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Raman spectroscopy is a widely used, powerful, and nondestructive tool for studying the vibrational properties of bulk and low-dimensional materials. Raman spectra can be simulated using first-principles methods, but due to the high computational cost calculations are usually limited only to fairly small unit cells, which makes it difficult to carry out simulations for alloys and defects. Here, we develop an efficient method for simulating Raman spectra of alloys, benchmark it against full density-functional theory calculations, and apply it to several alloys of two-dimensional transition metal dichalcogenides. In this method, the Raman tensor for the supercell mode is constructed by summing up the Raman tensors of the pristine system weighted by the projections of the supercell vibrational modes to those of the pristine system. This approach is not limited to 2D materials and should be applicable to any crystalline solids with defects and impurities. To efficiently evaluate vibrational modes of very large supercells, we adopt mass approximation, although it is limited to chemically and structurally similar atomic substitutions. To benchmark our method, we first apply it to Mo$_x$W$_{(1-x)}$S$_2$ monolayer in the H-phase, where several experimental reports are available for comparison. Second, we consider Mo$_x$W$_{(1-x)}$Te$_2$ in the T'-phase, which has been proposed to be 2D topological insulator, but where experimental results for the monolayer alloy are still missing. We show that the projection scheme also provides a powerful tool for analyzing the origin of the alloy Raman-active modes in terms of the parent system eigenmodes. Finally, we examine the trends in characteristic Raman signatures for dilute concentrations of impurities in MoS$_2$.

We study the plasmonic properties of arrays of atomic chains which comprise noble (Cu, Ag, and Au) and transition (Pd, Pt) metal atoms using time-dependent density-functional theory. We show that the response to the electromagnetic radiation is related to both physics, the geometry-dependent confinement of sp-valence electrons, and chemistry, the energy position of d-electrons in the different atomic species and the hybridization between d and sp electrons. As a result it is possible to tune the position of the surface plasmon resonance, split it to several peaks, and eventually achieve broadband absorption of radiation. Mixing the arrays with transition metals can strongly attenuate the plasmonic behaviour. We analyze the origin of these phenomena and show that they arise from rich interactions between single-particle electron-hole and collective electron excitations. The tunability of the plasmonic response of arrays of atomic chains, which can be realized on solid surfaces, opens wide possibilities for their applications. In the present study we obtain guidelines how the desired properties can be achieved.

The real-time-propagation formulation of time-dependent density-functional theory (RT-TDDFT) is an efficient method for modeling the optical response of molecules and nanoparticles. Compared to the widely adopted linear-response TDDFT approaches based on, e.g., the Casida equations, RT-TDDFT appears, however, lacking efficient analysis methods. This applies in particular to a decomposition of the response in the basis of the underlying single-electron states. In this work, we overcome this limitation by developing an analysis method for obtaining the Kohn-Sham electron-hole decomposition in RT-TDDFT. We demonstrate the equivalence between the developed method and the Casida approach by a benchmark on small benzene derivatives. Then, we use the method for analyzing the plasmonic response of icosahedral silver nanoparticles up to Ag$_{561}$. Based on the analysis, we conclude that in small nanoparticles individual single-electron transitions can split the plasmon into multiple resonances due to strong single-electron-plasmon coupling whereas in larger nanoparticles a distinct plasmon resonance is formed., Comment: 11 pages, 3 figures

The theory for the generation of Wannier functions within the generalized Pipek--Mezey approach [Lehtola, S.; J\'onsson, H. J. Chem. Theory Comput. 2014, 10, 642] is presented and an implementation thereof is described. Results are presented for systems with periodicity in one, two and three dimensions as well as isolated molecules. The generalized Pipek--Mezey Wannier functions (PMWF) are highly localized orbitals consistent with chemical intuition where a distinction is maintained between {\sigma}- and {\pi}-orbitals. The PMWF method is compared with the so-called maximally localized Wannier functions (MLWF) that are frequently used for the analysis of condensed matter calculations. Whereas PMWFs maximize the localization criterion of Pipek and Mezey, MLWFs maximize that of Foster and Boys and have the disadvantage of mixing {\sigma}- and {\pi}-orbitals in many cases. The PMWF orbitals turn out to be as localized as the MLWF orbitals as evidenced by cross-comparison of the values of the PMWF and MLWF objective functions for the two types of orbitals. Our implementation in the atomic simulation environment (ASE) is compatible with various representations of the wave function, including real-space grids, plane waves and linear combinations of atomic orbitals. The projector augmented wave formalism for the representation of atomic core electrons is also supported. Results of calculations with the GPAW software are described here, but our implementation can also use output from other electronic structure software such as ABINIT, NWChem and VASP., Comment: 17 pages, 5 figures

We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate that the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond., Comment: 11 pages, 6 figures

Quantum aspects, such as electron tunneling between closely separated metallic nanoparticles, are crucial for understanding the plasmonic response of nanoscale systems. We explore quantum effects on the response of the conductively coupled metallic nanoparticle dimer. This is realized by stretching a nanorod, which leads to the formation of a narrowing atomic contact between the two nanorod ends. Based on first-principles time-dependent density-functional-theory calculations, we find a discontinuous evolution of the plasmonic response as the nanorod is stretched. This is especially pronounced for the intensity of the main charge-transfer plasmon mode. We show the correlation between the observed discontinuities and the discrete nature of the conduction channels supported by the formed atomic-sized junction., Comment: Main text: 6 pages, 2 figures; Supplemental Material: 5 pages, 4 figures

We have recently shown that by using a scaling approach for randomly distributed topological defects in graphene, reliable estimates for transmission properties of macroscopic samples can be calculated based even on single-defect calculations [A. Uppstu et al., Phys. Rev. B 85, 041401 (2012)]. We now extend this approach of energy-dependent scattering cross sections to the case of adsorbates on graphene by studying hydrogen and carbon adatoms as well as epoxide and hydroxyl groups. We show that a qualitative understanding of resonant scattering can be gained through density functional theory results for a single-defect system, providing a transmission "fingerprint" characterizing each adsorbate type. This information can be used to reliably predict the elastic mean free path for moderate defect densities directly using ab-initio methods. We present tight-binding parameters for carbon and epoxide adsorbates, obtained to match the density-functional theory based scattering cross sections.

We show that transport in low-dimensional carbon structures with finite concentrations of scatterers can be modeled by utilising scaling theory and effective cross sections. Our reults are based on large scale numerical simulations of carbon nanotubes and graphene nanoribbons, using a tightbinding model with parameters obtained from first principles electronic structure calculations. As shown by a comprehensive statistical analysis, the scattering cross sections can be used to estimate the conductance of a quasi-1D system both in the Ohmic and localized regimes. They can be computed with good accuracy from the transmission functions of single defects, greatly reducing the computational cost and paving the way towards using first principles methods to evaluate the conductance of mesoscopic systems, consisting of millions of atoms., Comment: Submitted to Physical Review Letters

We have derived equations for nonadiabatic Ehrenfest molecular dynamics which conserve the total energy in the case of time-dependent discretization for electrons. A discretization is time-dependent in all cases where it or part of it depends on the positions of the nuclei, for example, in atomic orbital basis sets, and in the projector augmented-wave (PAW) method, where the augmentation functions depend on the nuclear positions. We have derived, implemented, and analyzed the energy conserving equations and their most common approximations for a 1D test system where we can achieve numerical results converged to a high accuracy. Based on the observations in 1D, we implement and analyze the Ehrenfest molecular dynamics in 3D using the PAW method and the time-dependent density functional formalism. We demonstrate the applicability of our method by carrying out calculations for small and medium sized molecules in both the adiabatic and the nonadiabatic regime., Comment: 12 pages, 10 figures

Several dissociated and two non-dissociated adsorption structures of the phenol molecule on the Si(001)-(2 \times 1) surface are studied using density functional theory with various exchange and correlation functionals. The relaxed structures and adsorption energies are obtained and it is found that the dissociated structures are energetically more favourable than the non-dissociated structures. However, the ground state energies alone do not determine which structure is obtained experimentally. To elucidate the situation core level shift spectra for Si 2p and C 1s states are simulated and compared with experimentally measured spectra. Several transition barriers were calculated in order to determine which adsorption structures are kinetically accessible. Based on these results we conclude that the molecule undergoes the dissociation of two hydrogen atoms on adsorption., Comment: 11 pages, 6 figures

We have calculated the absorption characteristics of different hybrid systems consisting of Ag, Ag2 or Ag3 atomic clusters and poly(methacrylic acid) (PMAA) using the time-dependent density-functional theory. The polymer is found to have an extensive structural-dependency on the spectral patterns of the hybrid systems relative to the bare clusters. The absorption spectrum can be `tuned' to the visible range for hybrid systems with an odd number of electrons per silver cluster, whereas for hybrid systems comprising an even number of electrons, the leading absorption edge can be shifted up to about 4.5 eV. The results give theoretical support to the experimental observations on the absorption in the visible range in metal cluster-polymer hybrid structures., Comment: Updated layout and minor changes in versions 2 and 3

We present for static density functional theory and time-dependent density functional theory calculations an all-electron method which employs high-order hierarchical finite element bases. Our mesh generation scheme, in which structured atomic meshes are merged to an unstructured molecular mesh, allows a highly nonuniform discretization of the space. Thus it is possible to represent the core and valence states using the same discretization scheme, i.e., no pseudopotentials or similar treatments are required. The nonuniform discretization also allows the use of large simulation cells, and therefore avoids any boundary effects., Comment: 11 pages, 9 figures; final (=published) version

We have modeled transport properties of nanostructures using the Green's function method within the framework of the density-functional theory. The scheme is computationally demanding so that numerical methods have to be chosen carefully. A typical solution to the numerical burden is to use a special basis-function set, which is tailored to the problem in question, for example, the atomic orbital basis. In this paper we present our solution to the problem. We have used the finite element method (FEM) with a hierarchical high-order polynomial basis, the so-called p-elements. This method allows the discretation error to be controlled in a systematic way. The p-elements work so efficiently that they can be used to solve interesting nanosystems described by non-local pseudopotentials. We demonstrate the potential of the implementation with two different systems. As a test system a simple Na-atom chain between two leads is modeled and the results are compared with several previous calculations. Secondly, we consider a thin hafnium dioxide (HfO2) layer on a silicon surface as a model for a gate structure of the next generation of microelectronics., Comment: 9 pages, 7 figures

Electron transport properties in nanostructures can be modeled, for example, by using the semiclassical Wigner formalism or the quantum mechanical Green's functions formalism. We compare the performance and the results of these methods in the case of magnetic resonant-tunneling diodes. We have implemented the two methods within the self-consistent spin-density-functional theory. Our numerical implementation of the Wigner formalism is based on the finite-difference scheme whereas for the Green's function formalism the finite-element method is used. As a specific application, we consider the device studied by Slobodskyy et all. [Phys. Rev. Lett. 90, 246601 (2003)] and analyze their experimental results. The Wigner and Green's functions formalisms give similar electron densities and potentials but, surprisingly, the former method requires much more computer resources in order to obtain numerically accurate results for currents. Both of the formalisms can successfully be used to model magnetic resonant tunneling diode structures., Comment: 13 pages and 12 figures

We have studied quantum wires using the Green's function technique and the density-functional theory, calculating the electronic structure and the conductance. All the numerics are implemented using the finite-element method with a high-order polynomial basis. For short wires, i.e. quantum point contacts, the zero-bias conductance shows, as a function of the gate voltage and at a finite temperature, a plateau at around 0.7G_0. (G_0 = 2e^2/h is the quantum conductance). The behavior, which is caused in our mean-field model by spontaneous spin polarization in the constriction, is reminiscent of the so-called 0.7-anomaly observed in experiments. In our model the temperature and the wire length affect the conductance-gate voltage curves in the same way as in the measured data., Comment: 8 pages

We use the effective-mass approximation and the density-functional theory with the local-density approximation for modeling two-dimensional nano-structures connected phase-coherently to two infinite leads. Using the non-equilibrium Green's function method the electron density and the current are calculated under a bias voltage. The problem of solving for the Green's functions numerically is formulated using the finite-element method (FEM). The Green's functions have non-reflecting open boundary conditions to take care of the infinite size of the system. We show how these boundary conditions are formulated in the FEM. The scheme is tested by calculating transmission probabilities for simple model potentials. The potential of the scheme is demonstrated by determining non-linear current-voltage behaviors of resonant tunneling structures., Comment: 13 pages,15 figures