References

Please, cite the following papers when using PyNAO

PyNAO and method papers

The papers on Py?NAO and its method

koval2018pynao: P. Koval, M. Barbry and D. Sanchez-Portal, PySCF-NAO: An efficient and flexible implementation of linear response time-dependent density functional theory with numerical atomic orbitals, Computer Physics Communications, 2019, 10.1016/j.cpc.2018.08.004
koval2010-mbptlcao: P. Koval, D. Foerster, and O. Coulaud, A Parallel Iterative Method for Computing Molecular Absorption Spectra, J. Chem. Theo. Comput. 2010, 10.1021/ct100280x

PySCF papers

PyNAO was originally part of the PySCF program package and currently dependent on it. Therefore, PySCF papers must be included when using PyNAO for your work.

Qiming2020-pyscf: Qiming Sun Xing Zhang Samragni Banerjee Peng Bao Marc Barbry Nick S. Blunt Nikolay A. Bogdanov George H. Booth Jia Chen Zhi-Hao Cui Janus J. Eriksen Yang Gao Sheng Guo Jan Hermann Matthew R. Hermes Kevin Koh Peter Koval Susi Lehtola Zhendong Li Junzi Liu Narbe Mardirossian James D. McClain Mario Motta Bastien Mussard Hung Q. Pham Artem Pulkin Wirawan Purwanto Paul J. Robinson Enrico Ronca Elvira R. Sayfutyarova Maximilian Scheurer Henry F. Schurkus James E. T. Smith Chong Sun Shi-Ning Sun Shiv Upadhyay Lucas K. Wagner Xiao Wang Alec White James Daniel Whitfield Mark J. Williamson Sebastian Wouters Jun Yang Jason M. Yu Tianyu Zhu Timothy C. Berkelbach Sandeep Sharma Alexander Yu. Sokolov Garnet Kin-Lic Chan Recent developments in the PySCF program package, (2020), The Journal of Chemical Physics, 153, 2, doi: 10.1063/5.0006074
Qiming2018-pyscf: Q. Sun, T. C. Berkelbach, N. S. Blunt, G. H. Booth, S. Guo, Z. Li, J. Liu, J. McClain, E. R. Sayfutyarova, S. Sharma, S. Wouters, G. K.-L. Chan (2018), PySCF: the Python‐based simulations of chemistry framework. WIREs Comput. Mol. Sci., 8, doi:10.1002/wcms.1340

Thesis

The methods for TDDFT has been extensively described in M. Barbry Ph.D thesis

Barbry2018thesis: Marc Barbry Plasmons in Nanoparticles: Atomistic Ab Initio Theory for Large Systems, 2018

Literature

koval2019GW: Peter Koval, Mathias Per Ljungberg, Moritz Müller, and Daniel Sánchez-Portal. Toward efficient gw calculations using numerical atomic orbitals: Benchmarking and application to molecular dynamics simulations. J. Chem. Theory Comput, 15(8):4564–4580, 2019
Fetter1971: A.L. Fetter and J.D. Walecka. Quantum Theory of Many-Particle Systems. McGraw-Hill, New York, 1971.
galitskii1958: F Aryasetiawan and O Gunnarsson. The GW method. Reports on Progress in Physics, 61(3):237–312, mar 1998.
aryasetiawan1998gw: Viktor Mikhailovich Galitskii and Arkadii Beinusovich Migdal. Application of quantum field theory methods to the many body problem. Sov. Phys. JETP, 7(96), 1958.
martin_GW_2016: Richard M. Martin, Lucia Reining, and David M. Ceperley. Interacting Electrons: Theory and Computational Approaches. Cambridge University Press, 2016.
Mattuck1976: R.D. Mattuck. A Guide to Feynman Diagrams in the Many-body Problem. Dover Books on Physics Series. Dover Publications, Incorporated, 1976.
hedin1965new: Lars Hedin. New method for calculating the one-particle Green’s function with application to the electron-gas problem. Physical Review, 139(3A):A796, 1965
martin_RPAchapter12: Richard M. Martin, Lucia Reining, and David M. Ceperley. The RPA and the GW approximation for the self-energy, pages 245–279. Cambridge University Press, 2016.
RPA: David Pines and David Bohm. A collective description of electron interactions: Ii. collective vs individual particle aspects of the interactions. Phys. Rev., 85:338–353, Jan 1952.
VanSetten2015: Michiel J. Van Setten, et al. GW100: Benchmarking G0W0 for Molecular Systems. J. Chem. Theory Comput., 11(12):5665–5687, 2015.
aryasetiawan2009: Ferdi Aryasetiawan and Silke Biermann. Generalized Hedin equations and σGσW approximation for quantum many-body systems with spin-dependent interactions. Journal of Physics: Condensed Matter, 21(6):064232, jan 2009
aryasetiawan2008: F. Aryasetiawan and S. Biermann. Generalized hedin’s equations for quantum many-body systems with spin-dependent interactions. Physical review letters, 100:116402, Mar 2008.
ahmed2014spin: Towfiq Ahmed, Robert C Albers, Alexander V Balatsky, Christoph Friedrich, and Jian-Xin Zhu. GW quasi-particle calculations with spin-orbit coupling for the light actinides. Physical Review B, 89(3):035104, 2014.
Koval2014: Peter Koval, Dietrich Foerster, and Daniel Sánchez-Portal. Fully self-consistent GW and quasiparticle self-consistent GW for molecules. Phys. Rev. B, 89(15):155417, apr 2014.
gui2018: Xin Gui, Christof Holzer, and Wim Klopper. Accuracy assessment of GW starting points for calculating molecular excitation energies using the Bethe–Salpeter formalism. Journal of chemical theory and computation, 14(4):2127–2136, 2018.
Blase2011: X. Blase, C. Attaccalite, and V. Olevano. First-principles GW calculations for fullerenes, porphyrins, phtalo-cyanine, and other molecules of interest for organic photovoltaic applications. Phys. Rev. B - Condens. Matter Mater. Phys., 83(11):1–9, 2011.
Godby1988: R. W. Godby, M. Schlüter, and L. J. Sham. Self-energy operators and exchange-correlation potentials in semiconductors. Phys. Rev. B, 37(17):10159–10175, jun 1988.
complexcontour: Donald J Newman and Joseph Bak. Complex analysis. Springer, 2010.
Lebegue2003: S. Lebgue, B. Arnaud, M. Alouani, and P. E. Bloechl. Implementation of an all-electron GW approximation based on the projector augmented wave method without plasmon pole approximation: Application to si, SiC, AlAs, InAs, NaH, and KH. Phys. Rev. B, 67(15):155208, April 2003.
talman2009numsbt: JD Talman. NumSBT: A subroutine for calculating spherical Bessel transforms numerically. Computer Physics Communications, 180(2):332–338, 2009.
Freysoldt2008: Christoph Freysoldt, Philipp Eggert, Patrick Rinke, Arno Schindlmayr, and Matthias Scheffler. Screening in two dimensions: gw calculations for surfaces and thin films using the repeated-slab approach. Phys. Rev. B, 77:235428, Jun 2008.
Ozaki2004: T. Ozaki and H. Kino. Numerical atomic basis orbitals from H to Kr. Phys. Rev. B, 69(19):195113, may 2004.
nao2001: Javier Junquera, Óscar Paz, Daniel Sánchez-Portal, and Emilio Artacho. Numerical atomic orbitals for linear-scaling calculations. Phys. Rev. B, 64(23):235111, nov 2001.
Foerster2011: Dietrich Foerster, Peter Koval, and Daniel Sánchez-Portal. An O( N3 ) implementation of Hedin’s GW approximation for molecules. J. Chem. Phys., 135(7):074105, aug 2011.
foerster2008: Dietrich Foerster. Elimination, in electronic structure calculations, of redundant orbital products. The Journal of chemical physics, 128(3):034108, 2008.
talman1984numerical: James D Talman. Numerical calculation of four-center coulomb integrals. The Journal of chemical physics, 80(5):2000–2008, 1984.
siesta2002: Jose M Soler, Emilio Artacho, Julian D Gale, Alberto García, Javier Junquera, Pablo Ordejon and Daniel Sanchez-Portal. The SIESTA method for ab initio order-N materials simulation, Journal of Physics: Condensed Matter, 14 (11), 2002.
siesta2020: Alberto Garcia, Nick Papior, Arsalan Akhtar, Emilio Artacho, Volker Blum, Emanuele Bosoni, Pedro Brandimarte, Mads Brandbyge, J. I. Cerda, Fabiano Corsetti, Ramon Cuadrado, Vladimir Dikan, Jaime Ferrer, Julian Gale, Pablo Garcia-Fernandez, V. M. Garcia-Suarez, Sandra Garcia, Georg Huhs, Sergio Illera, Richard Korytar, Peter Koval, Irina Lebedeva, Lin Lin, Pablo Lopez-Tarifa, Sara G. Mayo, Stephan Mohr, Pablo Ordejon, Andrei Postnikov, Yann Pouillon, Miguel Pruneda, Roberto Robles, Daniel Sanchez-Portal, Jose M. Soler, Rafi Ullah, Victor Wen-zhe Yu, and Javier Junquera. Siesta: Recent developments and applications, J. Chem. Phys. 152, 204108, 2020.
Barbry2015: M. Barbry, P. Koval, F. Marchesin, R. Esteban, A. G. Borisov, J. Aizpurua, and D. Sanchez-Portal. Atomistic Near-Field Nanoplasmonics: Reaching Atomic-Scale Resolution in Nanooptics. Nano Lett. 2015, 15, 5, 3410–3419