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YAMBO code
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<h2 id="excited-state-properties">Excited state properties</h2> <p>Yambo can calculate: </p> <ul><li><a href="/facts/Quasiparticle/Bpx2MNpb">Quasiparticle</a> energies: plasmon pole,<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a> COHSEX approximation,<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a> or real-axis</li> <li>Lifetimes<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> within the <a href="/facts/GW_approximation/L6zEgGzH">GW approximation</a></li> <li><a href="/facts/Optical_absorption/xBYKt7yS">Optical absorption</a>: RPA, Bethe Salpeter with or without Tamm-Dancoff approximation,<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> TDDFT in TD-LDA or LRC<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a><a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a></li> <li><a href="/facts/Electron_energy_loss_spectroscopy/jLd6sMUb">Electron energy loss spectroscopy</a></li> <li>Dynamical polarizability</li> <li>electron-phonon coupling (static<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> and dynamic<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> perturbation theory)</li> <li>magneto optical properties<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a></li> <li>surface spectroscopy<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a></li></ul> <h2 id="physical-systems">Physical systems</h2> <p>Yambo can treat molecules and periodic systems (both metallic an insulating) in three dimensions (crystalline solids) two dimensions (surfaces) and one dimension (e.g., <a href="/facts/Nanotube/UcEkk6Xn">nanotubes</a>, <a href="/facts/Nanowire/Ege0K9Ek">nanowires</a>, <a href="/facts/Polymer/eF32E50K">polymer</a> chains). It can also handle collinear (i.e., <a href="/facts/Spin_polarization/S36kxcj2">spin-polarized</a> <a href="/facts/Wave_function/KgM5ykjY">wave functions</a>) and non-collinear (<a href="/facts/Spinor/sKFNnEwP">spinors</a>) magnetic systems. </p><p>Typical systems are of the size of 10-100 atoms, or 10-400 electrons, per unit cell in the case of periodic systems. </p> <h2 id="theoretical-methods-and-approximations">Theoretical methods and approximations</h2> <p>Yambo relies on many-body perturbation theory and <a href="/facts/Time-dependent_density_functional_theory/Wwk8tlmM">time-dependent density functional theory</a>.<a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a><a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> Quasiparticle energies are calculated within the <a href="/facts/GW_approximation/L6zEgGzH">GW approximation</a><a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> for the self energy. Optical properties are calculated either by solving the <a href="/facts/Bethe%E2%80%93Salpeter_equation/zvqX0syJ">Bethe–Salpeter equation</a><a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a><a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a> or by using the adiabatic local density approximation within time-dependent density functional theory. </p> <h2 id="numerical-details">Numerical details</h2> <p>Yambo uses a <a href="/facts/Plane_wave/0aDUbNhQ">plane waves</a> basis set to represent the electronic (single-particle) wavefunctions. Core electrons are described with norm-conserving <a href="/facts/Pseudopotential/2ckPRjIr">pseudopotentials</a>. 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<a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a> and the random-integration method. </p> <h2 id="technical-details">Technical details</h2> <ul><li>Yambo is interfaced with plane-wave density-functional codes: <a href="/facts/ABINIT/UllthTNt">ABINIT</a>, <a href="/facts/PWscf/hzDru7DV">PWscf</a>, <a href="/facts/CPMD/IhUdV435">CPMD</a> and with the ETSF-io library.<a class="footnote-ref" id="fnref:20" href="#fn:20"><sup>20</sup></a> The utilities that interface these codes with Yambo are distributed along with the main program.</li> <li>The source code is written in Fortran 95 and C</li> <li>The code is parallelized using MPI running libraries</li></ul> <h2 id="user-interface">User interface</h2> <ul><li>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.</li> <li>A postprocessing tool, distributed along with the main program, helps with the analysis and visualization of the results.</li></ul> <h2 id="system-requirements-portability">System requirements, portability</h2> <ul><li><a href="/facts/Unix/0pNL2seI">Unix</a> based systems</li> <li><a href="/facts/Compiler/WNfCDFJe">Compilers</a> for the programming languages <a href="/facts/Fortran/m1KqjcMU">Fortran</a> 95 and <a href="/facts/C_(programming_language)/Ky2No763">C</a></li> <li>optional: <a href="/facts/The_Portland_Group/WdMgVKxw">PGI</a> Fortran compiler for <a href="/facts/GPU/PTK1RQVp">GPU</a> version (starting from 4.5 release)</li> <li>optional: <a href="http://www.unidata.ucar.edu/software/netcdf/">netcdf</a>, <a href="http://www.fftw.org/">fftw</a>, <a href="http://www.mpi-forum.org/">mpi</a> (for parallel execution), <a href="http://www.etsf.eu/fileformats">etsf-io</a>, <a href="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc">libxc</a>, <a href="http://www.hdfgroup.org/HDF5">hdf5</a></li> <li>Hardware requirements depend very much on the physical system under study and the chosen level of theory. For <a href="/facts/Random-access_memory/DuD4bxh6">random-access memory</a> (RAM) the requirements may vary from less than 1 GB to few GBs, depending on the problem.</li></ul> <h2 id="learning-yambo">Learning Yambo</h2> <p>The Yambo team provides a <a href="http://www.yambo-code.eu/wiki/index.php?title=Main_Page">wiki</a> web-page with a list of <a href="http://www.yambo-code.eu/wiki/index.php?title=Tutorials">tutorials</a> and <a href="http://www.yambo-code.eu/wiki/index.php?title=Lectures">lecture notes</a>. On the yambo web-site there is also a list of all <a href="http://www.yambo-code.eu/wiki/index.php?title=Thesis">thesis</a> done with the code. </p> <h2 id="non-distributed-part">Non-distributed part</h2> <p>Part of the YAMBO code is kept under a private repository. These are the features implemented and not yet distributed: </p> <ul><li>total energy using adiabatic-connection fluctuation-dissipation theorem <a class="footnote-ref" id="fnref:21" href="#fn:21"><sup>21</sup></a></li> <li>magnetic field<a class="footnote-ref" id="fnref:22" href="#fn:22"><sup>22</sup></a></li> <li>self-consistent GW<a class="footnote-ref" id="fnref:23" href="#fn:23"><sup>23</sup></a></li> <li>dynamical Bethe–Salpeter<a class="footnote-ref" id="fnref:24" href="#fn:24"><sup>24</sup></a></li> <li>finite-momentum Bethe-Salpeter</li> <li>real-time spectroscopy<a class="footnote-ref" id="fnref:25" href="#fn:25"><sup>25</sup></a></li> <li>advanced kernels for time-dependent density functional theory (Nanoquanta kernel<a class="footnote-ref" id="fnref:26" href="#fn:26"><sup>26</sup></a>).</li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="http://www.yambo-code.eu">Official website</a></li> <li><a href="https://github.com/yambo-code">Yambo</a> on <a href="/facts/GitHub/n1hNCsc3">GitHub</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>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. <a href="/wiki/ArXiv_(identifier)" target="_blank">/wiki/ArXiv_(identifier)</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>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. <a href="https://doi.org/10.1088%2F1361-648X%2Fab15d0" target="_blank">https://doi.org/10.1088%2F1361-648X%2Fab15d0</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>"What Can Yambo Do?". Yambo. Retrieved 2021-05-05. <a href="http://www.yambo-code.eu/about/" target="_blank">http://www.yambo-code.eu/about/</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>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. <a href="978-0-12-607754-4" target="_blank">978-0-12-607754-4</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>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. <a href="978-0-12-607754-4" target="_blank">978-0-12-607754-4</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>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. <a href="/wiki/ArXiv_(identifier)" target="_blank">/wiki/ArXiv_(identifier)</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>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. <a href="/wiki/ArXiv_(identifier)" target="_blank">/wiki/ArXiv_(identifier)</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>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. <a href="/wiki/Lucia_Reining" target="_blank">/wiki/Lucia_Reining</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>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. <a href="/wiki/Lucia_Reining" target="_blank">/wiki/Lucia_Reining</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>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. <a href="/wiki/ArXiv_(identifier)" target="_blank">/wiki/ArXiv_(identifier)</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>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. <a href="/wiki/ArXiv_(identifier)" target="_blank">/wiki/ArXiv_(identifier)</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>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. <a href="/wiki/ArXiv_(identifier)" target="_blank">/wiki/ArXiv_(identifier)</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>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. <a href="https://comptes-rendus.academie-sciences.fr/physique/articles/10.1016/j.crhy.2009.03.015/" target="_blank">https://comptes-rendus.academie-sciences.fr/physique/articles/10.1016/j.crhy.2009.03.015/</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>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. <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>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. 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Bibcode:2008CoPhC.179..748C. doi:10.1016/j.cpc.2008.05.007. <a href="/wiki/Bibcode_(identifier)" target="_blank">/wiki/Bibcode_(identifier)</a> <a href="#fnref:20" class="footnote-back-ref">↩</a></p></li> <li id="fn:21"><p>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. <a href="/wiki/ArXiv_(identifier)" target="_blank">/wiki/ArXiv_(identifier)</a> <a href="#fnref:21" class="footnote-back-ref">↩</a></p></li> <li id="fn:22"><p>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. 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