Phonons from Density-Functional Perturbation Theory using the All-Electron Full-Potential Linearized Augmented Plane-Wave Method FLEUR

Phonons are quantized vibrations of a crystal lattice that play a crucial role in understanding many properties of solids. Density functional theory (DFT) provides a state-of-the-art computational approach to lattice vibrations from first-principles. We present a successful software implementation for calculating phonons in the harmonic approximation, employing density-functional perturbation theory (DFPT) within the framework of the full-potential linearized augmented plane-wave (FLAPW) method as implemented in the electronic structure package FLEUR. The implementation, which involves the Sternheimer equation for the linear response of the wave function, charge density, and potential with respect to infinitesimal atomic displacements, as well as the setup of the dynamical matrix, is presented and the specifics due to the muffin-tin sphere centered LAPW basis-set and the all-electron nature are discussed. As a test, we calculate the phonon dispersion of several solids including an insulator, a semiconductor as well as several metals. The latter are comprised of magnetic, simple, and transition metals. The results are validated on the basis of phonon dispersions calculated using the finite displacement approach in conjunction with the FLEUR code and the phonopy package, as well as by some experimental results. An excellent agreement is obtained.Comment: 44 pages, 6 figure

Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism

Dissimilatory sulfate reduction (DSR)—an important reaction in the biogeochemical sulfur cycle—has been dated to the Palaeoarchaean using geological evidence, but its evolutionary history is poorly understood. Several lineages of bacteria carry out DSR, but in archaea only Archaeoglobus, which acquired DSR genes from bacteria, has been proven to catalyse this reaction. We investigated substantial rates of sulfate reduction in acidic hyperthermal terrestrial springs of the Kamchatka Peninsula and attributed DSR in this environment to Crenarchaeota in the Vulcanisaeta genus. Community profiling, coupled with radioisotope and growth experiments and proteomics, confirmed DSR by ‘Candidatus Vulcanisaeta moutnovskia’, which has all of the required genes. Other cultivated Thermoproteaceae were briefly reported to use sulfate for respiration but we were unable to detect DSR in these isolates. Phylogenetic studies suggest that DSR is rare in archaea and that it originated in Vulcanisaeta, independent of Archaeoglobus, by separate acquisition of qmoABC genes phylogenetically related to bacterial hdrA genes.This work was supported by the Russian Science Foundation (grant number 17-74-30025) and in part by the grant from the Russian Ministry of Science and Higher Education (to N.A.C., A.V.L., E.N.F., M.L.M., A.Y.M., N.V.P. and E.A.B.-O.). Sequencing of PCR amplicons was performed using the scientific equipment of the core research facility ‘Bioengineering’ by T. Kolganova. The proteomics analysis was performed at the Proteomics Facility of the Spanish National Center for Biotechnology (CNB-CSIC), which belongs to ProteoRed, PRB2-ISCIII, supported by grant PT13/0001 (to S.C., M.C.M. and M.F.). P.N.G. acknowledges funding from the UK Biotechnology and Biological Sciences Research Council (BBSRC) within the ERA NET-IB2 programme, grant number ERA-IB-14-030 and the European Union Horizon 2020 Research and Innovation programme (Blue Growth: Unlocking the Potential of Seas and Oceans) under grant agreement number 634486, as well as support from the Centre for Environmental Biotechnology project, part funded by the European Regional Development Fund (ERDF) through the Welsh Government, and support from the Centre of Environmental Biotechnology. D.Y.S. was supported by the SIAM/Gravitation Program (Dutch Ministry of Education, Culture and Science; grant 24002002) and RFBR grant 19-04-00401. F.L.S. and S.N. acknowledge support from the Wiener Wissenschafts, Forschungs- und Technologiefonds (Austria) through the grant VRG15-007. F.L.S. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation programme (grant agreement 803768). I.A.C.P. acknowledges support from the Fundação para a Ciência e Tecnologia (Portugal) through grant PTDC/BIA-BQM/29118/2017 and R&D unit MOSTMICRO-ITQB (UIDB/04612/2020 and UIDP/04612/2020)

Source-Free Exchange-Correlation Magnetic Fields in the FLAPW Method

A proposed modification of the exchange-correlation magnetic field in density functional theory is implemented into the all-electron full-potential linearized augmented-plane-wave code Fleur. By removing terms from the magnetic field that stem from source contributions not found for physical ones, a recent paper has shown that theprediction of Fe magnetic moments in iron pnictide materials can be improved vastly while conserving the accurate description of simpler materials. The theory justifyingthe idea is explored and the physicality of the modification is discussed. The interaction of the modification with different kinds of magnets is highlighted, the possibleconstraints in application are explained and justified and the results are compared to those from the original paper calculated via the Elk code. Furthermore, theeffect on the coupling parameters in a Heisenberg model is investigated to gain greater insight about how the modification works and why the improvements happen

Phonons from Density-Functional Perturbation Theory using the All-Electron Full-Potential Linearized Augmented Plane-Wave Method FLEUR

<p>The archive files contain the input and result files for the corresponding publication in IOP Electronic Structure - Technical Notes, as well as a short python script to plot them.</p&gt

Calculation Of Phonon Spectra With The FLAPW Method Using Density Functional Perturbation Theory

Computing phonons applying density functional perturbation theory (DFPT) within all-electron DFT methods is a well-known challenge due to the displacement of muffin-tin spheres and sphere-centered basis functions. In this talk, we present our current results of the phonon dispersion based on our implementation of the DFPT approach in the FLEUR code [1] (www.flapw.de), an implementation of the full-potential linearized augmented plane wave (FLAPW) method. We highlight the good agreement of our preliminary results with phonon dispersions obtained with the finite displacement method for which the FLEUR code has been combined with the phonopy tool (www.phonopy.github.io/phonopy/). We discuss the numerical challenges involved in calculating meV quantites on top of large ground state energies typical for all-electron methods and how we addressed them

Phonons from density-functional perturbation theory using the all-electron full-potential linearized augmented plane-wave method FLEUR *

Phonons are quantized vibrations of a crystal lattice that play a crucial role in understanding many properties of solids. Density functional theory provides a state-of-the-art computational approach to lattice vibrations from first-principles. We present a successful software implementation for calculating phonons in the harmonic approximation, employing density-functional perturbation theory within the framework of the full-potential linearized augmented plane-wave method as implemented in the electronic structure package FLEUR. The implementation, which involves the Sternheimer equation for the linear response of the wave function, charge density, and potential with respect to infinitesimal atomic displacements, as well as the setup of the dynamical matrix, is presented and the specifics due to the muffin-tin sphere centered linearized augmented plane-wavebasis-set and the all-electron nature are discussed. As a test, we calculate the phonon dispersion of several solids including an insulator, a semiconductor as well as several metals. The latter arecomprised of magnetic, simple, and transition metals. The results are validated on the basis of phonon dispersions calculated using the finite displacement approach in conjunction with theFLEUR code and the phonopy package, as well as by some experimental results. An excellent agreement is obtained

FLEUR

FLEUR is an all-electron DFT code based on the full-potential linearized augmented plane-wave method (FLAPW). It is mainly developed at the Forschungsentrum Jülich, Germany and available for the materials research community