164, 2019. URL: https://doi.org/10.1039/c9nr00866g, doi:10.1039/c9nr00866g.

  42. Gurvinder Singh, Krishan Kumar, and R. K. Moudgil. Alloying-induced spin Seebeck effect and spin figure of merit in pt-based bimetallic atomic wires of noble metals. Phys. Chem. Chem. Phys., 21(37):20965–20980, 2019. URL: https://doi.org/10.1039/c9cp01671f, doi:10.1039/c9cp01671f.

  43. Gurvinder Singh, Krishan Kumar, Baljinder Singh, and R. K. Moudgil. Ballistic phonon thermal transport across nano-junctions on aluminum and platinum nanowires. In AIP Conference Proceedings. Author(s), 2019. URL: https://doi.org/10.1063/1.5097098, doi:10.1063/1.5097098.

  44. Gaetano Calogero, Nick R. Papior, Bernhard Kretz, Aran Garcia-Lekue, Thomas Frederiksen, and Mads Brandbyge. Electron transport in nanoporous graphene: Probing the Talbot effect. Nano Lett., 19(1):576–581, December 2018. URL: https://doi.org/10.1021/acs.nanolett.8b04616, doi:10.1021/acs.nanolett.8b04616.

  45. Delwin Perera and Jochen Rohrer. Structure sensitivity of electronic transport across graphene grain boundaries. Phys. Rev. B, October 2018. URL: https://doi.org/10.1103/physrevb.98.155432, doi:10.1103/physrevb.98.155432.

  46. Zahra Nourbakhsh and Reza Asgari. Phosphorene as a nanoelectromechanical material. Phys. Rev. B, September 2018. URL: https://doi.org/10.1103/physrevb.98.125427, doi:10.1103/physrevb.98.125427.

  47. Gaetano Calogero, Nick R Papior, Peter Bøggild, and Mads Brandbyge. Large-scale tight-binding simulations of quantum transport in ballistic graphene. J. Phys. Condens. Matter, 30(36):364001, August 2018. URL: https://doi.org/10.1088/1361-648x/aad6f1, doi:10.1088/1361-648x/aad6f1.

  48. Bálint Fülöp, Zoltán Tajkov, János Pető, Péter Kun, János Koltai, László Oroszlány, Endre Tóvári, Hiroshi Murakawa, Yoshinori Tokura, Sándor Bordács, Levente Tapasztó, and Szabolcs Csonka. Exfoliation of single layer BiTeI flakes. 2D Mater., 5(3):031013, June 2018. URL: https://doi.org/10.1088/2053-1583/aac652, doi:10.1088/2053-1583/aac652.

  49. Zahra Nourbakhsh and Reza Asgari. Charge transport in doped zigzag phosphorene nanoribbons. Phys. Rev. B, June 2018. URL: https://doi.org/10.1103/physrevb.97.235406, doi:10.1103/physrevb.97.235406.

  50. Nick R Papior, Gaetano Calogero, and Mads Brandbyge. Simple and efficient LCAO basis sets for the diffuse states in carbon nanostructures. J. Phys. Condens. Matter, 30(25):25LT01, May 2018. URL: https://doi.org/10.1088/1361-648x/aac4dd, doi:10.1088/1361-648x/aac4dd.

  51. César Moreno, Manuel Vilas-Varela, Bernhard Kretz, Aran Garcia-Lekue, Marius V. Costache, Markos Paradinas, Mirko Panighel, Gustavo Ceballos, Sergio O. Valenzuela, Diego Peña, and Aitor Mugarza. Bottom-up synthesis of multifunctional nanoporous graphene. Science, 360(6385):199–203, April 2018. URL: https://doi.org/10.1126/science.aar2009, doi:10.1126/science.aar2009.

  52. Veronika Obersteiner, Georg Huhs, Nick Papior, and Egbert Zojer. Unconventional current scaling and edge effects for charge transport through molecular clusters. Nano Lett., 17(12):7350–7357, November 2017. URL: https://doi.org/10.1021/acs.nanolett.7b03066, doi:10.1021/acs.nanolett.7b03066.

  53. Thomas Groizard, Nick Papior, Boris Le Guennic, Vincent Robert, and Mikaël Kepenekian. Enhanced cooperativity in supported spin-crossover Metal–Organic frameworks. The Journal of Physical Chemistry Letters, 8(14):3415–3420, July 2017. URL: https://doi.org/10.1021/acs.jpclett.7b01248, doi:10.1021/acs.jpclett.7b01248.

  54. Peter Bøggild, José M. Caridad, Christoph Stampfer, Gaetano Calogero, Nick Rübner Papior, and Mads Brandbyge. A two-dimensional Dirac fermion microscope. Nat. Commun., June 2017. URL: https://doi.org/10.1038/ncomms15783, doi:10.1038/ncomms15783.

  55. Pedro Brandimarte, Mads Engelund, Nick Papior, Aran Garcia-Lekue, Thomas Frederiksen, and Daniel Sánchez-Portal. A tunable electronic beam splitter realized with crossed graphene nanoribbons. J. Chem. Phys., 146(9):092318, March 2017. URL: https://doi.org/10.1063/1.4974895, doi:10.1063/1.4974895.

  56. Nick Papior, Nicolás Lorente, Thomas Frederiksen, Alberto García, and Mads Brandbyge. Improvements on non-equilibrium and transport green function techniques: The next-generation transiesta. Comput. Phys. Commun., 212:8–24, March 2017. URL: https://doi.org/10.1016/j.cpc.2016.09.022, doi:10.1016/j.cpc.2016.09.022.

  57. missing author in Brede2023

  58. missing author in li-sanz-2023

arXiv publications

These publications are as far as we know in the review process.

  • D. Weckbecker, M. Fleischmann, R. Gupta, W. Landgraf, S. Leitherer, O. Pankratov, S. Sharma, V. Meded, S. Shallcross, Moiré ordered current loops in the graphene twist bilayer, 1901.04712

  • Y. Guan, O.V. Yazyev, Electronic transport in graphene with out-of-plane disorder, 2210.16629