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

The adsorption of C60 on Si(111) has been studied by means of first-principles density functional calculations. 
A 2x2 adatom surface reconstruction was used to simulate the terraces of the 7x7 reconstruction. 
The structure of several possible adsorption configurations was optimized using the ab initio atomic forces, finding good candidates for two different adsorption states observed experimentally. 
While the C60 molecule remains closely spherical, the silicon substrate appears quite soft, especially the adatoms, which move substantially to form extra C-Si bonds, at the expense of breaking Si-Si bonds. 
The structural relaxation has a much larger effect on the adsorption energies, which strongly depend on the adsorption configuration, than on the charge transfer.

/pdf/first-principles-study-of-the-adsorption-of-c60-on-si-111-33e9awahc9.pdf

First principles study of the adsorption of C60 on Si(111)

Atom scattering by soft-potential surfaces with one-rayleigh-phonon exchange

We discuss the application of the local-spin-density approximation (LSDA) and provide criteria to gauge the reliability of supercell models of $a\ensuremath{-}\mathrm{S}\mathrm{i}:\mathrm{H}$ and tetrahedral amorphous carbon $(ta\ensuremath{-}\mathrm{C}).$ We identify models of $a\ensuremath{-}\mathrm{S}\mathrm{i}:\mathrm{H}$ that exhibit a localization on dangling bond consistent with electron-spin-resonance (ESR) experiments and show that a LSDA level description of the electron states is essential to describe these states. We offer an ab initio calculation of a well-isolated floating bond state and show that neither the charge nor spin is well localized. Finally, we suggest the origin of the ESR signal in $ta\ensuremath{-}\mathrm{C}$ is $\ensuremath{\pi}$-bonded pairs at the Fermi level.

José M. Soler

Papers

First principles study of the adsorption of C60 on Si(111)

Atom scattering by soft-potential surfaces with one-rayleigh-phonon exchange

Application of local-spin-density approximation to a-Si and tetrahedral a-C

Resonance line shapes for He diffraction and determination of surface profile for Ni(110) + (1 × 2)H

Tunneling current through localized surface states