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

Practical quantum mechanical simulations of materials, which take into account explicitly the electronic degrees of freedom, are presently limited to about 1000 atoms. In contrast, the largest classical simulations, using empirical interatomic potentials, involve over 109 atoms. Much of this 106-factor difference is due to the existence of well-developed order-N algorithms for the classical problem, in which the computer time and memory scale linearly with the number of atoms N of the simulated system. Furthermore, such algorithms are well suited for execution in parallel computers, using rather small interprocessor communications. In contrast, nearly all quantum mechanical simulations involve a computational effort which scales as O(N 3 ), that is, as the cube of the number of atoms simulated. Such an intrinsically more expensive dependence is due to the delocalized character of the electron wavefunctions. Since the electrons are fermions, every one of the ~N occupied wavefunctions must be kept orthogonal to every other one, thus requiring ~N 2 constraints, each involving an integral over the whole system, whose size is also proportional to N.

Electronic Structure Calculations with Localized Orbitals: The Siesta Method

Publisher's Note: “Density, structure, and dynamics of water: The effect of van der Waals interactions” [J. Chem. Phys.134, 024516 (2011)]

The isothermal compressibility of water is essential to understand its anomalous properties. We compute it by ab initio molecular dynamics simulations of 200 molecules at five densities, using two different van der Waals density functionals. While both functionals predict compressibilities within ~30% of experiment, only one of them accurately reproduces, within the uncertainty of the simulation, the density dependence of the self-diffusion coefficient in the anomalous region. The discrepancies between the two functionals are explained in terms of the low- and high-density structures of the liquid.

Room temperature compressibility and the diffusivity anomaly of liquid water from first principles

Thermodynamics of the roughening transition in stepped surfaces

The presence of sharp peaks in the real part of the static dielectric response function are usually accepted as indication of charge or spin instabilities in a material. However, there are misconceptions that Fermi surface (FS) nesting guarantees a peak in the response function like in one-dimensional systems, and, in addition, response function matrix elements between empty and occupied states are usually considered of secondary importance and typically set to unity like in the free electron gas case. In this work, we explicitly show, through model systems and real materials, within the framework of density functional theory, that predictions about the peaks in the response function, using FS nesting and constant matrix elements yields erroneous conclusions. We find that the inclusion of the matrix elements completely alters the structure of the response function. In all the cases studied other than the one-dimensional case we find that the inclusion of matrix elements washes out the structure found with constant matrix elements. Our conclusion is that it is imperative to calculate the full response function, with matrix elements, when making predictions about instabilities in novel materials.

José M. Soler

Papers

Electronic Structure Calculations with Localized Orbitals: The Siesta Method

Publisher's Note: “Density, structure, and dynamics of water: The effect of van der Waals interactions” [J. Chem. Phys.134, 024516 (2011)]

Room temperature compressibility and the diffusivity anomaly of liquid water from first principles

Thermodynamics of the roughening transition in stepped surfaces

Critical analysis of the response function in low dimensional materials