YAMBO code

Yambo
Original author(s)	Andrea Marini
Developer(s)	Davide Sangalli, Claudio Attaccalite, Andrea Ferretti, Henrique Miranda, Myrta Gruning, Conor Hogan, Daniele Varsano, Dario A. Leon, Fulvio Paleari, Igancio Alliati, Nicola Spallanzani, Nalabothula Muralidhar, Elena Molteni, Alberto Guandalini, Pedro Melo, Ryan McMillan, Fabio Affinito, Alejandro Molina-Sanchez
Initial release	2008; 17 years ago
Stable release	5.2 / 31 August 2023; 20 months ago
Repository	github.com/yambo-code/yambo
Written in	Fortran, C
Operating system	Unix, Unix-like
Platform	x86, x86-64
Available in	English
Type	Many-body theory
License	GPL
Website	www.yambo-code.eu

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]

Excited state properties

Yambo can calculate:

Quasiparticle energies: plasmon pole,^[4] COHSEX approximation,^[4] or real-axis
Lifetimes^[5] within the GW approximation
Optical absorption: RPA, Bethe Salpeter with or without Tamm-Dancoff approximation,^[6] TDDFT in TD-LDA or LRC^[7]^[8]
Electron energy loss spectroscopy
Dynamical polarizability
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

^ Marini, Andrea; Hogan, Conor; Grüning, Myrta; Varsano, Daniele (2009). "yambo: An ab initio tool for excited state calculations". Computer Physics Communications. 180 (8): 1392–1403. arXiv:0810.3118. Bibcode:2009CoPhC.180.1392M. doi:10.1016/j.cpc.2009.02.003. S2CID 8269390.
^ 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. arXiv:1902.03837. Bibcode:2019JPCM...31F5902S. doi:10.1088/1361-648X/ab15d0. PMID 30943462.
^ "What Can Yambo Do?". Yambo. Retrieved 2021-05-05.
^ ^a ^b Aulbur, Wilfried G.; Jönsson, Lars; Wilkins, John W. (2000). "Quasiparticle Calculations in Solids". Solid State Physics. Vol. 54. Elsevier. pp. 1–218. doi:10.1016/s0081-1947(08)60248-9. ISBN 978-0-12-607754-4.
^ Marini, Andrea; Del Sole, Rodolfo; Rubio, Angel; Onida, Giovanni (30 October 2002). "Quasiparticle band-structure effects on thedhole lifetimes of copper within the GW approximation". Physical Review B. 66 (16): 161104(R). arXiv:cond-mat/0208575. Bibcode:2002PhRvB..66p1104M. doi:10.1103/physrevb.66.161104. hdl:10261/98481. S2CID 37797921.
^ Grüning, Myrta; Marini, Andrea; Gonze, Xavier (12 August 2009). "Exciton-Plasmon States in Nanoscale Materials: Breakdown of the Tamm−Dancoff Approximation". Nano Letters. 9 (8): 2820–2824. arXiv:0809.3389. Bibcode:2009NanoL...9.2820G. doi:10.1021/nl803717g. PMID 19637906. S2CID 28990507.
^ 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. 69 (15): 155112. Bibcode:2004PhRvB..69o5112B. doi:10.1103/physrevb.69.155112. hdl:10261/98108.
^ 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. 72 (12): 125203. Bibcode:2005PhRvB..72l5203B. doi:10.1103/physrevb.72.125203.
^ Marini, Andrea (4 September 2008). "Ab InitioFinite-Temperature Excitons". Physical Review Letters. 101 (10): 106405. arXiv:0712.3365. Bibcode:2008PhRvL.101j6405M. doi:10.1103/physrevlett.101.106405. PMID 18851235. S2CID 35012998.
^ 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. 107 (25): 255501. arXiv:1106.1459. Bibcode:2011PhRvL.107y5501C. doi:10.1103/physrevlett.107.255501. PMID 22243089. S2CID 44572818.
^ 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. 86 (12): 125139. arXiv:1205.1994. Bibcode:2012PhRvB..86l5139S. doi:10.1103/physrevb.86.125139. S2CID 119108665.
^ Hogan, Conor; Palummo, Maurizia; Del Sole, Rodolfo (2009). "Theory of dielectric screening and electron energy loss spectroscopy at surfaces". Comptes Rendus Physique. 10 (6): 560–574. Bibcode:2009CRPhy..10..560H. doi:10.1016/j.crhy.2009.03.015.
^ Runge, Erich; Gross, E. K. U. (19 March 1984). "Density-Functional Theory for Time-Dependent Systems". Physical Review Letters. 52 (12): 997–1000. Bibcode:1984PhRvL..52..997R. doi:10.1103/physrevlett.52.997.
^ Gross, E. K. U.; Kohn, Walter (23 December 1985). "Local density-functional theory of frequency-dependent linear response". Physical Review Letters. 55 (26): 2850–2852. Bibcode:1985PhRvL..55.2850G. doi:10.1103/physrevlett.55.2850. PMID 10032255.
^ Aryasetiawan, F; Gunnarsson, O (1 February 1998). "The GW method". Reports on Progress in Physics. 61 (3): 237–312. arXiv:cond-mat/9712013. Bibcode:1998RPPh...61..237A. doi:10.1088/0034-4885/61/3/002. S2CID 250874552.
^ Bethe-Salpeter equation: the origins
^ Strinati, G. (1988). "Application of the Green's functions method to the study of the optical properties of semiconductors". La Rivista del Nuovo Cimento. 11 (12): 1–86. Bibcode:1988NCimR..11l...1S. doi:10.1007/bf02725962. S2CID 122125343.
^ 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. 73 (20): 205119. arXiv:cond-mat/0601031. Bibcode:2006PhRvB..73t5119R. doi:10.1103/physrevb.73.205119. hdl:10261/97933. S2CID 26312984.
^ Caliste, D.; Pouillon, Y.; Verstraete, M.J.; Olevano, V.; Gonze, X. (2008). "Sharing electronic structure and crystallographic data with ETSF_IO". Computer Physics Communications. 179 (10): 748–758. Bibcode:2008CoPhC.179..748C. doi:10.1016/j.cpc.2008.05.007.
^ Marini, Andrea; García-González, P.; Rubio, Angel (5 April 2006). "First-Principles Description of Correlation Effects in Layered Materials". Physical Review Letters. 96 (13): 136404. arXiv:cond-mat/0510221. Bibcode:2006PhRvL..96m6404M. doi:10.1103/physrevlett.96.136404. hdl:10261/97928. PMID 16712011. S2CID 13324711.
^ Sangalli, Davide; Marini, Andrea (12 October 2011). "Anomalous Aharonov–Bohm Gap Oscillations in Carbon Nanotubes". Nano Letters. 11 (10): 4052–4057. arXiv:1106.5695. Bibcode:2011NanoL..11.4052S. doi:10.1021/nl200871v. PMID 21805987. S2CID 10946434.
^ Bruneval, Fabien; Vast, Nathalie; Reining, Lucia (6 July 2006). "Effect of self-consistency on quasiparticles in solids". Physical Review B. 74 (4): 045102. Bibcode:2006PhRvB..74d5102B. doi:10.1103/physrevb.74.045102.
^ Marini, Andrea; Del Sole, Rodolfo (23 October 2003). "Dynamical Excitonic Effects in Metals and Semiconductors". Physical Review Letters. 91 (17): 176402. arXiv:cond-mat/0308271. Bibcode:2003PhRvL..91q6402M. doi:10.1103/physrevlett.91.176402. PMID 14611364. S2CID 8472529.
^ 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. 84 (24): 245110. arXiv:1109.2424. Bibcode:2011PhRvB..84x5110A. doi:10.1103/physrevb.84.245110. S2CID 118694162.
^ 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. 91 (25): 256402. arXiv:cond-mat/0310495. Bibcode:2003PhRvL..91y6402M. doi:10.1103/physrevlett.91.256402. PMID 14754131. S2CID 17007016.