We have developed and implemented a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical linear combination of atomic orbitals basis set, which includes multiple-zeta and polarization orbitals. Exchange and correlation are treated with the local spin density or generalized gradient approximations. The basis functions and the electron density are projected on a real-space grid, in order to calculate the Hartree and exchange-correlation potentials and matrix elements, with a number of operations that scales linearly with the size of the system. We use a modified energy functional, whose minimization produces orthogonal wavefunctions and the same energy and density as the Kohn-Sham energy functional, without the need for an explicit orthogonalization. Additionally, using localized Wannier-like electron wavefunctions allows the computation time and memory required to minimize the energy to also scale linearly with the size of the system. Forces and stresses are also calculated efficiently and accurately, thus allowing structural relaxation and molecular dynamics simulations.

/pdf/the-siesta-method-for-ab-initio-order-n-materials-simulation-1q65k8c3vq.pdf

The SIESTA method for ab initio order-N materials simulation

In this work we briefly describe the most relevant features of WSXM, a freeware scanning probe microscopy software based on MS-Windows. The article is structured in three different sections: The introduction is a perspective on the importance of software on scanning probe microscopy. The second section is devoted to describe the general structure of the application; in this section the capabilities of WSXM to read third party files are stressed. Finally, a detailed discussion of some relevant procedures of the software is carried out.

https://nanoed.tul.cz/pluginfile.php/1608/mod_resource/content/1/view.pdf

WSXM: a software for scanning probe microscopy and a tool for nanotechnology.

/pdf/honeycomb-carbon-a-review-of-graphene-bjl5wl6ai8.pdf

Honeycomb Carbon: A Review of Graphene

We introduce the 2D counterpart of layered black phosphorus, which we call phosphorene, as an unexplored p-type semiconducting material. Same as graphene and MoS2, single-layer phosphorene is flexible and can be mechanically exfoliated. We find phosphorene to be stable and, unlike graphene, to have an inherent, direct, and appreciable band gap. Our ab initio calculations indicate that the band gap is direct, depends on the number of layers and the in-layer strain, and is significantly larger than the bulk value of 0.31–0.36 eV. The observed photoluminescence peak of single-layer phosphorene in the visible optical range confirms that the band gap is larger than that of the bulk system. Our transport studies indicate a hole mobility that reflects the structural anisotropy of phosphorene and complements n-type MoS2. At room temperature, our few-layer phosphorene field-effect transistors with 1.0 μm channel length display a high on-current of 194 mA/mm, a high hole field-effect mobility of 286 cm2/V·s, and an...

/pdf/phosphorene-an-unexplored-2d-semiconductor-with-a-high-hole-pehm34p0g2.pdf

Phosphorene: An Unexplored 2D Semiconductor with a High Hole Mobility

https://www.zora.uzh.ch/id/eprint/3175/3/PP_VandeVondele_CPCom_2005QuickManVO.pdf

QUICKSTEP: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach

Size distributions of fragments from multiply charged clusters have been determined. On a time scale of 0.1 ms with respect to ionization, triply charged CO/sub 2/ clusters of size nroughly-equal114 are found to fission extremely asymmetrically, their doubly charged fragments carrying 92% of the mass. For doubly charged CO/sub 2/ clusters, however, evaporation of neutral monomers is the only channel for delayed dissociation. A model, based on the liquid-drop approximation, can quantitatively account for the lower size limits of multiply charged clusters as well as for the distribution of fission fragments from (CO/sub 2/)/sub roughly-equal114/ /sup 3 +/. .AE

Dissociation channels for multiply charged clusters.

The electronic structure of porous metal-organic framework-5 (MOF-5) of composition ${\mathrm{Zn}}_{4}\mathrm{O}(1,4\text{\ensuremath{-}}\mathrm{benzenedicarboxylate}{)}_{3}$ was investigated with an ab initio density-functional-theory method. The unit cell volume and atomic positions were optimized with the well-known local-density approximation leading to a good agreement between the experimental and theoretical equilibrium structural parameters. Single crystal elastic constants (${C}_{11}$, ${C}_{12}$, and ${C}_{44}$) were then computed at the athermal limit in order to estimate fundamental figures for technological and engineering applications. Our calculations suggest that MOF-5 behaves as a soft and ductile material with a Young's modulus of the order of Oak wood. Particular attention was also focused on the study of oxygen, and carbon $K$ XANES spectra. The differences in their shapes and energy peak positions were discussed in relation to the bonding topology and to the different calculational methods used.

Ab initio study of metal-organic framework-5 Zn 4 O ( 1 , 4 − benzenedicarboxylate ) 3 : An assessment of mechanical and spectroscopic properties

From Coordination Polymer Macrocrystals to Nanometric Individual Chains

The adsorption and diffusion of single Pb atoms on $\mathrm{Si}(111)\ensuremath{-}(7\ifmmode\times\else\texttimes\fi{}7)$ surfaces have been studied by scanning tunneling microscopy (STM) and first-principles density functional calculations. STM experiments at temperatures from 100 to 130 K have revealed three regions of preferential adsorption, inside each half-unit cell, as well as real time diffusion events between them. The stable adsorption sites have been determined by first-principles calculations and by comparing simulated and measured STM images. The activation barriers for the motion inside the half-unit cells have been calculated and measured experimentally. A very good agreement between calculations and experiments has been found.

Single adatom adsorption and diffusion on Si ( 111 ) − ( 7 × 7 ) surfaces: Scanning tunneling microscopy and first-principles calculations

Density functional theory is used to study the electronic and atomic structure of small clusters of Na, Mg, Al and Pb. We study the quantityEN−1–EN, which has relevance to the processes of cluster growth and evaporation (EN is the total energy of the cluster withN atoms). By comparing the results of the jellium model with those of a more realistic model (although still simple) we are able to appreciate “structural” effects beyond the “electronic-shell effects” which form the essence of the predictions of the jellium model. The calculations predict formation of atomic shells and appreciable reconstruction as the cluster grows.

José M. Soler

Papers

Dissociation channels for multiply charged clusters.

Ab initio study of metal-organic framework-5 Zn 4 O ( 1 , 4 − benzenedicarboxylate ) 3 : An assessment of mechanical and spectroscopic properties

From Coordination Polymer Macrocrystals to Nanometric Individual Chains

Single adatom adsorption and diffusion on Si ( 111 ) − ( 7 × 7 ) surfaces: Scanning tunneling microscopy and first-principles calculations

Electronic and atomic structure of Na, Mg, Al and Pb clusters