Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method.

Electronic structure calculations have become an indispensable tool in many areas of materials science and quantum chemistry. Even though the Kohn-Sham formulation of the density-functional theory (DFT) simplifies the many-body problem significantly, one is still confronted with several numerical challenges. In this article we present the projector augmented-wave (PAW) method as implemented in the GPAW program package (https://wiki.fysik.dtu.dk/gpaw) using a uniform real-space grid representation of the electronic wavefunctions. Compared to more traditional plane wave or localized basis set approaches, real-space grids offer several advantages, most notably good computational scalability and systematic convergence properties. However, as a unique feature GPAW also facilitates a localized atomic-orbital basis set in addition to the grid. The efficient atomic basis set is complementary to the more accurate grid, and the possibility to seamlessly switch between the two representations provides great flexibility. While DFT allows one to study ground state properties, time-dependent density-functional theory (TDDFT) provides access to the excited states. We have implemented the two common formulations of TDDFT, namely the linear-response and the time propagation schemes. Electron transport calculations under finite-bias conditions can be performed with GPAW using non-equilibrium Green functions and the localized basis set. In addition to the basic features of the real-space PAW method, we also describe the implementation of selected exchange-correlation functionals, parallelization schemes, ΔSCF-method, x-ray absorption spectra, and maximally localized Wannier orbitals.

Quantum well states in two-dimensional gold clusters on MgO thin films.

The electronic structure of ultrasmall Au clusters on thin MgO/Ag(001) films has been analyzed by scanning tunneling spectroscopy and density functional theory. The clusters exhibit two-dimensional quantum well states, whose shapes resemble the eigenstates of a 2D electron gas confined in a parabolic potential. From the symmetry of the highest occupied (HOMO) and lowest unoccupied molecular orbital (LUMO) of a particular cluster, its electron filling and charge state is determined. In accordance with a Bader charge analysis, aggregates containing up to 20 atoms accumulate one to four extra electrons due to a charge transfer from the MgO/Ag interface. The HOMO-LUMO gap is found to close for clusters containing between 70 and 100 atoms.

Supported magnetic nanoclusters: soft landing of Pd clusters on a MgO surface.

Low-energy deposition of neutral Pd(N) clusters (N=2-7 and 13) on a MgO(001) surface F center (FC) was studied by spin-density-functional molecular dynamics simulations. The incident clusters are steered by an attractive "funnel" created by the FC, resulting in adsorption of the cluster, with one of its atoms bonded atop of the FC. The deposited Pd2-Pd6 clusters retain their gas-phase structures, while for N>6 surface-commensurate isomers are energetically more favorable. Adsorbed clusters with N>3 are found to remain magnetic at the surface.

Photoabsorption spectra of Na(+)(n) clusters: thermal line-broadening mechanisms.

Photoabsorption cross sections of small sodium cluster cations ( Na(+)(n), n = 3, 5, 7, and 9) were calculated at various temperatures with the time-dependent local-density approximation in conjunction with ab initio molecular dynamics simulations, yielding spectra that agree with measured ones without ad hoc line broadening or renormalization. Three thermal line-broadening mechanisms are revealed: (I) lifting of level degeneracies caused by symmetry-breaking ionic motions, (II) oscillatory shifts of the entire spectrum caused by breathing vibrations, and (III) cluster structural isomerizations.

COI oxidation on a single Pd atom supported on magnesia.

The oxidation of CO on single Pd atoms anchored to MgO(100) surface oxygen vacancies is studied with temperature-programmed-reaction mass spectrometry and infrared spectroscopy. In one-heating-cycle experiments, CO(2), formed from O(2) and CO preadsorbed at 90 K, is detected at 260 and 500 K. Ab-initio simulations suggest two reaction routes, with Pd(CO)(2)O(2) and PdCO(3)CO found as precursors for the low and high temperature channels, respectively. Both reactions result in annealing of the vacancy and induce migration and coalescence of the remaining Pd-CO to form larger clusters.

Structure and magnetism of neutral and anionic palladium clusters.

The properties of neutral and anionic Pd(N) clusters were investigated with spin-density-functional calculations. The ground-state structures are three dimensional for N>3 and they are magnetic with a spin triplet for 2 < or = N < or = 7 and a spin nonet for N = 13 neutral clusters. Structural and spin isomers were determined and an anomalous increase of the magnetic moment with temperature is predicted for a Pd7 ensemble. Vertical electron detachment and ionization energies were calculated and the former agrees well with measured values for Pd(-)(N).

Effect of long-term administration of ethanol to the rat: lipids, collagen and other proteins, and Mallory bodies in the liver.

Rats drank ethanol, on the average 1.20 g/100 g body weight, for various periods up to nearly 300 days. Experimental variables included a high-fat, low-protein diet, administration of additional ethanol by stomach tube, and CCl4 injections instead of ethanol. Growth was retarded by all the variables, especially by the high-fat, low-protein diet. The specific histological finding in the ethanol groups was the presence of Mallory bodies. Significant increase in total liver lipids was caused by ethanol, and rapid fat accumulation, inflammatory changes, and even fibrosis and cirrhosis by the high-fat, low-protein diet and the CCl4 injections. Ethanol raised the concentrations of collagen and soluble protein in the liver; the collagen content was increased also by the high-fat, low-protein diet and the CCl4 injections. The incorporation of proline to collagen was stimulated in incubated liver slices from both ethanol-treated and high-fat, low-protein-fed rats. These treatments also increased the concentration of free proline in the liver, thus augmenting the protein synthesis in fibroblasts.