Sharing electronic structure and crystallographic data with ETSF_IO

We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines.

Program summary

Program title: ETSF_IOCatalogue identifier: AEBG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBG_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Gnu Lesser General Public LicenseNo. of lines in distributed program, including test data, etc.: 63 156No. of bytes in distributed program, including test data, etc.: 363 390Distribution format: tar.gzProgramming language: Fortran 95Computer: All systems with a Fortran95 compilerOperating system: All systems with a Fortran95 compilerClassification: 7.3, 8External routines: NetCDF, http://www.unidata.ucar.edu/software/netcdfNature of problem: Store and exchange electronic structure data and crystallographic data independently of the computational platform, language and generating softwareSolution method: Implement a library based both on NetCDF file format and an open specification (http://etsf.eu/index.php?page=standardization)     

First-principles calculations of the YBa2Cu3O7/PrBa2Cu3O7 interface

We discuss results of spin-polarized electronic structure calculations for a 1 × 1 YBa₂Cu₃O₇/PrBa₂Cu₃O₇ supercell, obtained by the full-potential linear augmented plane wave (FLAPW) method as implemented in the WIEN2k package. The calculations are based on the generalized gradient approximation for the exchange correlation functional. The on-site Coulomb interaction of the correlated Cu 3d and Pr 4f electrons is considered by using the LSDA+U approach. The electronic states of the YBa₂Cu₃O₇/PrBa₂Cu₃O₇ interface are compared with the respective states in the PrBa₂Cu₃O₇ and YBa₂Cu₃O₇ bulk compounds, where we focus on the magnetic Pr atoms and the Cu atoms in the CuO₂ planes.     

Plato: A localised orbital based density functional theory code

The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation.

Program summary

Program title: PlatoCatalogue identifier: AEFC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 219 974No. of bytes in distributed program, including test data, etc.: 1 821 493Distribution format: tar.gzProgramming language: C/MPI and PERLComputer: Apple Macintosh, PC, Unix machinesOperating system: Unix, Linux and Mac OS XHas the code been vectorised or parallelised?: Yes, up to 256 processors testedRAM: Up to 2 Gbytes per processorClassification: 7.3External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTWNature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces.Solution method: Localised orbital based density functional theory.Restrictions: Tight-binding and density functional theory only, no exact exchange.Unusual features: Both atom centred and uniform meshes available. Can deal with arbitrary angular momenta for orbitals, whilst still retaining Slater–Koster tables for accuracy.Running time: Test cases will run in a few minutes, large calculations may run for several days.     

Structural studies on Si:H network by Raman, micro-photoluminescence, electron microscopy and ultraviolet ellipsometry: effect of Ar dilution to the SiH4-plasma

Structural characterization of the material has been performed using micro-Raman spectroscopy, ultraviolet (UV) ellipsometry, electron microscopy and micro-photoluminescence (PL) studies on Si:H films prepared at a wide range of Ar dilution to the SiH₄ plasma, defined by R(Ar)=Ar/SiH₄ and varying from 10 to 400. Microcrystallization in Si:H network was easily obtained introducing Ar as a diluent, however, increasing Ar dilution revealed a continuous transformation of the network from microcrystalline to amorphous dominated structure. An overall amorphization of the network and its initiation by the presence of an enormously high void density (∼81 vol.%) in an extended incubation layer (∼163 nm) is the result of extremely high Ar dilution (R(Ar)∼400), on the formation of Si:H films. Increasing porosity in the amorphous dominated matrix resulted in a significant increase in the photoluminescence intensity, contributing to a photoluminescent Si:H material available from extremely high Ar dilution to the SiH₄ plasma in rf glow discharge. Effect of Ar dilution inducing the growth morphology by controlling both the gas phase reactions and solid phase network modifications in Si:H network has been discussed.     

Ab-initio study of electronic and elastic properties of Mg(BH4)(NH2) complex hydride

Structural and electronic properties of complex hydride Mg(BH₄)(NH₂), applicable in hydrogen storage, were studied in framework of pseudopotential-density functional theory. This compound shows an indirect band gap of 4.95 eV which is categorized in insulator materials. The calculated total and partial density of states of this compound show that the hydrogen bonding in BH₄ anion is mainly covalent and the hydrogen-hydrogen repulsion is more in anion BH₄ than in anion NH₂. The calculated bulk modulus from Birch-Murnaghan equation of state is in close agreement with that obtained from the elastic constants. The obtained bulk modulus (19.27 GPa) shows this compound is more ductile than binary and ternary hydrides and it does not have a brittle structure. Therefore, it is a good candidate for hydrogenation and dehydrogenation cycles. The stability of the structure in ambient pressure is also declared by calculating the elastic coefficients. However, the existence of elastic anisotropy in the compound demonstrates the less compressibility of it along the c axis than a and b axes. The small amount of Poisson ratio indicates that it is more stable against shear compared to common borohydrides. This point is important for hydride stability in hydrogenation and dehydrogenation cycles.     

Ab initio study of solution energy and diffusion of caesium in uranium dioxide

The behaviour of caesium in nuclear fuels is investigated using density functional theory (DFT). In a first step, the incorporation and solution energies of Cs in pre-existing trap sites of UO₂ (vacancies, interstitials, U-O di-vacancy and Schottky trio defects) are calculated using the projector-augmented-wave (PAW) derived pseudopotentials as implemented in the Vienna ab initio simulation package (VASP). Correlation effects are taken into account within the DFT + U approach. The solubility of caesium is found to be very low, in agreement with experimental data. The migration of Cs is found to be highly anisotropic, it is controlled by uranium diffusion with an Arrhenius activation energy of 4.8 eV in hyperstoichiometric UO_2+x, in good agreement with experimental values.     

Hydrogen-induced enhancement of ductility of fcc iridium: A first-principles study

First-principles FLAPW-GGA calculations have been performed to understand the response of the structural, elastic and electronic properties of fcc Ir to the presence of interstitial hydrogen in comparison with fcc Pd. The Cauchy pressure and the Pugh's criterion (ratio of shear modulus and bulk modulus) were used to assess the trends for brittle/ductile behavior of Ir and Pd accompanying hydrogen insertion. An unconventional hydrogen-induced enhancement of ductility of iridium was predicted simultaneously with its “metallization” owing to the growth of the near-Fermi density of states.     

Effect of pressure on the structural and elastic properties of ZnS and MgS alloys in the B3 and B1 phases

From the first-principles calculations, we have investigated the elastic stiffness coefficients C₁₁, C₁₂, C₄₄ and the bulk modulus B of the II-VI semiconductors ZnS and MgS under hydrostatic pressure. The calculations are based on the density functional theory within the generalized gradient approximation (GGA) for exchange-correlation interaction. For the structural properties we have shown that ZnS adopt the rocksalt (NaCl or B1) structure over 11.87 GPa pressure, the same character is adopted by MgS over 0.8 GPa. The elastic coefficients have the same behavior for the different structures of alloys; they increase with increasing pressure values. Our results for the structural parameters and equilibrium phase elastic constants are in good agreement with the available theoretical and experimental data.     

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First Principles Investigation of Local Distortions in Doped La2CuO4

We present the results of first-principles cluster calculations of local distortions in doped La₂CuO₄. Local deformations of the CuO₆ octahedra associated with the presence of an additional extrinsic hole were determined using the density-functional (DF) method on various cluster models. The results indicate that a localized hole induces a contraction of the CuO(apical) distance from 2.40 to 2.28 Å. The contracted distance is in very good agreement with the anomalous, short CuO(apical) distance of 2.3 Å, observed recently by polarized Cu K-edge extended x-ray absorption fine structure (EXAFS) in La_1.85Sr_0.15CuO₄ and associated with the hole-rich stripe region.