Relaxation Of Atomic Positions Research Articles

Density functional calculations of atomic structure, charging effect, and static dielectric constant of two-dimensional systems based on B-splines

We have implemented a total-energy minimization scheme to allow for relaxation of atomic positions in density functional calculations for two-dimensional (2D) materials using a mixed basis set. The basis functions consist of products of 2D plane waves in the plane of the material and localized B-splines along the perpendicular direction. By using the mixed basis approach (MBA), we have studied the atomic relaxation and charge polarization of 2D systems under an applied electric field. In contrast to the conventional super-cell approach (SCA) which adopts repeated slabs sandwiched between vacuum regions, MBA makes no requirement of compensating background charge for treating electrically charged 2D systems due to carrier injection. With MBA we can avoid using a periodic sawtooth potential for systems under the applied field as commonly adopted in SCA. Furthermore, we introduced a simple method to determine the out-of-plane dielectric constants of 2D materials without the ambiguity of defining their effective thickness. This is achieved by calculating the linear response in charge polarization to the applied field. Selected 2D systems, including graphene and transition-metal dichalcogenides are tested. Our MBA results are consistent with previous SCA calculations when both approaches are equally applicable. However, for charged systems with high carrier density, we find significant deviation from SCA results obtained by imposing artificial charge neutrality condition.

Hydrogen Embrittlement at Cleavage Planes and Grain Boundaries in Bcc Iron-Revisiting the First-Principles Cohesive Zone Model.

Hydrogen embrittlement, which severely affects structural materials such as steel, comprises several mechanisms at the atomic level. One of them is hydrogen enhanced decohesion (HEDE), the phenomenon of H accumulation between cleavage planes, where it reduces the interplanar cohesion. Grain boundaries are expected to play a significant role for HEDE, since they act as trapping sites for hydrogen. To elucidate this mechanism, we present the results of first-principles studies of the H effect on the cohesive strength of α-Fe single crystal (001) and (111) cleavage planes, as well as on the Σ5(310)[001] and Σ3(112)[10] symmetrical tilt grain boundaries. The calculated results show that, within the studied range of concentrations, the single crystal cleavage planes are much more sensitive to a change in H concentration than the grain boundaries. Since there are two main types of procedures to perform ab initio tensile tests, different in whether or not to allow the relaxation of atomic positions, which can affect the quantitative and qualitative results, these methods are revisited to determine their effect on the predicted cohesive strength of segregated interfaces.

A topologically correct method of dislocations construction for atomistic modeling

We discuss the deep topological reasons why dislocation quadrupoles should be used for the construction of dislocations containing edge components. We demonstrate that contrary to all other currently used methods, this approach exactly preserves the topology of the order parameter field (atomic displacements in a crystal with defects relative to a defect-free crystal) of a dislocation-free crystal with periodic boundary conditions even for small simulation volumes and, thus, restores the verity of the material frame indifference principle, broken in other techniques. Using dislocation quadrupoles for edge and mixed dislocations, we have developed a careful procedure for relaxation of atomic positions around a dislocation core which enables one to achieve arbitrary low dislocation densities characteristic for real crystals. As a demonstration of the method capabilities, we have constructed a simulation volume with as low dislocation density as 1.5·1014m-2, which is realistic in deformed crystals, and one can easily lower this value as desired. All details of dislocation construction process are explicitly specified, making it very easy to reproduce our results. FCC Al crystal is used as a test case.

Adsorption of Water on Yttria-Stabilized Zirconia

Water adsorption on the cubic (111) surface of yttria-stabilized zirconia (YSZ) was investigated using density functional theory calculations. Relaxation of atomic positions away from ideal cubic lattice sites, in particular of the oxygen anion sublattice, is observed on including both phase-stabilizing dopants and water adsorption. A large slab model has been used to explore the effects of extended relaxation throughout the anionic sublattice and the role of vacancy–vacancy interactions on water adsorption. Dissociative adsorption of water to fill a surface vacancy site, accompanied by concerted oxygen movement in the vacancy cluster region of the slab, leads to a very strong adsorption of −2.20 eV, blocking surface sites for oxygen activation. We show that the use of larger slab models leads to a more detailed representation of the YSZ surface system.

GASP: software for geometric simulations of flexibility in polyhedral and molecular framework structures

Template-based geometric simulation is a specialised method for modelling flexible framework structures made up of rigid units using a simplified, localised physical model. The strengths of the method are its ability to handle large all-atom structural models rapidly and at minimal computational expense, and to provide insights into the links between local bonding and steric geometry and global flexibility. We review the implementation of geometric simulation in the ‘GASP’ software, and its application to the study of materials including zeolites, perovskites and metal–organic frameworks. The latest version (5) of GASP has significant improvements and extensions, in particular an improved algorithm for relaxation of atomic positions, and the capacity to handle both polyhedral and molecular structural units. GASP is freely available to researchers.

Van der Waals density functional study of the structural and electronic properties of La-doped phenanthrene

By the first principle calculations based on the van der Waals density functional theory, we study the crystal structures and electronic properties of La-doped phenanthrene. Two stable atomic geometries of La₁phenanthrene are obtained by relaxation of atomic positions from various initial structures. The structure-I is a metal with two energy bands crossing the Fermi level, while the structure-II displays a semiconducting state with an energy gap of 0.15 eV, which has an energy gain of 0.42 eV per unit cell compared to the structure-I. The most striking feature of La₁phenanthrene is that La 5d electrons make a significant contribution to the total density of state around the Fermi level, which is distinct from potassium doped phenanthrene and picene. Our findings provide an important foundation for the understanding of superconductivity in La-doped phenanthrene.

An insight into evolution of electronic, magnetic, optical, and vibrational properties of ultrathin Pd nanowires

We have studied evolution of the electronic, magnetic, optical, and vibrational properties of Pd nanowires (NWs) as we go from linear chains (LCs) (the ideal one-dimensional structure) to zigzag (ZZ) structure to 2 × 2 NWs. The 2 × 2 structure is found to be more stable and stiff, as compared to the LCs and ZZ NWs, with promising and versatile optical and vibrational properties. This 2 × 2 structure, built from the stacking of face-centered cubic (110) planes, has already been observed experimentally for silver NWs. Our calculations, which include relaxation of atomic positions, show that on stretching 2 × 2 NWs undergo a structural change from (110) stacking to a more symmetric (001) stacking, which culminates into a metastable state with stable magnetism. Furthermore, inclusion of spin orbit coupling beautifully illustrates its impact on the atomic magnetic moments in 2 × 2 NWs. Structure dependence of the axial anisotropy and azimuthal anisotropy is nicely brought out on comparison for the three structures. The charge density plots show charge accumulation transverse to NW axis for 2 × 2 NWs, consistent with their one-dimensional nature. A late start of the optical response, to the electric field perpendicular to the wire axis, indicates that well-aligned ultrathin Pd wires can effectively be used as polarizers of the light. Our systematic study also resolves discrepancies in the previous reports on Pd ZZ NWs.

Bulk and surface half-metallicity of CsS in CsCl structure: A density functional theory study

Abstract The electronic and magnetic properties of CsS in CsCl structure have been investigated. Comparisons between the total energies of CsS in different structures such as CsCl, zinc-blende, rocksalt, wurtzite and NiAs show that the CsCl structure is the most stable. Also we have done the full relaxation of atomic positions and cell parameters and we find out that CsCl with lattice parameter of 4.24 A is the most stable structure of CsS. According to our calculation in GGA approximation, CsS in CsCl structure is a half-metallic ferromagnet with a magnetic moment of 1 μ B per formula unit and half-metallic gap of 0.4 eV. We also consider CsS under stress and it is found that it preserves the half-metallicity up to lattice compression of 40%. The electronic and magnetic properties of (0 0 1), (1 1 0) and (1 1 1) surfaces of CsS in CsCl structure are also studied to find the robustness of half-metallicity at the surface. We find out that the half-metallicity of bulk CsS is lost only in Cs-terminated (0 0 1) surface but it is preserved in all of the other surfaces. In addition, we study the properties of CsS in GGA + U approximation and we realize that it is still a half-metal with a larger half-metallic gap of 1.76 eV. Finally, the Curie temperature is estimated in mean field approximation and it is found to be much more than the room temperature. All of the above properties cause the CsS compound to be a promising candidate for spintronic applications.

Magnetic ground state and electronic structure of CeRu2Al10

We present a combined theoretical and experimental study of the electronic structure for CeRu2Al10 based on ab initio band structure calculations and x-ray photoemission spectroscopy (XPS) data. Our calculations were performed for the base unit cell and for the hypothetical unit cell which enables antiferromagnetic ordering. The stability of the magnetic phase was investigated within fixed spin moment calculations. When additional 4f correlations are not included in the LSDA + U approach, CeRu2Al10 exhibits an unstable magnetic configuration with the difference in total energy per unit cell between the weakly magnetic state and the non-magnetic one of the order ∼0.3 meV. We found that Coulomb correlations among 4f electrons, when they are included in the LSDA + U approach, stabilize the magnetic structure. In the weakly correlated system (small U) an antiferromagnetic (AFM) ground state with the lowest total energy is preferred. The situation is, however, the opposite when the 4f correlations are strong. In this case the ferromagnetic (FM) ground state is preferred. By comparing our calculations with the experimental data we conclude that the 4f correlations in CeRu2Al10 are weak. We also carried out a structural relaxation of atomic positions within the Cmcm unit cell and we found that the Al atoms exhibit noticeable displacement from their positions known from x-ray diffraction (XRD) analysis.

Reversal of atomic contrast in scanning probe microscopy on (111) metal surfaces

We study the origin of atomic contrast on Cu(111) and Pt(111) surfaces probed by a non-contact atomic force microscope and scanning tunnelling microscope. First-principles simulations of the interaction between the atoms of the scanning tip and those of the probed surface show a dependence of the resulting contrast on the tip–sample distance and reveal a close relation between contrast changes and relaxation of atomic positions in both the tip and the sample. Contrast reversion around the distance where the short-range attractive atomic force reaches its maximum is predicted for both types of microscopies. We also demonstrate a relation between the maximal attractive force in a F–z atomic force spectroscopy and the chemical identity of the apex atom on the imaging tip.

Elastic Parameters of Various Rafted Structures of Model Ni-Base Alloys

Two-phase microstructure of ordered cube-shaped precipitates in the disordered matrix is characteristic of Ni-base superalloys. This microstructure degrades under the applied stress: depending on the stress direction, lattice misfit and elastic parameters of both constituent phases, the precipitates coalesce and change their overall shape. Various atomic configurations were modeled in this work representing various morphologies of precipitates developed under applied stress. A model Ni-base alloy containing six alloying elements typical of advanced Ni-based superalloys was used. Generated configurations were further subject to study of elastic parameters by means of computer straining experiments. Relaxation of atomic positions in the strained crystal blocks was implemented using molecular dynamics calculations with phenomenological Lennard-Jones pair potentials and interactions involving three coordination spheres. Changes of elastic parameters due to varying precipitates morphology are discussed.

Roles of γ-Fe 2O 3 in fly ash for mercury removal: Results of density functional theory study

First-principle calculations based on density function theory (DFT) are used to clarify the roles of γ-Fe 2O 3 in fly ash for removing mercury from coal-fired flue gases. In this study, the structure of key surface of γ-Fe 2O 3 is modeled and spin-polarized periodic boundary conditions with the partial relaxation of atom positions are employed. Binding energies of Hg on γ-Fe 2O 3 (0 0 1) perfect and defective surfaces are calculated for different adsorption sites and the potential adsorption sites are predicted. Additionally, electronic structure is examined to better understand the binding mechanism. It is found that mercury is preferably adsorbed on the bridge site of γ-Fe 2O 3 (0 0 1) perfect surface, with binding energy of −54.3 kJ/mol. The much stronger binding occurs at oxygen vacancy surface with binding energy of −134.6 kJ/mol. The calculations also show that the formation of hybridized orbital between Hg and Fe atom of γ-Fe 2O 3 (0 0 1) is responsible for the relatively strong interaction of mercury with the solid surface, which suggests that the presently described processes are all noncatalytic in nature. However, this is a reflection more of mercury's amalgamation ability.

The effect of the interface oxidation on tunneling conductance ofCo2MnSi/MgO/Co2MnSi magnetic tunnel junction

We investigate and discuss the effects of interfacial oxidation on electronic structures and tunnel conductanceof the Co2MnSi/MgO/Co2MnSi(001) magnetic tunnel junction (MTJ) on the basis of first-principles calculations. It is found thatthe MnSi termination tends to be oxidized compared with the Co termination because ofthe relaxation of atomic positions in the MnSi-terminated interface. Furthermore, we foundthat the single oxide layer inserted on both sides of the junction greatly decreases thetunnel conductance of the MTJ in parallel magnetization. We concluded that therelaxation of the Mn atomic position in the oxidized junction reduces the coupling of theΔ1 statesbetween the Co2MnSi electrode and the MgO barrier and causes significant interfacial scattering of the majority-spin electronswith Δ1 symmetry at the oxidized layer.

Roles of oxygen vacancy in the adsorption properties of CO and NO on Cu 2O(1 1 1) surface: Results of a first-principles study

First-principles calculations based on density functional theory (DFT) and the generalized gradient approximation (GGA) have been used to study the adsorption of CO and NO molecules on the Cu 2O(1 1 1) surface in the presence of oxygen vacancy. The calculations employ slab geometry and periodic boundary conditions with partial relaxation of atom positions. Two molecular orientations, X- and O-down (X = C, N), at two distinct sites, Cu 1C and oxygen vacancy sites, have been considered. Total energy calculations indicate that the Cu 1C position is relatively more favored than the oxygen vacancy site. The predicted binding energies are 144.5 kJ mol −1 (CO) and 124.1 kJ mol −1 (NO), respectively. The C–O and N–O stretching frequencies are unequally red-shifted upon adsorption. Upon adsorption at Cu 1C site, CO molecule was found to bind to Cu 1C atoms in vertical configuration whereas NO molecule adsorption in tilted mode. While upon adsorption at oxygen vacancy site, CO and NO molecules are both vertical to the Cu 2O(1 1 1) surface. Interestingly, we found that their adsorption properties on oxygen vacancy site are dependent on the defect density. As the density of defective sites increased, the adsorption energies of the defect-XO configuration increase and the N–O bond is continuously weakened whereas the C–O bond remains constant. Therefore, such a process favors the dissociation of the NO molecule and has a small influence on the adsorbed CO molecule.

Structural, Electronic, and Optical Properties of InxGa1-xAs Alloys by Full Potential Linear Augmented Plane Wave Method

Ab-initio calculations have been performed to determine the structural, electronic, and optical properties of InxGa1-xAs alloys for x=0.0, 0.25, 0.50, 0.75, and 1.0. The calculated lattice constants follow Vegard's law when we allow for relaxation of atomic positions. Our calculated dielectric function and critical points are in good qualitative agreement with experimental data. The critical point energies are fitted with a polynomial equation of indium concentration. The measured dielectric function and fitting parameters are in good agreement with our results. Our results will be useful for the design of optoelectronic devices using these materials.

Influence of superimposed normal stress on the [formula omitted] shear strength in perfect fcc metals

The influence of a stress applied perpendicularly to slip planes during the shear deformation of fcc crystals on the theoretical shear strength was studied for 〈112〉{111} slip system using first principles methods. A special relaxation procedure guaranteed that all stresses acting on the system were zero with the exception of the normal stress and the resolved shear stress. The theoretical shear strength was found to be a decreasing function of the applied tensile normal stress. The results were compared with similar calculations for rigid atomic planes and the role of relaxation of atomic positions within the planes was found to be important for correct description of the studied deformation process.

Density functional study of structures and mechanical properties of Y-doped α-SiAlONs

A 2 × 2 × 1 supercell of α-Si 3N 4 is used to model Y-doped α-SiAlON's (silicoalumino oxonitrides). Ab initio total energy calculations are performed at the DFT (GGA) level. A full relaxation of atomic positions is performed for stoichiometric α-Si 3N 4 and for a series of substituted structures with concentrations of Y, Al and O increasing up to the composition Y 0.5Si 9.5Al 2.5O 1.0N 15.0, similar to the observed solubility limits. The avoidance of neighboring AlX 4 (X = N,O) tetrahedra in highly doped structures indicates that the distribution of Al atoms in the framework of α-SiAlON's obeys the same Loewenstein rule as in aluminosilicate zeolite structures. An increase of the lattice parameters and cell volumes is observed with increasing degree of the doping. Changes are more pronounced for the insertion of Y than for Si-N/Al-O substitution. An introduction of a Y 3+ cation into the interstitial position in the cage, however, causes a local contraction of the structure. Via the contraction a more efficient Y–N bonding is formed, leading to the stabilization of the Y-doped structure. The pronounced increase of the cell volume and the lattice parameters with Y-doping is due to three framework Al/Si framework substitutions compensating the extraframework Y 3+ cation. The calculated bulk modulus ( B 0) ranges from 223 GPa for pure α-Si 3N 4 to 197 GPa for Y 0.5Si 9.5Al 2.5O 1.0N 15.0. The slope of the decrease of B 0 with the degree of doping depends on the Y-content. For constant concentration of Y an increasing content of O causes a linear decrease of B 0.

Size dependence of tetrahedral bond lengths in CdSe nanocrystals

The structural characteristics of organically passivated CdSe nanocrystals (NCs) were investigated with x-ray diffraction and extended x-ray absorption fine structure. As the NC size decreases, the axial bond length R(1) for an atomic tetrahedron extends but the equatorial bond length R(2) contracts, with a similar tendency of distortion for the lattice parameters of the wurtzite structure. The authors suggest that the observed hexagonal distortion is attributed to the surface stress of the NCs related to the organic passivation effect and the relaxation of atomic positions at the stacking fault interface.

First-principles calculation of LaNi5 surface

The spin-polarized, all-electron, ab initio calculations have been performed for the electronic structure of the surface of crystal LaNi5 using the self-consistent cluster-embedding (SCCE) calculation method. The geometrical surface structure of crystal LaNi5 and its electronic structure having the lowest ground-state energy are obtained, with the full relaxation of atomic positions along the direction perpendicular to the surface. On the surface of crystal LaNi5, the La atom protruded, and the Ni atoms caved in, so the surface becomes uneven which increases the contacting area. The effective volume of the surface layer rises by 9%. The Fermi level of the LaNi5 surface, which is contributed by mainly Ni 3d electrons, is much higher than that of body LaNi5. The valence band is not fully filled. For the first two layers of LaNi5 surface, there are 1.15 electrons transferred from La to Ni, and the two layers have small opposite spin magnetic moments which shows the paramagnet. All calculated results show that the properties of LaNi5 surface are significantly different from that of body LaNi5, but very similar to that of hydride LaNi5H7. So the geometrical surface structure of crystal LaNi5 is in favor of the absorption of hydrogen.

A DFT study of amorphous silicon oxynitride

We study amorphous silicon oxynitride, a-SiNO, for the entire compositional range between SiO2 and Si3N4. Structural models are constructed using an empirical bond switch algorithm. The continuous random alternating networks (CRAN) generated have well-defined bond topology as to represent the perfect chemical order in such materials. Consequently, the models comprise Si–O and Si–N bonds only and constitute an extension of the classical model of vitreous silica presented by Zachariasen. Models consisting of 108–126 atoms are subsequently optimized using standard density functional methods, including full relaxation of atomic positions and cell geometries. Extensive ab initio (Car–Parrinello) molecular dynamic simulations are carried out for 10–50ps to test for the chemical and structural stability of the amorphous networks at elevated temperatures. The results show that changes of physical and structural properties within the Si–N–O phase diagram are close to what can be expected from Vegard’s rule. E.g., the addition of N into SiO2 stiffens the network and decreases the insulating character of the material, while elastic properties such as the bulk modulus increase. The elastic properties, namely the bulk modulus, give rise to propose two distinct regions within the ternary phase diagram, with Si2N2O approximately separating both region. At this composition, the dependence of B0 on the N content abruptly changes its slope.