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.
Copyright (C) 1998-2009 ABINIT group (XG,DCA,RC)
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~abinit/COPYING or
http://www.gnu.org/copyleft/gpl.txt .
For the initials of contributors, see ~abinit/doc/developers/contributors.txt .
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Content:
A. Introduction
In the section B. List of suggestions, you will find several references we suggest you to cite in your papers that have benefited from ABINIT. However, we wish first to clarify the spirit in which the present document (Acknowledgments) has been written. The users of the code have no formal obligations with respect to the ABINIT group (within the limits of the GNU General Public License). However, it is common practice in the scientific literature, to acknowledge the efforts of people that have made the research possible.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) It is expected also that the authors make the ABINIT group aware of the existence of their papers. This operation can be done by the automatic Web registration procedure.
B. List of suggestions
First, an overview ...The two first papers Ref.[1] and Ref.[2] in this list of suggestions should be considered for citation in all the papers that have benefited from the ABINIT project. Moreover, if you used the GW part of ABINIT, the suggestion to cite Ref.[2] is even stronger. Self-consistent GW should be acknowledged by citing Ref.[13]. Massive parallelism (coupled band / FFT) should refer to Ref.[14]. Use of PAW should refer to Ref.[15]. Use of the phonon or electric field response features of ABINIT should be acknowledged by citing Ref.[7] and Ref.[8] (and Ref.[12] for thermodynamical properties), while the response to strain should be acknowledged by citing Ref.[9]. Computation of non-linear properties (e.g. Raman scattering) should be acknowledged by citing Ref.[11]. When pseudopotentials were generated thanks to the FHI98PP code, Ref. [10] is suggested.
Now, the detailed and complete list of suggestions :
- B.1. At least, the two papers that describe the ABINIT project should be
mentioned in the bibliography section of your paper:
[1] 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."
[2] 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."
These references might be properly abbreviated, of course.
Note that the second should be cited especially if you are using the GW part of ABINIT, as the authors of this part are not in the list of authors of the first paper. 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). - 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:
[3] 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. 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 :
[4] 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.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 :
[5] 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.4. The potential-based conjugate-gradient algorithm, used when
iscf=5 is not published. However,
a few elements have already been explained in :
[6] X. Gonze, Phys. Rev. B 54, 4383 (1996) "Towards a potential-based conjugate gradient algorithm for order-N self-consistent total energy calculations" - 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
[7] 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
[8] 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
[9] 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 :
[10] 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 :
[11] 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 :
[12] 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 :
[13] 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 :
[14] 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 :
[15] 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 Projector-Augmented Wave method as implemented in ABINIT is used
the following paper should be mentioned :
[16] 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.14. If the LDA+U method as implemented in ABINIT is used, the following paper should
be mentioned:
[16] 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.15. If the extrapolar method to speed up the SCF cycles is used (non-zero iprcel),
the following paper should be mentioned:
[17] 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.16. If the ETSF file format is used, through the ETSF_IO library,
the following paper should be mentioned:
[18] 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.17. Other references can be found in the files explaining the input variables. Please, pay a special attention to the "suggested citations", as they refer to papers closely associated to ABINIT.
C. Examples
The following examples might be enlarged : many explanatory sentences might be added, especially if they are placed in the technical section of a paper. On the other hand, perhaps not all the features that are mentioned below have been used, in which case some sentences might be removed.- C.1. Ground-state calculations.
The present results have been obtained thanks the use of the ABINIT code [1, 2, 3, 15]. It relies on an efficient Fast Fourier Transform algorithm [4] for the conversion of wavefunctions between real and reciprocal space, on the adaptation to a fixed potential of the band-by-band conjugate gradient method [5] and on a potential-based conjugate-gradient algorithm for the determination of the self-consistent potential [6]. Massive parallelism in ABINIT is described in Ref.[14]. - 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.[7], while Ref.[8] 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.[9], 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.[11], 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.[12].
Goto : ABINIT home Page | Suggested acknowledgments | List of input variables | Tutorial home page | Bibliography
Help files : New user's guide | Abinis (main) | Abinis (respfn) | Mrgddb | Anaddb | AIM (Bader) | Cut3D | Optic | Mrgscr
ABINITv6.12.1 Production release
