YAMBO code

Yambo is a computer software package for studying many-body theory aspects of solids and molecule systems. [1] [2] It calculates the excited state properties of physical systems from first principles, e.g., from quantum mechanics law without the use of empirical data. It is an open-source software released under the GNU General Public License (GPL). However the main development repository is private and only a subset of the features available in the private repository are cloned into the public repository and thus distributed.[3]

Yambo
Original author(s)Andrea Marini
Developer(s)Conor Hogan, Myrta Gruning, Daniele Varsano, Davide Sangalli, Andrea Ferretti, Pedro Melo, Ryan McMillan, Fabio Affinito, Alejandro Molina-Sanchez, Henrique Miranda
Initial release2008 (2008)
Stable release
4.5 / 2 January 2020 (2020-01-02)
Repositorygithub.com/yambo-code/yambo
Written inFortran, C
Operating systemUnix, Unix-like
Platformx86, x86-64
Available inEnglish
TypeMany-body theory
LicenseGPL
Websitewww.yambo-code.org

Excited state properties

Yambo can calculate:

  • electron-phonon coupling (static[9] and dynamic[10] perturbation theory)
  • magneto optical properties[11]
  • surface spectroscopy[12]


Physical systems

Yambo can treat molecules and periodic systems (both metallic an insulating) in three dimensions (crystalline solids) two dimensions (surfaces) and one dimension (e.g., nanotubes, nanowires, polymer chains). It can also handle collinear (i.e., spin-polarized wave functions) and non-collinear (spinors) magnetic systems.

Typical systems are of the size of 10-100 atoms, or 10-400 electrons, per unit cell in the case of periodic systems.

Theoretical methods and approximations

Yambo relies on many-body perturbation theory and time-dependent density functional theory.[13][14] Quasiparticle energies are calculated within the GW approximation[15] for the self energy. Optical properties are calculated either by solving the Bethe–Salpeter equation[16][17] or by using the adiabatic local density approximation within time-dependent density functional theory.

Numerical details

Yambo uses a plane waves basis set to represent the electronic (single-particle) wavefunctions. Core electrons are described with norm-conserving pseudopotentials. The choice of a plane-wave basis set enforces the periodicity of the systems. Isolated systems, and systems that are periodic in only one or two directions can be treated by using a supercell approach. For such systems Yambo offers two numerical techniques for the treatment of the Coulomb integrals: the cut-off[18] and the random-integration method.

Technical details
  • Yambo is interfaced with plane-wave density-functional codes: ABINIT, PWscf, CPMD and with the ETSF-io library.[19] The utilities that interface these codes with Yambo are distributed along with the main program.
  • The source code is written in Fortran 95 and C
  • The code is parallelized using MPI running libraries

User interface
  • Yambo has a command line user interface. Invoking the program with specific option generates the input with default values for the parameters consistent with the present data on the system.
  • A postprocessing tool, distributed along with the main program, helps with the analysis and visualization of the results.

System requirements, portability
  • Unix based systems
  • Compilers for the programming languages Fortran 95 and C
  • optional: PGI Fortran compiler for GPU version (starting from 4.5 release)
  • optional: netcdf, fftw, mpi (for parallel execution), etsf-io, libxc, hdf5
  • Hardware requirements depend very much on the physical system under study and the chosen level of theory. For random-access memory (RAM) the requirements may vary from less than 1 GB to few GBs, depending on the problem.

Learning Yambo

The Yambo team provides a wiki web-page with a list of tutorials and lecture notes. On the yambo web-site there is also a list of all thesis done with the code.

Non-distributed part

Part of the YAMBO code is kept under a private repository. These are the features implemented and not yet distributed:

  • total energy using adiabatic-connection fluctuation-dissipation theorem [20]
  • magnetic field[21]
  • self-consistent GW[22]
  • dynamical Bethe–Salpeter[23]
  • finite-momentum Bethe-Salpeter
  • real-time spectroscopy[24]
  • advanced kernels for time-dependent density functional theory (Nanoquanta kernel[25]).

References
  1. Marini, Andrea; Hogan, Conor; Grüning, Myrta; Varsano, Daniele (2009). "yambo: An ab initio tool for excited state calculations". Computer Physics Communications. Elsevier BV. 180 (8): 1392–1403. arXiv:0810.3118. doi:10.1016/j.cpc.2009.02.003. ISSN 0010-4655.
  2. Sangalli, D; Ferretti, A; Miranda, H; Attaccalite, C; Marri, I; Cannuccia, E; Melo, P; Marsili, M; Paleari, F; Marrazzo, A; Prandini, G; Bonfà, P; Atambo, M O; Affinito, F; Palummo, M; Molina-Sánchez, A; Hogan, C; Grüning, M; Varsano, D; Marini, A (2019). "Many-body perturbation theory calculations using the yambo code". Journal of Physics: Condensed Matter. 31 (32): 325902. doi:10.1088/1361-648X/ab15d0. ISSN 0953-8984.
  3. http://www.yambo-code.org/about/
  4. Aulbur, Wilfried G.; Jönsson, Lars; Wilkins, John W. (2000). "Quasiparticle Calculations in Solids". Solid State Physics. 54. Elsevier. pp. 1–218. doi:10.1016/s0081-1947(08)60248-9. ISBN 978-0-12-607754-4. ISSN 0081-1947.
  5. Marini, Andrea; Del Sole, Rodolfo; Rubio, Angel; Onida, Giovanni (30 October 2002). "Quasiparticle band-structure effects on thedhole lifetimes of copper within theGWapproximation". Physical Review B. American Physical Society (APS). 66 (16): 161104(R). doi:10.1103/physrevb.66.161104. hdl:10261/98481. ISSN 0163-1829.
  6. Grüning, Myrta; Marini, Andrea; Gonze, Xavier (12 August 2009). "Exciton-Plasmon States in Nanoscale Materials: Breakdown of the Tamm−Dancoff Approximation". Nano Letters. American Chemical Society (ACS). 9 (8): 2820–2824. arXiv:0809.3389. doi:10.1021/nl803717g. ISSN 1530-6984.
  7. Botti, Silvana; Sottile, Francesco; Vast, Nathalie; Olevano, Valerio; Reining, Lucia; Weissker, Hans-Christian; Rubio, Angel; Onida, Giovanni; Del Sole, Rodolfo; Godby, R. W. (23 April 2004). "Long-range contribution to the exchange-correlation kernel of time-dependent density functional theory". Physical Review B. American Physical Society (APS). 69 (15): 155112. doi:10.1103/physrevb.69.155112. hdl:10261/98108. ISSN 1098-0121.
  8. Botti, Silvana; Fourreau, Armel; Nguyen, François; Renault, Yves-Olivier; Sottile, Francesco; Reining, Lucia (6 September 2005). "Energy dependence of the exchange-correlation kernel of time-dependent density functional theory: A simple model for solids". Physical Review B. American Physical Society (APS). 72 (12): 125203. doi:10.1103/physrevb.72.125203. ISSN 1098-0121.
  9. Marini, Andrea (4 September 2008). "Ab InitioFinite-Temperature Excitons". Physical Review Letters. American Physical Society (APS). 101 (10): 106405. arXiv:0712.3365. doi:10.1103/physrevlett.101.106405. ISSN 0031-9007.
  10. Cannuccia, Elena; Marini, Andrea (14 December 2011). "Effect of the Quantum Zero-Point Atomic Motion on the Optical and Electronic Properties of Diamond and Trans-Polyacetylene". Physical Review Letters. American Physical Society (APS). 107 (25): 255501. arXiv:1106.1459. doi:10.1103/physrevlett.107.255501. ISSN 0031-9007.
  11. Sangalli, Davide; Marini, Andrea; Debernardi, Alberto (27 September 2012). "Pseudopotential-based first-principles approach to the magneto-optical Kerr effect: From metals to the inclusion of local fields and excitonic effects". Physical Review B. American Physical Society (APS). 86 (12): 125139. arXiv:1205.1994. doi:10.1103/physrevb.86.125139. ISSN 1098-0121.
  12. Hogan, Conor; Palummo, Maurizia; Del Sole, Rodolfo (2009). "Theory of dielectric screening and electron energy loss spectroscopy at surfaces". Comptes Rendus Physique. Elsevier BV. 10 (6): 560–574. doi:10.1016/j.crhy.2009.03.015. ISSN 1631-0705.
  13. Runge, Erich; Gross, E. K. U. (19 March 1984). "Density-Functional Theory for Time-Dependent Systems". Physical Review Letters. American Physical Society (APS). 52 (12): 997–1000. doi:10.1103/physrevlett.52.997. ISSN 0031-9007.
  14. Gross, E. K. U.; Kohn, Walter (23 December 1985). "Local density-functional theory of frequency-dependent linear response". Physical Review Letters. American Physical Society (APS). 55 (26): 2850–2852. doi:10.1103/physrevlett.55.2850. ISSN 0031-9007.
  15. Aryasetiawan, F; Gunnarsson, O (1 February 1998). "TheGWmethod". Reports on Progress in Physics. IOP Publishing. 61 (3): 237–312. arXiv:cond-mat/9712013. doi:10.1088/0034-4885/61/3/002. ISSN 0034-4885.
  16. Bethe-Salpeter equation: the origins
  17. Strinati, G. (1988). "Application of the Green's functions method to the study of the optical properties of semiconductors". La Rivista del Nuovo Cimento. Springer Science and Business Media LLC. 11 (12): 1–86. doi:10.1007/bf02725962. ISSN 1826-9850.
  18. Rozzi, Carlo A.; Varsano, Daniele; Marini, Andrea; Gross, Eberhard K. U.; Rubio, Angel (26 May 2006). "Exact Coulomb cutoff technique for supercell calculations". Physical Review B. American Physical Society (APS). 73 (20): 205119. doi:10.1103/physrevb.73.205119. hdl:10261/97933. ISSN 1098-0121.
  19. Caliste, D.; Pouillon, Y.; Verstraete, M.J.; Olevano, V.; Gonze, X. (2008). "Sharing electronic structure and crystallographic data with ETSF_IO". Computer Physics Communications. Elsevier BV. 179 (10): 748–758. doi:10.1016/j.cpc.2008.05.007. ISSN 0010-4655.
  20. Marini, Andrea; García-González, P.; Rubio, Angel (5 April 2006). "First-Principles Description of Correlation Effects in Layered Materials". Physical Review Letters. American Physical Society (APS). 96 (13): 136404. doi:10.1103/physrevlett.96.136404. hdl:10261/97928. ISSN 0031-9007.
  21. Sangalli, Davide; Marini, Andrea (12 October 2011). "Anomalous Aharonov–Bohm Gap Oscillations in Carbon Nanotubes". Nano Letters. American Chemical Society (ACS). 11 (10): 4052–4057. arXiv:1106.5695. doi:10.1021/nl200871v. ISSN 1530-6984.
  22. Bruneval, Fabien; Vast, Nathalie; Reining, Lucia (6 July 2006). "Effect of self-consistency on quasiparticles in solids". Physical Review B. American Physical Society (APS). 74 (4): 045102. doi:10.1103/physrevb.74.045102. ISSN 1098-0121.
  23. Marini, Andrea; Del Sole, Rodolfo (23 October 2003). "Dynamical Excitonic Effects in Metals and Semiconductors". Physical Review Letters. American Physical Society (APS). 91 (17): 176402. arXiv:cond-mat/0308271. doi:10.1103/physrevlett.91.176402. ISSN 0031-9007.
  24. Attaccalite, C.; Grüning, M.; Marini, A. (13 December 2011). "Real-time approach to the optical properties of solids and nanostructures: Time-dependent Bethe-Salpeter equation". Physical Review B. American Physical Society (APS). 84 (24): 245110. arXiv:1109.2424. doi:10.1103/physrevb.84.245110. ISSN 1098-0121.
  25. Marini, Andrea; Del Sole, Rodolfo; Rubio, Angel (16 December 2003). "Bound Excitons in Time-Dependent Density-Functional Theory: Optical and Energy-Loss Spectra". Physical Review Letters. American Physical Society (APS). 91 (25): 256402. arXiv:cond-mat/0310495. doi:10.1103/physrevlett.91.256402. ISSN 0031-9007.
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