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

Basis sets of atomic orbitals are very efficient for density functional calculations but lack a systematic variational convergence. We present a method to optimize numerical atomic orbitals variationally, using a single parameter to control their range. The efficiency of the basis generation scheme is tested and compared with other schemes for multiple $\ensuremath{\zeta}$ basis sets. The scheme is shown to be comparable in quality to other widely used schemes albeit offering better performance for linear-scaling computations.

https://arxiv.org/pdf/cond-mat/0207548.pdf

Systematic generation of finite-range atomic basis sets for linear-scaling calculations

It is known that ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions, based on the generalized gradient approximation (GGA) to density functional theory (DFT), with commonly used functionals fail to produce structural and diffusive properties in reasonable agreement with experiment. This is true for canonical, constant temperature simulations where the density of the liquid is fixed to the experimental density. The equilibrium density, at ambient conditions, of DFT water has recently been shown by Schmidt et al. [J. Phys. Chem. B, 113, 11959 (2009)] to be underestimated by different GGA functionals for exchange and correlation, and corrected by the addition of interatomic pair potentials to describe van der Waals (vdW) interactions. In this contribution we present a DFT-AIMD study of liquid water using several GGA functionals as well as the van der Waals density functional (vdW-DF) of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)]. As expected, we find that the density of water is grossly underestimated by GGA functionals. When a vdW-DF is used, the density improves drastically and the experimental diffusivity is reproduced without the need of thermal corrections. We analyze the origin of the density differences between all the functionals. We show that the vdW-DF increases the population of non-H-bonded interstitial sites, at distances between the first and second coordination shells. However, it excessively weakens the H-bond network, collapsing the second coordination shell. This structural problem is partially associated to the choice of GGA exchange in the vdW-DF. We show that a different choice for the exchange functional is enough to achieve an overall improvement both in structure and diffusivity.

/pdf/density-structure-and-dynamics-of-water-the-effect-of-van-1zndam84ro.pdf

Density, structure, and dynamics of water: The effect of van der Waals interactions

We present a detailed method to construct uniform meshes for fast Fourier transforms in electronic-structure calculations. We show that a drastic reduction in the mesh size can be frequently achieved by using an unconventional set of primitive lattice vectors. The same method can be applied also to obtain optimum sets of special points for Brillouin-zone integrals, generalizing previous schemes.

Optimal meshes for integrals in real- and reciprocal-space unit cells.

Using first-principles density-functional calculations, gold monatomic wires are found to exhibit a zigzag shape which remains under tension, becoming linear just before breaking. At room temperature they are found to spin, which explains the extremely long apparent interatomic distances shown by electron microscopy. The zigzag structure is stable if the tension is relieved, the wire holding its chainlike shape even as a free-standing cluster. This unexpected metallic-wire stiffness stems from the transverse quantization in the wire, as shown in a simple free electron model.

/pdf/stiff-monatomic-gold-wires-with-a-spinning-zigzag-geometry-16zw6tgtxd.pdf

Stiff Monatomic Gold Wires with a Spinning Zigzag Geometry

/pdf/density-structure-and-dynamics-of-water-the-effect-of-van-435rzv50ky.pdf

José M. Soler

Papers

Systematic generation of finite-range atomic basis sets for linear-scaling calculations

Density, structure, and dynamics of water: The effect of van der Waals interactions

Optimal meshes for integrals in real- and reciprocal-space unit cells.

Stiff Monatomic Gold Wires with a Spinning Zigzag Geometry

Density, structure and dynamics of water: the effect of Van der Waals interactions