Siesta code

Figure 6.18. (Top) STM image of the flfe-plane of TTF-TCNQ taken at 63 K (Ft = 50 mV, /t = 1 nA). The image area is 5.3 nm x 5.3 nm. Reprinted with permission from Z. Z. Wang, J. C. Girard, C. Pasquier, D. Jerome and K. Bechgaard, Physical Review B, 67,121401 (2003). Copyright (2003) by the American Physical Society. (Bottom) Simulation of the STM image of the afe-plane of TTF-TCNQ, obtained with DFT calculations in the GGA performed with the Siesta code (Soler et al, 2002) using the Tersoff-Hamann approximation (see Section 4.2). The value of the charge density is 2 x 10 electrons/a.u., which is about 0.2 nm above the surface. Courtesy of Drs P. Ordejon and E. Canadell.

In this work we recalculate the structures of Au clusters with 6scalar relativistic Troullier-Martins pseudo-potentials , respectively, and within the SIESTA code" . In Fig 2 we present our results for the structures and relative binding energies. We see that GGA leads to planar structures whereas LDA favors 3D structures for n>7 clusters. Thus, in addition to relativistic effects, the observed planarity of Au clusters is accounted for using only the GGA level of theory. 

The relaxation of the structure in the KMC-DR method was done using an approach based on the density functional theory and linear combination of atomic orbitals implemented in the Siesta code [97]. The minimum basis set of localized numerical orbitals of Sankey type [98] was used for all atoms except silicon atoms near the interface, for which polarization functions were added to improve the description of the SiOx layer. The core electrons were replaced with norm-conserving Troullier-Martins pseudopotentials [99] (Zr atoms also include 4p electrons in the valence shell). Calculations were done in the local density approximation (LDA) of DFT. The grid in the real space for the calculation of matrix elements has an equivalent cutoff energy of 60 Ry. The standard diagonalization scheme with Pulay mixing was used to get a self-consistent solution. In the framework of the KMC-DR method, it is not necessary to perform an accurate optimization of the structure, since structure relaxation is performed many times. 

We use the DFT SIESTA code [13], which implements the generalized gradient approximation (GGA), Perdew-Burke-Emzerhof (PBE) density functional [14], norm-conserving pseudopotentials and periodic boundary conditions. A localized double- polarized (DZP) basis set was used for valence electrons. 

SIESTA code, the interactions of valence electrons with the atomic ionic cores are described by the norm-conserving pseudopotentials with the partial core correction of 0.6 au. on the oxygen atom. We used the optimized-zeta plus polarization (DZP) basis sets with medium localization in the SIESTA code. A mesh cutloff energy of 350 Ry, which defines the equivalent plane wave cut-off for the grid, was used. The forces on atomic ions are obtained by the Heilman IFeynman theorem and were used to relax atomic ionic positions to the minimum energy. The atomic forces within the supercell were minimized to within 0.035 eV/A and 0.05 eV/A in the SIESTA and CASTEP codes respectively. 

Abstract SIESTA was developed as an approach to compute the electronic properties and perform atomistic simulations of complex materials from first principles. Very large systems, with an unprecedented number of atoms, can be studied while keeping the computational cost at a reasonable level. The SIESTA code is fi-eely available for the academic community (http //www.uam.es/siesta), and this has made it a widely used tool for the study of materials. It has been applied to a large variety of systems including surfaces, adsorbates, nanotubes, nanoclusters, biological molecules, amorphous semiconductors, ferroelectric films, low-dimensional metals, etc. Here we present a thorough review of the applications in materials science to date. 

Density functional theory (DFT), developed within solid state physics, is based on the theorem of Hohenberg and Kohn that the ground state energy of a system depends on the electron density. It can be applied to calculations performed either with localised basis sets or by combination of plane waves. Both approaches have been applied to microporous solids, although the plane wave methods have been used more commonly. The SIESTA code, for example,permits DFT calculations using localised basis sets as does GAUSSIAN. 

In 2008, Artacho et al. presented developments and applicability of the Siesta method for a large variation of systems [37]. Within the Siesta code the plane wave basis for the electron density is combined with numerical atomic orbitals of finite support. In their article, Artacho et al. demonstrate linear scalability of the Siesta program using a system with more than 4,000 atoms [37]. 

There are multiple methods for TS searches [26]. As an example, the one implemented in the SIESTA code [6] is the constrained optimization scheme [27, 28]. Initially, the distance between atoms participating in the bond that forms or breaks is constrained at an estimated value, and the total energy of the system is minimized with respect to all the other degrees of freedom. Then, this procedure is repeated with a new distance until the TS is found so that all forces on atoms vanish and the total energy is a maximum along the reaction coordinate but a minimum with respect to the remaining degrees of freedom. 

For the study of low-dimensional magnetic systems we use in this paper an alternative method that has been recently applied successfully to quite varied systems, ranging from metal nanostructures to biomolecules, showing accuracy and flexibility. We have used the Siesta code 12,13,14,15 which... 

For completeness we have also calculated with the Siesta code and with the TB-LMTO GGA method the electronic structure and the magnetization for a free standing Fe monolayer. The magnetic moments found with the SZSP and DZSP basis sets are 3.19 fis and 3.23 hb respectively, in good agreement with the TB-LMTO result (3.15 /ub). This corresponds to an enhancement of about 0.15 hb with respect to the (100) surface, due to the loss of coordination. 

Table 1. Properties of Fe2 obtained with the Siesta code. We use GGA with a pseudopotential energy cutoff of 150 Ry and an energy shift of 0.001 Ry for both single (SZSP) and double C, (DZSP) basis. The total spin in all the cases is S = 3fi. Bond lengths r (bohrs), binding energies E), (eV/atom), and vibrational frequencies We (cm ) are shown. The binding energies Ei, are calculated with respect to spherical D Fe atoms. Other calculations and experimental results are given for comparison.

The SIESTA method provides a very general scheme to perform a range of calculations from very fast to very accurate, depending on the needs and stage of the simulation, of all kinds of molecule, material and surface. It allows DPT simulations of more than a thousand atoms in modest PC workstations, and over a hundred thousand atoms in parallel platforms [400], The numerious appUcations of the Siesta DFT LCAO method can be found on the Siesta code site [344]. These appUcations include nanotubes, surface phenomena and amorphous solids. 

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