Acknowledgments

This file provides a description of suggested acknowledgments and references to be inserted in scientific papers whose results have been obtained thanks to ABINIT. It discusses also briefly the problem of co-authorship.

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Copyright (C) 1998-2017 ABINIT group (XG,DCA,RC)
This file is distributed under the terms of the GNU General Public License, see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt .
For the initials of contributors, see ~abinit/doc/developers/contributors.txt .

Content:

• A. Introduction
• B. List of suggestions
• C. Example

A. Introduction

Please note the following :

• 1) The ABINIT project, in order to be viable, should be known as a robust tool, that has been tested, and that has allowed good scientific research. This will be facilitated if the ABINIT project is mentioned properly in research papers.
• 2) Some recent ideas and algorithms are coded, and it would be fair to cite these.
• 3) You might also register on the ABINIT forum. Indirectly, this also helps the ABINIT developer group, because the total number of registered people on the ABINIT forum is often cited as an indicator of the user community size.

B. List of suggestions

The first general ABINIT paper, Ref.[1], in the list of suggestions below, should be cited in papers that have benefited from the ABINIT project, irrespective of their content. There are three other ABINIT papers, Ref.[2], [3],[4], that might as well be considered, irrespective of the content of the paper, because these papers are quite general as well, although they are older (2009, 2005 and 2002).
There are also many articles that are more focused: they describe some specific capability of ABINIT. The following list is actually not complete ... More references will be proposed by ABINIT itself (see the end of the output file), in the files explaining the input variables, as well as in the references of the four general papers ...
Use of PAW should refer to Ref.[6]. Self-consistent GW should be acknowledged by citing Ref.[14]. Massive parallelism (coupled band / FFT) should refer to Ref.[16]. Use of the phonon or electric field response features of ABINIT should be acknowledged by citing Ref.[8] and Ref.[9] (and Ref.[13] for thermodynamical properties), while the response to strain should be acknowledged by citing Ref.[10]. Computation of non-linear properties (e.g. Raman scattering) should be acknowledged by citing Ref.[12]. When pseudopotentials were generated thanks to the FHI98PP code, Ref. [11] is suggested. When pseudopotentials were generated thanks to the ONCVPSP code, Ref. [22] is suggested. Computations using the Van der Waals DFT-D functional (Grimme) should be acknowledged by citing Ref.[23].

Now, the detailed and complete list of suggestions :

• B.1. At least, the most recent paper that describe the ABINIT project should be mentioned in the bibliography section of your paper (bibtex format):
  [1] X.Gonze, F.Jollet, F.Abreu Araujo, D.Adams, B.Amadon, T.Applencourt, C.Audouze, J.-M.Beuken, J.Bieder, A.Bokhanchuk, E.Bousquet, F.Bruneval, D.Caliste, M.Cote, F.Dahm, F.Da Pieve, M.Delaveau, M.Di Gennaro, B.Dorado, C.Espejo, G.Geneste, L.Genovese, A.Gerossier, M.Giantomassi, Y.Gillet, D.R.Hamann, L.He, G.Jomard, J.Laflamme Janssen, S.Le Roux, A.Levitt, A.Lherbier, F.Liu, I.Lukacevic, A.Martin, C.Martins, M.J.T.Oliveira, S.Ponce, Y.Pouillon, T.Rangel, G.-M.Rignanese, A.H.Romero, B.Rousseau, O.Rubel, A.A.Shukri, M.Stankovski, M.Torrent, M.J.Van Setten, B.Van Troeye, M.J.Verstraete, D.Waroquier, J.Wiktor, B.Xue, A.Zhou, J.W.Zwanziger. Computer Physics Communications 205, 106 (2016).
  "Recent developments in the ABINIT software package." A version of this paper, that is not formatted for Computer Phys. Comm. is available here. The licence allows the authors to put it on the Web.
  The second (bibtex format) and third (bibtex format) general ABINIT papers are as follows :
  [2] X. Gonze, B. Amadon, P.M. Anglade, J.-M. Beuken, F. Bottin, P. Boulanger, F. Bruneval, D. Caliste, R. Caracas, M. Cote, T. Deutsch, L. Genovese, Ph. Ghosez, M. Giantomassi, S. Goedecker, D. Hamann, P. Hermet, F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet, M.J.T. Oliveira, G. Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf, M. Torrent, M.J. Verstraete, G. Zérah, J.W. Zwanziger. Computer Physics Communications 180, 2582-2615 (2009).
  "ABINIT : first-principles approach to material and nanosystem properties" A version of this paper, that is not formatted for Computer Phys. Comm. is available here. The licence allows the authors to put it on the Web.
  [3] X. Gonze, G.-M. Rignanese, M. Verstraete, J.-M. Beuken, Y. Pouillon, R. Caracas, F. Jollet, M. Torrent, G. Zerah, M. Mikami, Ph. Ghosez, M. Veithen, J.-Y. Raty, V. Olevano, F. Bruneval, L. Reining, R. Godby, G. Onida, D.R. Hamann, and D.C. Allan. Zeit. Kristallogr. 220, 558-562 (2005).
  "A brief introduction to the ABINIT software package." The .pdf of the latter paper is available here. Note that it should not redistributed (Copyright by Oldenburg Wissenshaftverlag, the licence allows the authors to put it on the Web).
  The very first paper on the ABINIT project might also be considered for citation (bibtex format):
  [4] X. Gonze, J.-M. Beuken, R. Caracas, F. Detraux, M. Fuchs, G.-M. Rignanese, L. Sindic, M. Verstraete, G. Zerah, F. Jollet, M. Torrent, A. Roy, M. Mikami, Ph. Ghosez, J.-Y. Raty, D.C. Allan. Computational Materials Science 25, 478-492 (2002).
  "First-principles computation of material properties : the ABINIT software project."
  These four references might be properly abbreviated, of course.
  
  
• B.2. In the body of the paper, or in the acknowledgments (can obviously be modified, according to the context), either mention "The present results have been obtained through the use of the ABINIT code, a common project of the Université Catholique de Louvain, Corning Incorporated, and other contributors (URL http://www.abinit.org)" or refer to the following note:
  [5] The ABINIT code is a common project of the Université Catholique de Louvain, Corning Incorporated, and other contributors (URL http://www.abinit.org).
  Actually, four other institutions have significantly contributed to the ABINIT effort : the Université de Liège, the Commissariat à l'Energie Atomique, Mitsubishi Chemical Corp., the Ecole Polytechnique Palaiseau. These (or one of these) might be also cited, just before "and other contributors."
  
  
• B.3. If the Projector-Augmented Wave method as implemented in ABINIT is used the following paper should be mentioned (bibtex format) :
  [6] M. Torrent, F. Jollet, F. Bottin, G. Zerah, and X. Gonze Comput. Mat. Science 42, 337, (2008) " Implementation of the Projector Augmented-Wave Method in the ABINIT code. Application to the study of iron under pressure. " .


• B.4. The determination of wavefunctions in a fixed trial potential is done according to a state-by-state (or band-by-band) conjugate gradient algorithm. The reference is :
  [7] M.C. Payne, M.P. Teter, D.C. Allan, T.A. Arias and J.D. Joannopoulos, Rev. Mod. Phys. 64, 1045 (1992), "Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients"
  Note however : the algorithm in that paper was originally designed to perform the potential self-consistency concurrently, but this is not done in ABINIT.
  
  
• B.5. Many ingredients needed for the calculations of responses to atomic displacements or homogeneous electric fields (dynamical matrices, effective charges and dielectric constants), as well as the Fourier interpolation implemented in the 'anaddb' code are described in
  [8] X. Gonze, Phys. Rev. B55, 10337 (1997) "First-principles responses of solids to atomic displacements and homogeneous electric fields: implementation of a conjugate-gradient algorithm"
  and
  [9] X. Gonze and C. Lee, Phys. Rev. B55, 10355 (1997) "Dynamical matrices, Born effective charges, dielectric permittivity tensors, and interatomic force constants from density-functional perturbation theory".
  
  
• B.6. The methods used for the calculation of responses to homogeneous strain (elastic tensors, piezoelectric tensors, and internal force-response tensors) are described in
  [10] D. R. Hamann, X. Wu, K. M. Rabe, and D. Vanderbilt, Phys. Rev. B71, 035117 (2005) " Metric tensor formulation of strain in density-functional perturbation theory."


• B.7. If the Fritz-Haber-Institute pseudopotential code is used, the following paper should be mentioned :
  [11] M. Fuchs, M. Scheffler, Comput. Phys. Commun. 119, 67 (1999) "Ab initio pseudopotentials for electronic structure calculations of poly-atomic systems using density-functional theory".


• B.8. If the "static" non-linear capabilities of ABINIT are used (Raman efficiencies, electro-optic coefficients ... ), the following paper should be mentioned :
  [12] M. Veithen, X. Gonze, and Ph. Ghosez, Phys. Rev. B 71, 125107 (2005) "Nonlinear optical susceptibilities, Raman efficiencies, and electrooptic tensors from firstprinciples density functional theory ".


• B.9. If the integration over the phonon degrees of freedom if used (thmflag), the following paper should be mentioned :
  [13] C. Lee, X. Gonze, Phys. Rev. B 51, 8610 (1995) "Ab-initio calculation of the thermodynamic properties and atomic temperature factors of SiO2 alpha-quartz and stishovite. ".


• B.10. If the self-consistent capabilities of ABINIT beyond DFT are used (GW, COHSEX, HF, etc), the following paper should be mentioned :
  [14] F. Bruneval, N. Vast, L. Reining, Phys. Rev. B 74, 045102 (2006) "Effect of self-consistency on quasiparticles in solids ".


• B.11. If the completeness relationship is used to speed up the convergence with respect to the number of bands in a GW calculation (input variables gwcomp and gwencomp), the following paper should be mentioned :
  [15] F. Bruneval, X. Gonze, Phys. Rev. B 78, 085125 (2008) "Accurate GW self-energies in a plane-wave basis using only a few empty states: towards large systems ".


• B.12. If the massive parallelism of ABINIT (coupled band / FFT or even coupled band / FFT / k points ) is used, the following paper should be mentioned :
  [16] F. Bottin, S. Leroux, A. Knyazev, G. Zerah, Comput. Mat. Science 42, 329, (2008) "Large scale ab initio calculations based on three levels of parallelization " (available on Arxiv.org).


• B.13. If the LDA+U method as implemented in ABINIT is used, the following paper should be mentioned:
  [17] B. Amadon, F. Jollet and M. Torrent, Phys. Rev. B 77, 155104 (2008) " γ and β cerium: LDA+U calculations of ground-state parameters. "


• B.14. If the extrapolar method to speed up the SCF cycles is used (non-zero iprcel), the following paper should be mentioned:
  [18] P.-M. Anglade, X. Gonze, Phys. Rev. B 78, 045126 (2008) " Preconditioning of self-consistent-field cycles in density functional theory : the extrapolar method "


• B.15. If the ETSF file format is used, through the ETSF_IO library, the following paper should be mentioned:
  [19] D. Caliste, Y. Pouillon, M.J. Verstraete, V. Olevano, X. Gonze, Comput. Physics Communications 179, 748 (2008). " Sharing electronic structure and crystallographic data with ETSF_IO."


• B.16. In the core of the ABINIT code, one finds a remarkable Fast Fourier Transform routine, that has been written by S. Goedecker. Its speed is really crucial for the code, and moreover, its availability makes the whole package more portable. The ideas on which this routine is based are published in :
  [20] S. Goedecker, SIAM J. on Scientific Computing 18, 1605 (1997) "Fast radix 2, 3, 4 and 5 kernels for Fast Fourier Transformations on computers with overlapping multiply-add instructions".


• B.17. The potential-based conjugate-gradient algorithm, used when iscf=5 is not published. However, a few elements have already been explained in :
  [21] X. Gonze, Phys. Rev. B 54, 4383 (1996) "Towards a potential-based conjugate gradient algorithm for order-N self-consistent total energy calculations"


• B.18. If the ONCVPSP pseudopotentials are used, the following paper should be mentioned :
  [22] D.R. Hamann, Phys. Rev. B 88, 085117 (2013) "Optimized norm-conserving Vanderbilt pseudopotentials"


• B.19. If the Van Der Waals DFT-D (Grimme) functionals are used, the following paper should be mentioned :
  [23] B. Van Troeye, M. Torrent, and X. Gonze. Phys. Rev. B93, 144304 (2016) "Interatomic force constants including the DFT-D dispersion contribution"


• B.20. If the temperature dependence of the electronic structure or the zero-point motion effect on the electronic structure are computed, the following two papers should be mentioned :
  [24] S. Ponce, G. Antonius, P. Boulanger, E. Cannuccia, A. Marini, M. Cote and X. Gonze. Computational Material Science 83, 341 (2014) "Verification of first-principles codes: Comparison of total energies, phonon frequencies, electron--phonon coupling and zero-point motion correction to the gap between ABINIT and QE/Yambo"
  [25] S. Ponce, Y. Gillet, J. Laflamme Janssen, A. Marini, M. Verstraete and X. Gonze. J. Chem. Phys. 143, 102813 (2015). "Temperature dependence of the electronic structure of semiconductors and insulators "

C. Examples

• C.1. Ground-state calculations (PAW).
  The present results have been obtained thanks the use of the ABINIT code [1, 2, 3, 4, 5]. Massive parallelism in ABINIT is described in Ref.[16].


• C.2. Response-function calculations.
  The following sentence can be considered, in addition of those of example C.1 :
  Technical details on the computation of responses to atomic displacements and homogeneous electric fields can be found in Ref.[8], while Ref.[9] presents the subsequent computation of dynamical matrices, Born effective charges, dielectric permittivity tensors, and interatomic force constants. Details on the computation of responses to the strain perturbation can be found in Ref.[10], which describes the computation of the elastic, piezoelectric, and internal force-response tensors. Details on the computation of non-linear responses can be found in Ref.[12], which describes the computation of the nonlinear optical susceptibilities, Raman efficiencies, and electrooptic tensors from density functional perturbation theory. Details on the computation of thermodynamical properties (entropy, free energy, specific heat, atomic temperature factors) obtained by integration over the phonon degrees of freedom can be found in Ref.[13].