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Sample records for ab initio density

  1. Accurate ab initio spin densities

    CERN Document Server

    Boguslawski, Katharina; Legeza, Örs; Reiher, Markus

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys. 2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CA...

  2. The density matrix renormalization group for ab initio quantum chemistry

    CERN Document Server

    Wouters, Sebastian

    2014-01-01

    During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. Its underlying wavefunction ansatz, the matrix product state (MPS), is a low-rank decomposition of the full configuration interaction tensor. The virtual dimension of the MPS, the rank of the decomposition, controls the size of the corner of the many-body Hilbert space that can be reached with the ansatz. This parameter can be systematically increased until numerical convergence is reached. The MPS ansatz naturally captures exponentially decaying correlation functions. Therefore DMRG works extremely well for noncritical one-dimensional systems. The active orbital spaces in quantum chemistry are however often far from one-dimensional, and relatively large virtual dimensions are required to use DMRG for ab initio quantum chemistry (QC-DMRG). The QC-DMRG algorithm, its computational cost, and its properties are discussed. Two important aspects to reduce the computational co...

  3. Ab initio molecular dynamics using hybrid density functionals

    Science.gov (United States)

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost

    2008-06-01

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  4. The ab-initio density matrix renormalization group in practice.

    Science.gov (United States)

    Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic

    2015-01-21

    The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

  5. Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions.

    Science.gov (United States)

    Changlani, Hitesh J; Zheng, Huihuo; Wagner, Lucas K

    2015-09-14

    We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U(∗)/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.

  6. Mechanisms for catalytic carbon nanofiber growth studied by ab initio density functional theory calculations

    DEFF Research Database (Denmark)

    Abild-Pedersen, Frank; Nørskov, Jens Kehlet; Rostrup-Nielsen, Jens;

    2006-01-01

    Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported...

  7. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

    Science.gov (United States)

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  8. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

    Science.gov (United States)

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  9. Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions

    Energy Technology Data Exchange (ETDEWEB)

    Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K. [Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green St., Urbana, Illinois 61801 (United States)

    2015-09-14

    We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.

  10. Ab-initio density functional theory study of a WO3 NH3-sensing mechanism

    Institute of Scientific and Technical Information of China (English)

    Hu Ming; Zhang Jie; Wang Wei-Dan; Qin Yu-Xiang

    2011-01-01

    WO3 bulk and various surfaces are studied by an ab-initio density functional theory technique.The band structures and electronic density states of WO3 bulk are investigated.The surface energies of different WO3 surfaces are compared and then the(002)surface with minimum energy is computed for its NH3 sensing mechanism which explains the results in the experiments.Three adsorption sites are considered.According to the comparisons of the energy and the charge change between before and after adsorption in the optimal adsorption site O1c,the NH3 sensing mechanism is obtained.

  11. Ab initio molecular dynamics with nuclear quantum effects at classical cost: ring polymer contraction for density functional theory

    CERN Document Server

    Marsalek, Ondrej

    2015-01-01

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive pro...

  12. Molecular orbital ab initio and density functional theoretical study on reaction between PH2 and NO

    Institute of Scientific and Technical Information of China (English)

    HU; Zhengfa(胡正发); WANG; Zhenya(王振亚); LI; Haiyang(李海洋); ZHOU; Shikang(周士康)

    2002-01-01

    The theoretical study of reaction between PH2 and NO on the ground state potential energy surface is reported by using molecular orbital ab initio calculation and density function theory (DFT). Equilibrium structural parameters, harmonic vibrational frequencies, total energies and zero point energies of all species during reaction are computed by HF, MP2 (full) and B3LYP theory levels with the medium basis set 6-31G*. Theoretical results indicate that intermediate IM1(H2PNO) is firstly formed by overcoming a small energy barrier TS1, and then two four-membered ring transient states TS2 and TS5, with energy barriers 103.3 and 102.6 kJ/mol respectively,then H-migration and isomerization are completed and the products PN and H2O are formed. The reaction is exothermic one with -189.6 k J/mol released.

  13. Ab initio density functional theory investigation of structural and electronic properties of silicon carbide nanotube bundles

    Energy Technology Data Exchange (ETDEWEB)

    Moradian, Rostam [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Nano Science and Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of); Department of Nano Science, Computational Physical Science Research Laboratory, Institute for Studies in Theoretical Physics and Mathematics (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)], E-mail: moradian.rostam@gmail.com; Behzad, Somayeh; Chegel, Raad [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of)

    2008-10-01

    By using ab initio density functional theory the structural and electronic properties of isolated and bundled (8,0) and (6,6) silicon carbide nanotubes (SiCNTs) are investigated. Our results show that for such small diameter nanotubes the inter-tube interaction causes a very small radial deformation, while band splitting and reduction of the semiconducting energy band gap are significant. We compared the equilibrium interaction energy and inter-tube separation distance of (8,0) SiCNT bundle with (10,0) carbon nanotube (CNT) bundle where they have the same radius. We found that there is a larger inter-tube separation and weaker inter-tube interaction in the (8,0) SiCNT bundle with respect to (10,0) CNT bundle, although they have the same radius.

  14. Ab initio density functional theory investigation of Li-intercalated silicon carbide nanotube bundles

    Energy Technology Data Exchange (ETDEWEB)

    Moradian, Rostam [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Nano Science and Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of); Computational Physical Science Research Laboratory, Department of Nano Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), PO Box 19395-5531, Tehran (Iran, Islamic Republic of)], E-mail: moradian.rostam@gmail.com; Behzad, Somayeh; Chegel, Raad [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of)

    2009-06-15

    We present the results of ab initio density functional theory calculations on the energetic, and geometric and electronic structure of Li-intercalated (6,6) silicon carbide nanotube (SiCNT) bundles. Our results show that intercalation of lithium leads to the significant changes in the geometrical structure. The most prominent effect of Li intercalation on the electronic band structure is a shift of the Fermi energy which occurs as a result of charge transfer from lithium to the SiCNTs. All the Li-intercalated (6,6) SiCNT bundles are predicted to be metallic representing a substantial change in electronic properties relative to the undoped bundle, which is a wide band gap semiconductor. Both inside of the nanotube and the interstitial space are susceptible for intercalation. The present calculations suggest that the SiCNT bundle is a promising candidate for the anode material in battery applications.

  15. Ab initio downfolding for electron-phonon-coupled systems: Constrained density-functional perturbation theory

    Science.gov (United States)

    Nomura, Yusuke; Arita, Ryotaro

    2015-12-01

    We formulate an ab initio downfolding scheme for electron-phonon-coupled systems. In this scheme, we calculate partially renormalized phonon frequencies and electron-phonon coupling, which include the screening effects of high-energy electrons, to construct a realistic Hamiltonian consisting of low-energy electron and phonon degrees of freedom. We show that our scheme can be implemented by slightly modifying the density functional-perturbation theory (DFPT), which is one of the standard methods for calculating phonon properties from first principles. Our scheme, which we call the constrained DFPT, can be applied to various phonon-related problems, such as superconductivity, electron and thermal transport, thermoelectricity, piezoelectricity, dielectricity, and multiferroicity. We believe that the constrained DFPT provides a firm basis for the understanding of the role of phonons in strongly correlated materials. Here, we apply the scheme to fullerene superconductors and discuss how the realistic low-energy Hamiltonian is constructed.

  16. Density functional and ab initio investigation of S2N2 and (SN)2

    Science.gov (United States)

    Moon, Jiwon; Chae, Myoungju; Kim, Joonghan

    2017-03-01

    Quantum chemical calculations were performed to calculate the molecular properties of the 1Ag state of disulfur dinitride, S2N2, and the 1A1 state of the SN dimer, (SN)2, using density functional theory (DFT) and ab initio methods. The molecular structure of (SN)2 is a trapezoid instead of a rectangle. Because the multireference character of (SN)2 is considerable, most hybrid DFTs poorly describe its molecular properties. In contrast, old generalized gradient approximations give qualitatively correct descriptions of the molecular properties of (SN)2. Multi-state second-order multiconfigurational perturbation theory gives results that are close to those from multireference configuration interaction with the Davidson correction. The multireference character should be considered when calculating the molecular properties of poly sulfur nitride systems.

  17. Thermal Conductivity of Pure Noble Gases at Low Density from Ab Initio Prandtl Number

    Science.gov (United States)

    Song, Bo; Wang, Xiaopo; Liu, Zhigang

    2013-03-01

    The experimental data reported in the literature after 2000 have been investigated for the viscosity and thermal conductivity of helium-4, neon, and argon at low density. The well-established values of thermal conductivity by transient hot-wire measurements are not reliable enough for noble gases in the low-pressure gas region. These facts motivate us to determine the thermal conductivity from accurate viscosity data and the ab initio Prandtl number, with an uncertainty of 0.25 % for temperatures ranging between 200 K and 700 K. The theoretical accuracy is superior to the accuracy of the best measurements. The calculated results are accurate enough to be applied as standard values for the thermal conductivity of helium-4, neon, and argon over the considered temperature range.

  18. Electronic Transport in Monolayer Graphene with Extreme Physical Deformation: ab Initio Density Functional Calculation

    CERN Document Server

    Gao, Haiyuan; Li, Meijiao; Guo, Zhendong; Chen, Hongshen; Jin, Zhonghe; Yu, Bin

    2011-01-01

    Electronic transport properties of monolayer graphene with extreme physical bending up to 90o angle are studied using ab Initio first-principle calculations. The importance of key structural parameters including step height, curvature radius and bending angle are discussed how they modify the transport properties of the deformed graphene sheet comparing to the corresponding flat ones. The local density of state reveals that energy state modification caused by the physical bending is highly localized. It is observed that the transport properties of bent graphene with a wide range of geometrical configurations are insensitive to the structural deformation in the low-energy transmission spectra, even in the extreme case of bending. The results support that graphene, with its superb electromechanical robustness, could serve as a viable material platform in a spectrum of applications such as photovoltaics, flexible electronics, OLED, and 3D electronic chips.

  19. Molecular Kohn-Sham exchange-correlation potential from the correlated ab initio electron density

    Science.gov (United States)

    Gritsenko, Oleg V.; van Leeuwen, Robert; Baerends, Evert Jan

    1995-09-01

    The molecular Kohn-Sham (KS) exchange-correlation potential vxc has been constructed for LiH from the correlated ab initio density ρ by means of the simple iterative procedure developed by van Leeuwen and Baerends [Phys. Rev. A 49, 2421 (1994)]. The corresponding KS energy characteristics, such as the kinetic energy of noninteracting particles Ts, kinetic part of the exchange-correlation energy Tc, and energy of the highest occupied molecular orbital ɛN, have been obtained with reasonable accuracy. A relation between the form of vxc and the electronic structure of LiH has been discussed. Test calculations for the two-electron H2 molecule have shown the efficiency of the procedure.

  20. Ab-initio simulations of materials using VASP: Density-functional theory and beyond.

    Science.gov (United States)

    Hafner, Jürgen

    2008-10-01

    During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science-promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces

  1. Matrix Product Operators, Matrix Product States, and ab initio Density Matrix Renormalization Group algorithms

    CERN Document Server

    Chan, Garnet Kin-Lic; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-01-01

    Current descriptions of the ab initio DMRG algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab-initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational par...

  2. Ab initio density matrix renormalization group study of magnetic coupling in dinuclear iron and chromium complexes

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Travis V.; Morokuma, Keiji, E-mail: morokuma@fukui.kyoto-u.ac.jp [Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103 (Japan); Kurashige, Yuki; Yanai, Takeshi [Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585 (Japan)

    2014-02-07

    The applicability of ab initio multireference wavefunction-based methods to the study of magnetic complexes has been restricted by the quickly rising active-space requirements of oligonuclear systems and dinuclear complexes with S > 1 spin centers. Ab initio density matrix renormalization group (DMRG) methods built upon an efficient parameterization of the correlation network enable the use of much larger active spaces, and therefore may offer a way forward. Here, we apply DMRG-CASSCF to the dinuclear complexes [Fe{sub 2}OCl{sub 6}]{sup 2−} and [Cr{sub 2}O(NH{sub 3}){sub 10}]{sup 4+}. After developing the methodology through systematic basis set and DMRG M testing, we explore the effects of extended active spaces that are beyond the limit of conventional methods. We find that DMRG-CASSCF with active spaces including the metal d orbitals, occupied bridging-ligand orbitals, and their virtual double shells already capture a major portion of the dynamic correlation effects, accurately reproducing the experimental magnetic coupling constant (J) of [Fe{sub 2}OCl{sub 6}]{sup 2−} with (16e,26o), and considerably improving the smaller active space results for [Cr{sub 2}O(NH{sub 3}){sub 10}]{sup 4+} with (12e,32o). For comparison, we perform conventional MRCI+Q calculations and find the J values to be consistent with those from DMRG-CASSCF. In contrast to previous studies, the higher spin states of the two systems show similar deviations from the Heisenberg spectrum, regardless of the computational method.

  3. The Structure, Density, and Local Environment Distribution in Ab Initio Liquid Water

    Science.gov (United States)

    Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto

    2014-03-01

    We have performed extensive ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions in the canonical (NVT) and isothermal-isobaric (NPT) ensembles to understand the individual and collective importance of exact exchange, van der Waals interactions, and nuclear quantum effects on the structural properties of liquid water. AIMD simulations which include these effects result in oxygen-oxygen radial distribution functions which are in excellent agreement with experiments and a liquid water structure having an equilibrium density within 1% of the experimental value of 1 g/cm3. A detailed analysis of the distribution of local structure in ambient liquid water has revealed that the inherent potential energy surface is bimodal with respect to high- and low-density molecular environments, consistent with the existence of polymorphism in the amorphous phases of water. With these findings in mind, the methodology presented herein overcomes the well-known limitations of semi-local density functional theory (GGA-DFT) providing a detailed and accurate microscopic description of ambient liquid water. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500.

  4. Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

    Science.gov (United States)

    Marsalek, Ondrej; Markland, Thomas E

    2016-02-07

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

  5. Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

    Science.gov (United States)

    Hafner, Jürgen

    2010-09-29

    During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

  6. Experimental (electrochemistry) and theoretical (ab initio and density functional theory) studies of hydrogen and sulfide adsorption on palladium (100) surface.

    OpenAIRE

    2001-01-01

    The adsorption of H And S2- species on Pd (100) has been studied with ab initio, density-functional calculations and electrochemical methods. A cluster of five Pd atoms with a frozen geometry described the surface. The computational calculations were performed through the GAUSSIAN94 program, and the basis functions adapted to a pseudo-potential obtained by using the Generator Coordinate Method adapted to the this program. Using the cyclic voltammetry technique through a Model 283 Potentiostat...

  7. Electronic and thermoelectric properties of InN studied using ab initio density functional theory and Boltzmann transport calculations

    Energy Technology Data Exchange (ETDEWEB)

    Borges, P. D., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu; Scolfaro, L., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu [Department of Physics, Texas State University, San Marcos, Texas 78666 (United States)

    2014-12-14

    The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.

  8. Ab initio joint density-functional theory of solvated electrodes, with model and explicit solvation

    Science.gov (United States)

    Arias, Tomas

    2015-03-01

    First-principles guided design of improved electrochemical systems has the potential for great societal impact by making non-fossil-fuel systems economically viable. Potential applications include improvements in fuel-cells, solar-fuel systems (``artificial photosynthesis''), supercapacitors and batteries. Economical fuel-cell systems would enable zero-carbon footprint transportation, solar-fuel systems would directly convert sunlight and water into hydrogen fuel for such fuel-cell vehicles, supercapacitors would enable nearly full recovery of energy lost during vehicle braking thus extending electric vehicle range and acceptance, and economical high-capacity batteries would be central to mitigating the indeterminacy of renewable resources such as wind and solar. Central to the operation of all of the above electrochemical systems is the electrode-electrolyte interface, whose underlying physics is quite rich, yet remains remarkably poorly understood. The essential underlying technical challenge to the first principles studies which could explore this physics is the need to properly represent simultaneously both the interaction between electron-transfer events at the electrode, which demand a quantum mechanical description, and multiscale phenomena in the liquid environment such as the electrochemical double layer (ECDL) and its associated shielding, which demand a statistical description. A direct ab initio approach to this challenge would, in principle, require statistical sampling and thousands of repetitions of already computationally demanding quantum mechanical calculations. This talk will begin with a brief review of a recent advance, joint density-functional theory (JDFT), which allows for a fully rigorous and, in principle, exact representation of the thermodynamic equilibrium between a system described at the quantum-mechanical level and a liquid environment, but without the need for costly sampling. We then shall demonstrate how this approach applies in

  9. Linear optical properties and their bond length dependence of yttrium bromide from ab initio and density functional theory calculations

    Energy Technology Data Exchange (ETDEWEB)

    Alipour, Mojtaba, E-mail: malipour@shirazu.ac.ir [Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454 (Iran, Islamic Republic of); Mohajeri, Afshan, E-mail: amohajeri@shirazu.ac.ir [Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454 (Iran, Islamic Republic of)

    2011-08-25

    Graphical abstract: The electronic properties such as the static dipole polarizability, anisotropy of the polarizability, and dipole moment of yttrium bromide, YBr (X{sup 1}{Sigma}) have been theoretically studied. Highlights: {yields} Conventional ab initio and density functional theory methods were employed to study linear optical properties of YBr molecule. {yields} Properties derivatives and their level of theory dependence were studied. {yields} Electron correlation effects and rovibrational corrections have also been discussed. - Abstract: We have employed conventional ab initio and density functional theory methods to study the electronic properties such as the mean static dipole polarizability, {alpha}-bar, anisotropy of the polarizability, {Delta}{alpha}, and dipole moment, {mu}, of yttrium bromide. The bond length dependence of properties is determined at different levels of theory and appropriate expansions around experimental internuclear distance have been presented. Moreover, the first and second geometrical derivatives for each property are quantified and their level of theory dependence has been analyzed. To study the effect of molecular rotation and vibration on the electronic properties, the rovibrational corrections have also been carried out. It is found that these corrections are less pronounced for considered properties of YBr. In all calculations, the electron correlation effects have been considered and discussed. The obtained results show that the electron correlation is more significant in the calculation of the mean and the anisotropy of dipole polarizability.

  10. Ab initio van der waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like

    DEFF Research Database (Denmark)

    Møgelhøj, Andreas; Kelkkanen, Kari André; Wikfeldt, K Thor

    2011-01-01

    The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations in the NVE ensemble using van der Waals (vdW) density-functional theory, i.e., using the new exchange-correlation functionals optPBE-vdW and vdW-DF2, where the latter has softer nonlocal...... shows some resemblance with experiment for high-density water ( Soper , A. K. and Ricci , M. A. Phys. Rev. Lett. 2000 , 84 , 2881 ), but not directly with experiment for ambient water. Considering the accuracy of the new functionals for interaction energies, we investigate whether the simulation...... protocol could cause the deviation. An O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from low-density liquid water, as extrapolated from experiments, reproduces near-quantitatively the experimental O-O PCF for ambient water. This suggests the possibility that the new functionals...

  11. Ab initio density functional theory investigation of crystalline bundles of polygonized single-walled silicon carbide nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Moradian, Rostam; Behzad, Somayeh; Chegel, Raad [Physics Department, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of)], E-mail: moradian.rostam@gmail.com

    2008-11-19

    By using ab initio density functional theory, the structural characterizations and electronic properties of two large-diameter (13, 13) and (14, 14) armchair silicon carbide nanotube (SiCNT) bundles are investigated. Full structural optimizations show that the cross sections of these large-diameter SiCNTs in the bundles have a nearly hexagonal shape. The effects of inter-tube coupling on the electronic dispersions of large-diameter SiCNT bundles are demonstrated. By comparing the band structures of the triangular lattices of (14, 14) SiCNTs with nearly hexagonal and circular cross sections we found that the polygonization of the tubes in the bundle leads to a further dispersion of the occupied bands and an increase in the bandgap by 0.18 eV.

  12. Ab initio density functional theory investigation of crystalline bundles of polygonized single-walled silicon carbide nanotubes.

    Science.gov (United States)

    Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

    2008-11-19

    By using ab initio density functional theory, the structural characterizations and electronic properties of two large-diameter (13, 13) and (14, 14) armchair silicon carbide nanotube (SiCNT) bundles are investigated. Full structural optimizations show that the cross sections of these large-diameter SiCNTs in the bundles have a nearly hexagonal shape. The effects of inter-tube coupling on the electronic dispersions of large-diameter SiCNT bundles are demonstrated. By comparing the band structures of the triangular lattices of (14, 14) SiCNTs with nearly hexagonal and circular cross sections we found that the polygonization of the tubes in the bundle leads to a further dispersion of the occupied bands and an increase in the bandgap by 0.18 eV.

  13. Optimizing electronic structure and quantum transport at the graphene-Si(111) interface: an ab initio density-functional study.

    Science.gov (United States)

    Tayran, Ceren; Zhu, Zhen; Baldoni, Matteo; Selli, Daniele; Seifert, Gotthard; Tománek, David

    2013-04-26

    We use ab initio density-functional calculations to determine the interaction of a graphene monolayer with the Si(111) surface. We find that graphene forms strong bonds to the bare substrate and accommodates the 12% lattice mismatch by forming a wavy structure consisting of free-standing conductive ridges that are connected by ribbon-shaped regions of graphene, which bond covalently to the substrate. We perform quantum transport calculations for different geometries to study changes in the transport properties of graphene introduced by the wavy structure and bonding to the Si substrate. Our results suggest that wavy graphene combines high mobility along the ridges with efficient carrier injection into Si in the contact regions.

  14. Ab initio quasi-particle approximation bandgaps of silicon nanowires calculated at density functional theory/local density approximation computational effort

    Energy Technology Data Exchange (ETDEWEB)

    Ribeiro, M., E-mail: ribeiro.jr@oorbit.com.br [Office of Operational Research for Business Intelligence and Technology, Principal Office, Buffalo, Wyoming 82834 (United States)

    2015-06-21

    Ab initio calculations of hydrogen-passivated Si nanowires were performed using density functional theory within LDA-1/2, to account for the excited states properties. A range of diameters was calculated to draw conclusions about the ability of the method to correctly describe the main trends of bandgap, quantum confinement, and self-energy corrections versus the diameter of the nanowire. Bandgaps are predicted with excellent accuracy if compared with other theoretical results like GW, and with the experiment as well, but with a low computational cost.

  15. Modeling the diffraction process of molecular crystals: computation of X-ray scattering intensities from ab initio electron densities

    NARCIS (Netherlands)

    Bruning, W.; Feil, D.

    1992-01-01

    An algorithm for calculating the scattering factors of atomic fragments in molecules as defined by the Stockholder recipe is presented. This method allows the calculation, from ab initio molecular wave functions, of structure factors including individual anisotropic atomic temperature factors. These

  16. Ionic dissociations of chlorosulfonic acid in microsolvated clusters: A density functional theory and ab initio MO study

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Ionic dissociation of chlorosulfonic acid (HSO3Cl) in the molecular clusters HSO3Cl-(H2O)n (n = 1-4) and HSO3Cl-NH3-(H2O)n (n = 0-3) was investigated by density functional theory and ab initio molecular orbital theory. The equilibrium structures, binding energies, and thermodynamic properties, such as relative enthalpy and relative Gibbs free energy, and were calculated using the hybrid density func- tional (B3LYP) method and the second order M?ller-Plesset approximation (MP2) method with the 6-311++G** basis set. Chlorosulfonic acid was found to require a minimum of three water molecules for ionization to occur and at least one water molecule to protonate ammonia. The corresponding clusters with fewer water molecules were found to be strongly hydrogen-bonded. The related properties and acid strength of chlorosulfonic acid were discussed and compared to the acid strengths of perchloric acid and sulfuric acid in the context of clusters with ammonia and water. The relative stabilities of these clusters were also investigated.

  17. Reciprocity Theorems for Ab Initio Force Calculations

    CERN Document Server

    Wei, C; Mele, E J; Rappe, A M; Lewis, Steven P.; Rappe, Andrew M.

    1996-01-01

    We present a method for calculating ab initio interatomic forces which scales quadratically with the size of the system and provides a physically transparent representation of the force in terms of the spatial variation of the electronic charge density. The method is based on a reciprocity theorem for evaluating an effective potential acting on a charged ion in the core of each atom. We illustrate the method with calculations for diatomic molecules.

  18. Ab initio and density functional theory evidence on the rate-limiting step in the Morita-Baylis-Hillman reaction.

    Science.gov (United States)

    Roy, Dipankar; Sunoj, Raghavan B

    2007-11-08

    The first ab initio and DFT studies on the mechanism of the MBH reaction show that the rate-limiting step involves an intramolecular proton transfer in the zwitterionic intermediate generated by the addition of enolate to electrophile. The activation barrier for the C-C bond-formation is found to be 20.2 kcal/mol lower than the proton-transfer step for the MBH reaction between methyl vinyl ketone and benzaldehyde catalyzed by DABCO.

  19. A simple local correlation energy functional for spherically confined atoms from ab initio correlation energy density.

    Science.gov (United States)

    Vyboishchikov, Sergei F

    2017-09-03

    We propose a simple method of calculating the electron correlation energy density e_c(r) and the correlation potential V_c(r) from second-order Møller-Plesset amplitudes and its generalization for the case of a Configuration Interaction wavefunction, based on Nesbet's theorem. The correlation energy density obtained by this method for free and spherically confined Be and He atoms was employed to fit a local analytical density functional based on Wigner's functional. The functional is capable to reproduce a strong increase of the correlation energy with decreasing the confined radius for the Be atom. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Insights on co-catalyst-promoted enamine formation between dimethylamine and propanal through ab initio and density functional theory study.

    Science.gov (United States)

    Patil, Mahendra P; Sunoj, Raghavan B

    2007-10-26

    The mechanistic details on enamine formation between dimethylamine and propanal are unraveled using the ab initio and density functional theory methods. The addition of secondary amine to the electrophile and simultaneous proton transfer results in a carbinolamine intermediate, which subsequently undergoes dehydration to form enamine. The direct addition of amine as well as the dehydration of the resulting carbinolamine intermediate is predicted to possess fairly high activation barrier implying that a unimolecular process is unlikely to be responsible for enamine formation. Different models are therefore proposed which could explain the relative ease of enamine formation under neat condition as well as under the influence of methanol as the co-catalyst. The explicit inclusion of either the reagent or the co-catalyst is considered in the transition states as stabilizing agents. The participation of the reagent or the co-catalyst as a monofunctional ancillary species is found to stabilize the transition states relative to the unassisted or the direct addition/dehydration pathways. The reduction in enthalpy of activation is found to be much more dramatic when two co-catalysts participate in an active bifunctional mode in the rate-determining dehydration step. The transition structures exhibited characteristic features of a relay proton transfer mechanism. The free energy of activation associated with the two methanol-assisted pathway is found to be 16.7 kcal/mol lower than that of the unassisted pathway. The results are found to be in concurrence with the available reports on the rate acceleration by co-catalysts in the Michael reaction between enamine and methyl vinyl ketone under neat conditions.

  1. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

    Science.gov (United States)

    Roemelt, Michael

    2015-07-01

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.

  2. Ab Initio Density Functional Calculations and Infra-Red Study of CO Interaction with Pd Atoms on θ-Al2O3 (010) Surface.

    Science.gov (United States)

    Narula, Chaitanya K; Allard, Lawrence F; Wu, Zili

    2017-07-24

    The ab initio density functional theoretical studies show that energetics favor CO oxidation on single Pd atoms supported on θ-alumina. The diffuse reflectance infra-red spectroscopy (DRIFTS) results show that carbonates are formed as intermediates when single supported Pd atoms are exposed to a gaseous mixture of CO + O2. The rapid agglomeration of Pd atoms under CO oxidation conditions even at 6 °C leads to the presence of Pd particles along with single atoms during CO oxidation experiments. Thus, the observed CO oxidation has contributions from both single Pd atoms and Pd particles.

  3. S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

    Science.gov (United States)

    Chaudret, Robin; Gresh, Nohad; Narth, Christophe; Lagardère, Louis; Darden, Thomas A; Cisneros, G Andrés; Piquemal, Jean-Philip

    2014-09-04

    We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar

  4. Giant magnetoresistance An ab-initio description

    CERN Document Server

    Binder, J

    2000-01-01

    A new theoretical concept to study the microscopic origin of Giant Magnetoresistance (GMR) from first principles is presented. The method is based on ab-initio electronic structure calculations within the spin density functional theory using a Screened KORRINGA-KOHNROSTOKER method. Scattering at impurity atoms in the multilayers is described by means of a GREEN's-function method. The scattering potentials are calculated self-consistently. The transport properties are treated quasi-classically solving the BOLTZMANN equation including the electronic structure of the layered system and the anisotropic scattering. The solution of the BOLTZMANN equation is performed iteratively taking into account both scattering out and scattering in terms (vertex corrections). The method is applied to Co/Cu and Fe/Cr multilayers. Trends of scattering cross sections, residual resistivities and GMR ratios are discussed for various transition metal impurities at different positions in the Co/Cu or Fe/Cr multilayers. Furthermore the...

  5. Electronically Excited States of Vitamin B12: Benchmark Calculations Including Time-Dependent Density Functional Theory and Correlated Ab Initio Methods

    CERN Document Server

    Kornobis, Karina; Wong, Bryan M; Lodowski, Piotr; Jaworska, Maria; Andruniów, Tadeusz; Rudd, Kenneth; Kozlowski, Pawel M; 10.1021/jp110914y

    2011-01-01

    Time-dependent density functional theory (TD-DFT) and correlated ab initio methods have been applied to the electronically excited states of vitamin B12 (cyanocobalamin or CNCbl). Different experimental techniques have been used to probe the excited states of CNCbl, revealing many issues that remain poorly understood from an electronic structure point of view. Due to its efficient scaling with size, TD-DFT emerges as one of the most practical tools that can be used to predict the electronic properties of these fairly complex molecules. However, the description of excited states is strongly dependent on the type of functional used in the calculations. In the present contribution, the choice of a proper functional for vitamin B12 was evaluated in terms of its agreement with both experimental results and correlated ab initio calculations. Three different functionals, i.e. B3LYP, BP86, and LC-BLYP, were tested. In addition, the effect of relative contributions of DFT and HF to the exchange-correlation functional ...

  6. Ab initio-driven nuclear energy density functional method. A proposal for safe/correlated/improvable parametrizations of the off-diagonal EDF kernels

    Energy Technology Data Exchange (ETDEWEB)

    Duguet, T. [IRFU/Service de Physique Nucleaire, CEA, Centre de Saclay, Gif-sur-Yvette (France); Instituut voor Kern- en Stralingsfysica, KU Leuven, Leuven (Belgium); Michigan State University, National Superconducting Cyclotron Laboratory and Department of Physics and Astronomy, East Lansing, MI (United States); Bender, M. [Centre d' Etudes Nucleaires de Bordeaux Gradignan, Universite Bordeaux, UMR5797, Gradignan (France); Centre d' Etudes Nucleaires de Bordeaux Gradignan, CNRS/IN2P3, UMR5797, Gradignan (France); Ebran, J.P. [CEA, DAM, DIF, Arpajon (France); Lesinski, T.; Soma, V. [IRFU/Service de Physique Nucleaire, CEA, Centre de Saclay, Gif-sur-Yvette (France)

    2015-12-15

    This programmatic paper lays down the possibility to reconcile the necessity to resum many-body correlations into the energy kernel with the fact that safe multi-reference energy density functional (EDF) calculations cannot be achieved whenever the Pauli principle is not enforced, as is for example the case when many-body correlations are parametrized under the form of empirical density dependencies. Our proposal is to exploit a newly developed ab initio many-body formalism to guide the construction of safe, explicitly correlated and systematically improvable parametrizations of the off-diagonal energy and norm kernels that lie at the heart of the nuclear EDF method. The many-body formalism of interest relies on the concepts of symmetry breaking and restoration that have made the fortune of the nuclear EDF method and is, as such, amenable to this guidance. After elaborating on our proposal, we briefly outline the project we plan to execute in the years to come. (orig.)

  7. Use of ab initio quantum chemical methods in battery technology

    Energy Technology Data Exchange (ETDEWEB)

    Deiss, E. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.

  8. Ab initio valence calculations in chemistry

    CERN Document Server

    Cook, D B

    1974-01-01

    Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge

  9. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting tr

  10. Ab initio calculations and modelling of atomic cluster structure

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter

    2004-01-01

    The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical...

  11. Ab initio study of alanine polypeptide chain twisting

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.

    2006-01-01

    chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...

  12. Molecular structures and vibrational frequencies of xanthine and its methyl derivatives (caffeine and theobromine) by ab initio Hartree-Fock and density functional theory calculations

    Science.gov (United States)

    Ucun, Fatih; Sağlam, Adnan; Güçlü, Vesile

    2007-06-01

    The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine and theobromine) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis set level. The calculations were utilized to the CS symmetries of the molecules. The obtained vibrational frequencies and optimised geometric parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.

  13. Ab initio and density functional computations of the vibrational spectrum, molecular geometry and some molecular properties of the antidepressant drug sertraline (Zoloft) hydrochloride

    Science.gov (United States)

    Sagdinc, Seda; Kandemirli, Fatma; Bayari, Sevgi Haman

    2007-02-01

    Sertraline hydrochloride is a highly potent and selective inhibitor of serotonin (5HT). It is a basic compound of pharmaceutical application for antidepressant treatment (brand name: Zoloft). Ab initio and density functional computations of the vibrational (IR) spectrum, the molecular geometry, the atomic charges and polarizabilities were carried out. The infrared spectrum of sertraline is recorded in the solid state. The observed IR wave numbers were analysed in light of the computed vibrational spectrum. On the basis of the comparison between calculated and experimental results and the comparison with related molecules, assignments of fundamental vibrational modes are examined. The X-ray geometry and experimental frequencies are compared with the results of our theoretical calculations.

  14. Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

    Science.gov (United States)

    Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

    2011-11-01

    Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.

  15. Ab initio phonon scattering by dislocations

    Science.gov (United States)

    Wang, Tao; Carrete, Jesús; van Roekeghem, Ambroise; Mingo, Natalio; Madsen, Georg K. H.

    2017-06-01

    Heat management in thermoelectric and power devices as well as in random access memories poses a grand challenge and can make the difference between a working and an abandoned device design. Despite the prevalence of dislocations in all these technologies, the modeling of their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce an efficient ab initio approach based on Green's functions computed by two-dimensional reciprocal space integration. By combining elasticity theory and density functional theory, we calculate the scattering strength of a 90∘ misfit edge dislocation in Si. Because of the breakdown of the Born approximation, earlier literature models fail, even qualitatively. We find that a dislocation density larger than 109cm-2 is necessary to substantially influence thermal conductivity at room temperature and above. We quantify how much of the reduction of thermal conductivity measured in nanograined samples can be explained by realistic dislocation concentrations.

  16. Ensemble v-representable ab-initio density functional calculation of energy and spin in atoms: atest of exchange-correlation approximations

    CERN Document Server

    Kraisler, Eli; Kelson, Itzhak

    2010-01-01

    The total energies and the spin states for atoms and their first ions with Z = 1-86 are calculated within the the local spin-density approximation (LSDA) and the generalized-gradient approximation (GGA) to the exchange-correlation (xc) energy in density-functional theory. Atoms and ions for which the ground-state density is not pure-state v-representable, are treated as ensemble v- representable with fractional occupations of the Kohn-Sham system. A newly developed algorithm which searches over ensemble v-representable densities [E. Kraisler et al., Phys. Rev. A 80, 032115 (2009)] is employed in calculations. It is found that for many atoms the ionization energies obtained with the GGA are only modestly improved with respect to experimental data, as compared to the LSDA. However, even in those groups of atoms where the improvement is systematic, there remains a non-negligible difference with respect to the experiment. The ab-initio electronic configuration in the Kohn-Sham reference system does not always equ...

  17. Large-Scale Hybrid Density Functional Theory Calculations in the Condensed-Phase: Ab Initio Molecular Dynamics in the Isobaric-Isothermal Ensemble

    Science.gov (United States)

    Ko, Hsin-Yu; Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto

    Hybrid functionals are known to alleviate the self-interaction error in density functional theory (DFT) and provide a more accurate description of the electronic structure of molecules and materials. However, hybrid DFT in the condensed-phase has a prohibitively high associated computational cost which limits their applicability to large systems of interest. In this work, we present a general-purpose order(N) implementation of hybrid DFT in the condensed-phase using Maximally localized Wannier function; this implementation is optimized for massively parallel computing architectures. This algorithm is used to perform large-scale ab initio molecular dynamics simulations of liquid water, ice, and aqueous ionic solutions. We have performed simulations in the isothermal-isobaric ensemble to quantify the effects of exact exchange on the equilibrium density properties of water at different thermodynamic conditions. We find that the anomalous density difference between ice I h and liquid water at ambient conditions as well as the enthalpy differences between ice I h, II, and III phases at the experimental triple point (238 K and 20 Kbar) are significantly improved using hybrid DFT over previous estimates using the lower rungs of DFT This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.

  18. Discovering chemistry with an ab initio nanoreactor

    OpenAIRE

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-01-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerat...

  19. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  20. Ab initio Bogoliubov coupled cluster theory

    Science.gov (United States)

    Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas

    2014-09-01

    Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.

  1. Toward Reliable Prediction of Hyperfine Coupling Constants Using Ab Initio Density Matrix Renormalization Group Method: Diatomic (2)Σ and Vinyl Radicals as Test Cases.

    Science.gov (United States)

    Lan, Tran Nguyen; Kurashige, Yuki; Yanai, Takeshi

    2014-05-13

    The density matrix renormalization group (DMRG) method is used in conjunction with the complete active space (CAS) procedure, the CAS configuration interaction (CASCI), and the CAS self-consistent field (CASSCF) to evaluate hyperfine coupling constants (HFCCs) for a series of diatomic (2)Σ radicals (BO, CO(+), CN, and AlO) and vinyl (C2H3) radical. The electron correlation effects on the computed HFCC values were systematically investigated using various levels of active space, which were increasingly extended from single valence space to large-size model space entailing double valence and at least single polarization shells. In addition, the core correlation was treated by including the core orbitals in active space. Reasonably accurate results were obtained by the DMRG-CASSCF method involving orbital optimization, while DMRG-CASCI calculations with Hartree-Fock orbitals provided poor agreement of the HFCCs with the experimental values. To achieve further insights into the accuracy of HFCC calculations, the orbital contributions to the total spin density were analyzed at a given nucleus, which is directly related to the FC term and is numerically sensitive to the level of correlation treatment and basis sets. The convergence of calculated HFCCs with an increasing number of renormalized states was also assessed. This work serves as the first study on the performance of the ab initio DMRG method for HFCC prediction.

  2. Empirical D3 Dispersion as a Replacement for ab Initio Dispersion Terms in Density Functional Theory-Based Symmetry-Adapted Perturbation Theory.

    Science.gov (United States)

    Sedlak, Robert; Řezáč, Jan

    2017-04-11

    In density functional theory-based symmetry-adapted perturbation theory (DFT-SAPT) interaction energy calculations, the most demanding step is the calculation of the London dispersion term. For this bottleneck to be avoided and DFT-SAPT to be made applicable to larger systems, the ab initio dispersion terms can be replaced by one calculated empirically at an almost negligible cost ( J. Phys. Chem. A 2011 ; 115 , 11321 - 11330 ). We present an update of this approach that improves accuracy and makes the method applicable to a wider range of systems. It is based on Grimme's D3 dispersion correction for DFT, where the damping function is changed to one suitable for the calculation of the complete dispersion energy. The best results have been achieved with the Tang-Toennies damping function. It has been parametrized on the S66×8 data set for which we report density fitting DFT-SAPT/aug-cc-pVTZ interaction energy decomposition. The method has been validated on a diverse set of noncovalent systems including difficult cases such as very compact noncovalent complexes of charge-transfer type. The root-mean-square errors in the complete test set are 0.73 and 0.42 kcal mol(-1) when charge-transfer complexes are excluded. The proposed empirical dispersion terms can also be used outside the DFT-SAPT framework, e.g., for the estimation of the amount of dispersion in a calculation where only the total interaction energy is known.

  3. The pressure-induced ringwoodite to Mg-perovskite and periclase post-spinel phase transition: a Bader's topological analysis of the ab initio electron densities

    Science.gov (United States)

    Parisi, Filippo; Sciascia, Luciana; Princivalle, Francesco; Merli, Marcello

    2012-02-01

    In order to characterize the pressure-induced decomposition of ringwoodite (γ-Mg2SiO4), the topological analysis of the electron density ρ( r), based upon the theory of atoms in molecules (AIM) developed by Bader in the framework of the catastrophe theory, has been performed. Calculations have been carried out by means of the ab initio CRYSTAL09 code at the HF/DFT level, using Hamiltonians based on the Becke- LYP scheme containing hybrid Hartree-Fock/density functional exchange-correlation terms. The equation of state at 0 K has been constructed for the three phases involved in the post-spinel phase transition (ringwoodite → Mg-perovskite + periclase) occurring at the transition zone-lower mantel boundary. The topological results show that the decomposition of the ringwoodite at high pressures is caused by a conflict catastrophe. Furthermore, topological evidences of the central role played by the oxygen atoms to facilitate the pressure-induced ringwoodite decomposition and the subsequent phase transition have been noticed.

  4. Ab initio-driven nuclear energy density functional method. A proposal for safe/correlated/improvable parametrizations of the off-diagonal EDF kernels

    CERN Document Server

    Duguet, T; Ebran, J -P; Lesinski, T; Somà, V

    2015-01-01

    This programmatic paper lays down the possibility to reconcile the necessity to resum many-body correlations into the energy kernel with the fact that safe multi-reference energy density functional (EDF) calculations cannot be achieved whenever the Pauli principle is not strictly enforced, as is for example the case when many-body correlations are parametrized under the form of empirical density dependencies. Our proposal is to exploit a newly developed ab initio many-body formalism to guide the construction of safe, explicitly correlated and systematically improvable parametrizations of the {\\it off-diagonal} energy and norm kernels that lie at the heart of the nuclear EDF method. The many-body formalism of interest relies on the concepts of symmetry breaking {\\it and} restoration that have made the fortune of the nuclear EDF method and is, as such, amenable to this guidance. After elaborating on our proposal, we briefly outline the project we plan to execute in the years to come.

  5. Doping-enhanced hyperpolarizabilities of silicon clusters: a global ab initio and density functional theory study of Si10 (Li, Na, K)n (n=1, 2) clusters.

    Science.gov (United States)

    Karamanis, Panaghiotis; Marchal, Remi; Carbonniére, Philippe; Pouchan, Claude

    2011-07-28

    A global theoretical study of the (hyper)polarizabilities of alkali doped Si(10) is presented and discussed. First, a detailed picture about the low lying isomers of Si(10)Li, Si(10)Na, Si(10)K, Si(10)Li(2), Si(10)Na(2), and Si(10)K(2) has been obtained in a global manner. Then, the microscopic first (hyper)polarizabilities of the most stable configurations have been determined by means of ab initio methods of high predictive capability such as those based on the Møller-Plesset perturbation and coupled cluster theory, paying extra attention to the (hyper)polarizabilities of the open shell mono-doped systems Si(10)Li, Si(10)Na, Si(10)K, and the influence of spin contamination. These results were used to assess the performance of methods of low computational cost based on density functional theory (DFT) in the reliable computation of these properties in order to proceed with an in-depth study of their evolution as a function of the alkali metal, the cluster composition, and the cluster structure. The most interesting outcomes of the performed (hyper)polarizability study indicate that while alkali doping leaves the per atom polarizability practically unaffected, influences dramatically the hyperpolarizabilities of Si(10). The lowest energy structures of the mono-doped clusters are characterized by significantly enhanced hyperpolarizabilities as compared to the analogue neutral or charged bare silicon clusters Si(10) and Si(11), while, certain patterns governed by the type and the number of the doping agents are followed. The observed hyperpolarizability increase is found to be in close connection with specific cluster to alkali metal charge transfer excited states and to the cluster structures. Moreover, an interesting correlation between the anisotropy of the electron density, and the hyperpolarizabilities of these systems has been observed. Finally, it is important to note that the presented method assessment points out that among the various DFT functionals used

  6. Ab Initio Calculations of Oxosulfatovanadates

    DEFF Research Database (Denmark)

    Frøberg, Torben; Johansen, Helge

    1996-01-01

    Restricted Hartree-Fock and multi-configurational self-consistent-field calculations together with secondorder perturbation theory have been used to study the geometry, the electron density, and the electronicspectrum of (VO2SO4)-. A bidentate sulphate attachment to vanadium was found to be stable...

  7. Ab initio calculation of tight-binding parameters

    Energy Technology Data Exchange (ETDEWEB)

    McMahan, A.K.; Klepeis, J.E.

    1997-12-01

    We calculate ab initio values of tight-binding parameters for the f- electron metal Ce and various phases of Si, from local-density functional one-electron Hamiltonian and overlap matrix elements. Our approach allows us to unambiguously test the validity of the common minimal basis and two-center approximations as well as to determine the degree of transferability of both nonorthogonal and orthogonal hopping parameters in the cases considered.

  8. Ab initio centroid path integral molecular dynamics: Application to vibrational dynamics of diatomic molecular systems

    Science.gov (United States)

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

    2004-01-01

    An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

  9. Structure, energetics, and electronic properties of the surface of a promoted MoS{sub 2} catalyst: An ab initio local density functional study

    Energy Technology Data Exchange (ETDEWEB)

    Raybaud, P.; Hafner, J.; Kresse, G.; Kasztelan, S.; Toulhoat, H.

    2000-02-15

    The determination of the local structure of cobalt- or nickel-promoted MoS{sub 2}-based hydrodesulfurization catalysts is of interest for understanding the mechanism leading to an increased activity brought by cobalt or nickel, the so-called synergetic effect. For that reason, the authors carried out ab initio calculations using density functional theory under the generalized gradient approximation for periodic systems. The edge substitution model emerges as the most stable structure and provides an excellent agreement with local structures experimentally determined on real catalysts by in situ extended X-ray absorption fine structure. The authors studied the absorption of sulfur on the active edge surface of the promoted MoS{sub 2} catalyst and determined the equilibrium coverage under sulfiding conditions. It is demonstrated that the incorporation of promoter atoms has a strong influence on the sulfur-metal bond energy at the surface and in particular leads to a reduction of the equilibrium S coverage of the active metal sites. A comparative study on the effects of Co, Ni, and Cu atoms as promoters was performed. Detailed results on the surface electronic structure of promoted MoS{sub 2} are presented.

  10. Atomic scale analysis of the GaP/Si(100) heterointerface by in situ reflection anisotropy spectroscopy and ab initio density functional theory

    Science.gov (United States)

    Supplie, Oliver; Brückner, Sebastian; Romanyuk, Oleksandr; Döscher, Henning; Höhn, Christian; May, Matthias M.; Kleinschmidt, Peter; Grosse, Frank; Hannappel, Thomas

    2014-12-01

    A microscopic understanding of the formation of polar-on-nonpolar interfaces is a prerequisite for well-defined heteroepitaxial preparation of III-V compounds on (100) silicon for next-generation high-performance devices. Energetically and kinetically driven Si(100) step formations result in majority domains of monohydride-terminated Si dimers oriented either parallel or perpendicular to the step edges. Here, the intentional variation of the Si(100) surface reconstruction controls the sublattice orientation of the heteroepitaxial GaP film, as observed by in situ reflection anisotropy spectroscopy (RAS) in chemical vapor ambient and confirmed by benchmarking to surface science analytics in ultrahigh vacuum. Ab initio density functional calculations of both abrupt and compensated interfaces are carried out. For P-rich chemical potentials at abrupt interfaces, Si-P bonds are energetically favored over Si-Ga bonds, in agreement with in situ RAS experiments. The energetically most favorable interface is compensated with an intermixed interfacial layer. In situ RAS reveals that the GaP sublattice orientation depends on the P chemical potential during nucleation, which agrees with a kinetically limited formation of abrupt interfaces.

  11. Structure, reactivity and spectroscopic properties of minerals from lateritic soils : insights from ab initio calculations

    OpenAIRE

    Balan, Etienne; Lazzeri, M.; Mauri, F.; Calas, G.

    2007-01-01

    We review here some recent applications of ab initio calculations to the modelling of spectroscopic and energetic properties of minerals, which are key components of lateritic soils or govern their geochemical properties. Quantum mechanical ab initio calculations are based on density functional theory and density functional perturbation theory. Among the minerals investigated, zircon is a typical resistant primary mineral. Its resistance to weathering is at the origin of the peculiar geochemi...

  12. Equations of state of heavy metals: ab initio approaches; Equations d'etat des metaux lourds: approches ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, S.; Jollet, F.; Jomard, G.; Siberchicot, B.; Torrent, M.; Zerah, G.; Amadon, B.; Bouchet, J.; Richard, N.; Robert, G. [CEA Bruyeres-le-Chatel, 91 (France)

    2005-07-01

    The determination of equations of states of heavy metals through ab initio calculation, i.e. without any adjustable parameter, allows to access to pressure and temperature thermodynamic conditions sometimes inaccessible to experiment. To perform such calculations, density functional theory (DFT) is a good starting point: when electronic densities are homogeneous enough, the local density approximation (LDA) remarkably accounts for thermodynamic properties of heavy metals, such as tantalum, or the light actinides, as well for static properties - equilibrium volume, elastic constants - as for dynamical quantities like phonon spectra. For heavier elements, like neptunium or plutonium, relativistic effects and strong electronic interactions must be taken into account, which requires more sophisticated theoretical approaches. (authors)

  13. High-performance ab initio density matrix renormalization group method: Applicability to large-scale multireference problems for metal compounds

    Science.gov (United States)

    Kurashige, Yuki; Yanai, Takeshi

    2009-06-01

    This article presents an efficient and parallelized implementation of the density matrix renormalization group (DMRG) algorithm for quantum chemistry calculations. The DMRG method as a large-scale multireference electronic structure model is by nature particularly efficient for one-dimensionally correlated systems, while the present development is oriented toward applications for polynuclear transition metal compounds, in which the macroscopic one-dimensional structure of electron correlation is absent. A straightforward extension of the DMRG algorithm is proposed with further improvements and aggressive optimizations to allow its application with large multireference active space, which is often demanded for metal compound calculations. Special efficiency is achieved by making better use of sparsity and symmetry in the operator and wave function representations. By accomplishing computationally intensive DMRG calculations, the authors have found that a large number of renormalized basis states are required to represent high entanglement of the electron correlation for metal compound applications, and it is crucial to adopt auxiliary perturbative correction to the projected density matrix during the DMRG sweep optimization in order to attain proper convergence to the solution. Potential energy curve calculations for the Cr2 molecule near the known equilibrium precisely predicted the full configuration interaction energies with a correlation space of 24 electrons in 30 orbitals [denoted by (24e,30o)]. The energies are demonstrated to be accurate to 0.6mEh (the error from the extrapolated best value) when as many as 10 000 renormalized basis states are employed for the left and right DMRG block representations. The relative energy curves for [Cu2O2]2+ along the isomerization coordinate were obtained from DMRG and other correlated calculations, for which a fairly large orbital space (32e,62o) is modeled as a full correlation space. The DMRG prediction nearly overlaps

  14. Coupling of Magnetization and Structural Distortions in Multiferroic BiFeO3:an Ab Initio Density Functional Theory Study

    Institute of Scientific and Technical Information of China (English)

    FENG Hong-Jian; LIU Fa-Min

    2008-01-01

    The coupling between magnetism and structural distortions in BiFeO3 (BFO) is investigated using density functional theory by considering the spin-orbit effect.Computational results show that the resulting magnetization M is rotated by reversal of sense of rotation of the oxygen octahedra in the double cell.The resulting magnetization is determined by the antiferrodistortive (AFD) distortions and ferroelectric (FE) displacements.This work clarifies the previous view that magnetism is only coupled with,and determined by,FE displacements.The excellent ferroelectricity is attributed significantly to the anomaly of Born effective charge of Bi,which is caused by the stereochemically active long pair of Bi 6s.

  15. Ab Initio Density Functional Theory Investigation of the Interaction between Carbon Nanotubes and Water Molecules during Water Desalination Process

    Directory of Open Access Journals (Sweden)

    Loay A. Elalfy

    2013-01-01

    Full Text Available Density functional theory calculations using B3LYP/3-21G level of theory have been implemented on 6 carbon nanotubes (CNTs structures (3 zigzag and 3 armchair CNTs to study the energetics of the reverse osmosis during water desalination process. Calculations of the band gap, interaction energy, highest occupied molecular orbital, lowest unoccupied molecular orbital, electronegativity, hardness, and pressure of the system are discussed. The calculations showed that the water molecule that exists inside the CNT is about 2-3 Å away from its wall. The calculations have proven that the zigzag CNTs are more efficient for reverse osmosis water desalination process than armchair CNTs as the reverse osmosis process requires pressure of approximately 200 MPa for armchair CNTs, which is consistent with the values used in molecular dynamics simulations, while that needed when using zigzag CNTs was in the order of 60 MPa.

  16. Ab initio and coupled-perturbed density functional theory estimation of zero-field splittings in MnII transition metal complexes.

    Science.gov (United States)

    Zein, Samir; Neese, Frank

    2008-08-28

    The paper presents a method comparison for the prediction of zero-field splitting (ZFS) parameters in a series of Mn (II) coordination complexes. The test set consists of Mn (II) complexes that are experimentally well-characterized by X-ray diffraction and high-field electron paramagnetic resonance. Their ZFS parameters have been calculated using density functional theory (DFT) as well as complete active space self-consistent field (CASSCF) methods. It is shown that the recently introduced coupled-perturbed spin-orbit coupling (CP-SOC) approach [ Neese, F. J. Chem. Phys. 2007, 127, 164112 ] together with hybrid-DFT functionals leads to a slope of the correlation line (plot of experimental vs calculated D values) that is essentially unity provided that the direct spin-spin interaction is properly included in the treatment. This is different from our previous DFT study on the same series of complexes where a severe overestimation of the D parameter has been found [ Zein, S. ; Duboc, C. ; Lubitz, W. ; Neese, F. Inorg. Chem. 2008, 47, 134 ]. CASSCF methods have been used to evaluate the ZFS in an "ab initio ligand-field" type treatment. The study demonstrates that a substantial part of the relevant physics is lost in such a treatment since only excitations within the manganese d-manifold are accounted for. Thus, a severe underestimation of the D parameter has been found. Because the CASSCF calculations in combination with quasidegenerate perturbation theory treats the SOC to all orders, we have nevertheless verified that second-order perturbation theory is an adequate approximation in the case of the high-spin d (5) configuration.

  17. A Comparison of Density Functional Theory with Ab initio Approaches for Systems Involving First Transition Row Metals

    Science.gov (United States)

    Ricca, Alessandra; Bauschlicher, Charles W.; Langhoff, Stephen R. (Technical Monitor)

    1994-01-01

    Density functional theory (DFT) is found to give a better description of the geometries and vibrational frequencies of FeL and FeL(sup +) systems than second order Moller Plesset perturbation theory (MP2). Namely, the DFT correctly predicts the shift in the CO vibrational frequency between free CO and the Sigma(sup -) state of FeCO and yields a good result for the Fe-C distance in the quartet states of FeCH4(+) 4 These are properties where the MP2 results are unsatisfactory. Thus DFT appears to be an excellent approach for optimizing the geometries and computing the zero-point energies of systems containing first transition row atoms. Because the DFT approach is biased in favor of the 3d(exp 7) occupation, whereas the more traditional approaches are biased in favor of the 3d(exp 6) occupation, differences are found in the relative ordering of states. It is shown that if the dissociation is computed to the most appropriate atomic asymptote and corrected to the ground state asymptote using the experimental separations, the DFT results are in good agreement with high levels of theory. The energetics at the DFT level are much superior to the MP2 and in most cases in good agreement with high levels of theory.

  18. Adsorption of TCDD molecule onto CNTs and BNNTs: Ab initio van der Waals density-functional study

    Science.gov (United States)

    Darvish Ganji, M.; Alinezhad, H.; Soleymani, E.; Tajbakhsh, M.

    2015-03-01

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCCD) is one of the most dangerous compounds that infect the environment and hence its removal is crucial for safety in human life. In this work, we have investigated the interaction of TCDD with boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs) by using the density functional theory (DFT) calculations. Our first-principles results have been validated by experiment and also other theoretical values for the similar system. The adsorption energies for TCDD molecule on the BNNTs and CNT are calculated. It was found that TCDD adsorption ability of BNNT is slightly stronger than that of CNT and TCDD molecule prefers to be adsorbed on BNNTs with molecular axis parallel to the tube axis. The results obtained indicate that TCDD is weakly bound to the outer surface of all the considered nanotubes and the obtained adsorption energy values and binding distance are typical for the physisorption. We also evaluated the influence of curvature and introduced defects on the TCDD adsorption ability of BNNTs. Furthermore, we have analyzed the electronic structure and charge population for the energetically most favorable complexes and the results indicate that no significant hybridization between the respective orbitals of the two entities was accomplished.

  19. Operator evolution for ab initio nuclear theory

    CERN Document Server

    Schuster, Micah D; Johnson, Calvin W; Jurgenson, Eric D; Navratil, Petr

    2014-01-01

    The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally-invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square-radius and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range and find at short ranges an increased contribution from such ind...

  20. Discovering chemistry with an ab initio nanoreactor

    Science.gov (United States)

    Martinez, Todd

    Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.

  1. Ab initio alpha-alpha scattering

    CERN Document Server

    Elhatisari, Serdar; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G

    2015-01-01

    Processes involving alpha particles and alpha-like nuclei comprise a major part of stellar nucleosynthesis and hypothesized mechanisms for thermonuclear supernovae. In an effort towards understanding alpha processes from first principles, we describe in this letter the first ab initio calculation of alpha-alpha scattering. We use lattice effective field theory to describe the low-energy interactions of nucleons and apply a technique called the adiabatic projection method to reduce the eight-body system to an effective two-cluster system. We find good agreement between lattice results and experimental phase shifts for S-wave and D-wave scattering. The computational scaling with particle number suggests that alpha processes involving heavier nuclei are also within reach in the near future.

  2. An ab initio study of hydroxylated graphane

    Science.gov (United States)

    Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola

    2017-09-01

    Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.

  3. Discovering chemistry with an ab initio nanoreactor

    Science.gov (United States)

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-12-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.

  4. Ab initio electronic properties of dual phosphorus monolayers in silicon

    DEFF Research Database (Denmark)

    Drumm, Daniel W.; Per, Manolo C.; Budi, Akin

    2014-01-01

    In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon......, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device...

  5. Ab-initio study of transition metal hydrides

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Ramesh [Dept. of Physics, Feroze Gandhi Insititute of Engineering and Technology, Raebareli-229001 (India); Shukla, Seema, E-mail: sharma.yamini62@gmail.com; Dwivedi, Shalini, E-mail: sharma.yamini62@gmail.com; Sharma, Yamini, E-mail: sharma.yamini62@gmail.com [Theoretical Condensed Matter Physics Laboratory, Dept. of Physics Feroze Gandhi College, Raebareli-229001 (India)

    2014-04-24

    We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.

  6. Accurate Prediction of Hyperfine Coupling Constants in Muoniated and Hydrogenated Ethyl Radicals: Ab Initio Path Integral Simulation Study with Density Functional Theory Method.

    Science.gov (United States)

    Yamada, Kenta; Kawashima, Yukio; Tachikawa, Masanori

    2014-05-13

    We performed ab initio path integral molecular dynamics (PIMD) simulations with a density functional theory (DFT) method to accurately predict hyperfine coupling constants (HFCCs) in the ethyl radical (CβH3-CαH2) and its Mu-substituted (muoniated) compound (CβH2Mu-CαH2). The substitution of a Mu atom, an ultralight isotope of the H atom, with larger nuclear quantum effect is expected to strongly affect the nature of the ethyl radical. The static conventional DFT calculations of CβH3-CαH2 find that the elongation of one Cβ-H bond causes a change in the shape of potential energy curve along the rotational angle via the imbalance of attractive and repulsive interactions between the methyl and methylene groups. Investigation of the methyl-group behavior including the nuclear quantum and thermal effects shows that an unbalanced CβH2Mu group with the elongated Cβ-Mu bond rotates around the Cβ-Cα bond in a muoniated ethyl radical, quite differently from the CβH3 group with the three equivalent Cβ-H bonds in the ethyl radical. These rotations couple with other molecular motions such as the methylene-group rocking motion (inversion), leading to difficulties in reproducing the corresponding barrier heights. Our PIMD simulations successfully predict the barrier heights to be close to the experimental values and provide a significant improvement in muon and proton HFCCs given by the static conventional DFT method. Further investigation reveals that the Cβ-Mu/H stretching motion, methyl-group rotation, methylene-group rocking motion, and HFCC values deeply intertwine with each other. Because these motions are different between the radicals, a proper description of the structural fluctuations reflecting the nuclear quantum and thermal effects is vital to evaluate HFCC values in theory to be comparable to the experimental ones. Accordingly, a fundamental difference in HFCC between the radicals arises from their intrinsic molecular motions at a finite temperature, in

  7. On the hierarchical parallelization of ab initio simulations

    CERN Document Server

    Ruiz-Barragan, Sergi; Shiga, Motoyuki

    2016-01-01

    A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.

  8. Ab initio calculation of the Hoyle state

    CERN Document Server

    Epelbaum, Evgeny; Lee, Dean; Meißner, Ulf-G

    2011-01-01

    The Hoyle state plays a crucial role in the hydrogen burning of stars heavier than our sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle^{1} as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago^{2,3}, nuclear theorists have not yet uncovered the nature of this state from first principles. In this letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of properties of the Hoyle state and in agreement with the experimentally observed energy. These lattice simulations provide insight into the structure of this unique state and new clues as to the amount of fine...

  9. Ab initio phase diagram of iridium

    Science.gov (United States)

    Burakovsky, L.; Burakovsky, N.; Cawkwell, M. J.; Preston, D. L.; Errandonea, D.; Simak, S. I.

    2016-09-01

    The phase diagram of iridium is investigated using the Z methodology. The Z methodology is a technique for phase diagram studies that combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. In the direct Z method, the solid phases along the melting curve are determined by comparing the solid-liquid equilibrium boundaries of candidate crystal structures. The inverse Z method involves quenching the liquid into the most stable solid phase at various temperatures and pressures to locate a solid-solid boundary. Although excellent agreement with the available experimental data (to ≲65 GPa) is found for the equation of state (EOS) of Ir, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes our ab initio data to higher pressure (P ) . Our results suggest the existence of a random-stacking hexagonal close-packed structure of iridium at high P . We offer an explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.

  10. Phonocatalysis. An ab initio simulation experiment

    Directory of Open Access Journals (Sweden)

    Kwangnam Kim

    2016-06-01

    Full Text Available Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  11. Ab initio materials physics and microscopic electrodynamics of media

    OpenAIRE

    2016-01-01

    We argue that the amazing progress of first-principles materials physics necessitates a revision of the Standard Approach to electrodynamics of media. We hence subject this Standard Approach to a thorough critique, which shows both its inherent conceptual problems and its practical inapplicability to modern ab initio calculations. We then go on to show that the common practice in ab initio materials physics has overcome these difficulties by taking a different, microscopic approach to electro...

  12. Finite Elements in Ab Initio Electronic-Structure Calulations

    Science.gov (United States)

    Pask, J. E.; Sterne, P. A.

    Over the course of the past two decades, the density functional theory (DFT) (see e.g., [1]) of Hohenberg, Kohn, and Sham has proven to be an accurate and reliable basis for the understanding and prediction of a wide range of materials properties from first principles (ab initio), with no experimental input or empirical parameters. However, the solution of the Kohn-Sham equations of DFT is a formidable task and this has limited the range of physical systems which can be investigated by such rigorous, quantum mechanical means. In order to extend the interpretive and predictive power of such quantum mechanical theories further into the domain of "real materials", involving nonstoichiometric deviations, defects, grain boundaries, surfaces, interfaces, and the like; robust and efficient methods for the solution of the associated quantum mechanical equations are critical. The finite-element (FE) method (see e.g., [2]) is a general method for the solution of partial differential and integral equations which has found wide application in diverse fields ranging from particle physics to civil engineering. Here, we discuss its application to large-scale ab initio electronic-structure calculations.

  13. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Chaka, Anne M.; Felmy, Andrew R.

    2014-03-28

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

  14. Ab initio thermodynamic model for magnesium carbonates and hydrates.

    Science.gov (United States)

    Chaka, Anne M; Felmy, Andrew R

    2014-09-04

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

  15. An Efficient Approach to Ab Initio Monte Carlo Simulation

    CERN Document Server

    Leiding, Jeff

    2013-01-01

    We present a Nested Markov Chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, is used to substantially decorrelate configurations at which the potential of interest is evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure is maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature \\beta^0), which is otherwise unconstrained. Local density approximation (LDA) results are presented for shocked states in argon at pressures from 4 to 60 GPa. Depending on the quality of the reference potential, the acceptance probability is enhanced by factors of 1.2-28 relative to unoptimized NMC sampling, and the procedure's efficiency is found to be competitive with that of standard ab initio...

  16. X-ray absorption Debye-Waller factors from ab initio molecular dynamics

    Science.gov (United States)

    Vila, F. D.; Lindahl, V. E.; Rehr, J. J.

    2012-01-01

    An ab initio equation of motion method is introduced to calculate the temperature-dependent mean-square vibrational amplitudes σ2 which appear in the Debye-Waller factors in x-ray absorption, x-ray scattering, and related spectra. The approach avoids explicit calculations of phonon modes, and is based instead on calculations of the displacement-displacement time correlation function from ab initio density functional theory molecular dynamics simulations. The method also yields the vibrational density of states and thermal quantities such as the lattice free energy. Illustrations of the method are presented for a number of systems and compared with other methods and experiment.

  17. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    Science.gov (United States)

    Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

  18. Ab initio study of alanine polypeptide chains twisting

    CERN Document Server

    Solovyov, I A; Solovyov, A V; Yakubovitch, A V; Greiner, Walter; Solov'yov, Andrey V.; Solov'yov, Ilia A.; Yakubovitch, Alexander V.

    2005-01-01

    We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable corres...

  19. High-throughput ab-initio dilute solute diffusion database

    Science.gov (United States)

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-07-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.

  20. Ab initio dynamical exchange interactions in frustrated antiferromagnets

    Science.gov (United States)

    Simoni, Jacopo; Stamenova, Maria; Sanvito, Stefano

    2017-08-01

    The ultrafast response to an optical pulse excitation of the spin-spin exchange interaction in transition metal antiferromagnets is studied within the framework of the time-dependent spin-density functional theory. We propose a formulation for the full dynamical exchange interaction, which is nonlocal in space, and it is derived starting from ab initio arguments. Then, we investigate the effect of the laser pulse on the onset of the dynamical process. It is found that we can distinguish two types of excitations, both activated immediately after the action of the laser pulse. While the first one can be associated to a Stoner-like excitation and involves the transfer of spin from one site to another, the second one is related to the ultrafast modification of a Heisenberg-like exchange interaction and can trigger the formation of spin waves in the first few hundred femtoseconds of the time evolution.

  1. Ab initio investigation of the mechanical properties of copper

    Institute of Scientific and Technical Information of China (English)

    Liu Yue-Lin; Gui Li-Jiang; Jin Shuo

    2012-01-01

    Employing the ab initio total energy method based on the density functional theory with the generalized gradient approximation,we have systematically investigated the theoretical mechanical properties of copper (Cu).The theoretical tensile strengths are calculated to be 25.3 GPa,5.9 GPa,and 37.6 GPa for the fcc Cu single crystal in the [001],[110],and [111] directions,respectively.Among the three directions,the [110] direction is the weakest one due to the occurrence of structure transition at the lower strain and the weakest interaction of atoms between the (110) planes,while the [111] direction is the strongest direction because of the strongest interaction of atoms between the (111) planes.In terms of the elastic constants of Cu single crystal,we also estimate some mechanical quantities of polycrystalline Cu,including bulk modulus B,shear modulus G,Young's modulus Ep,and Poisson's ratio v.

  2. Quantum plasmonics: from jellium models to ab initio calculations

    Directory of Open Access Journals (Sweden)

    Varas Alejandro

    2016-08-01

    Full Text Available Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.

  3. Ab initio electronic structure and optical conductivity of bismuth tellurohalides

    CERN Document Server

    Schwalbe, Sebastian; Starke, Ronald; Schober, Giulio A H; Kortus, Jens

    2016-01-01

    We investigate the electronic structure, dielectric and optical properties of bismuth tellurohalides BiTeX (X = I, Cl, Br) by means of all-electron density functional theory. In particular, we present the ab initio conductivities and dielectric tensors calculated over a wide frequency range, and compare our results with the recent measurements by Akrap et al. , Makhnev et al. , and Rusinov et al. . We show how the low-frequency branch of the optical conductivity can be used to identify characteristic intra- and interband transitions between the Rashba spin-split bands in all three bismuth tellurohalides. We further calculate the refractive indices and dielectric constants, which in turn are systematically compared to previous predictions and measurements. We expect that our quantitative analysis will contribute to the general assessment of bulk Rashba materials for their potential use in spintronics devices.

  4. Local structure analysis in ab initio liquid water

    Science.gov (United States)

    Santra, Biswajit; DiStasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto

    2015-09-01

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyse the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I ), was unimodal with most water molecules characterised by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I ) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high-density- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water. Analysis of the LSI autocorrelation function uncovered a persistence time of ∼ 4 ps - a finding consistent with the fact that natural thermal fluctuations are responsible for transitions between these distinct yet transient local aqueous environments in ambient liquid water.

  5. Ab initio calculations of third-order elastic constants and related properties for selected semiconductors

    OpenAIRE

    Lopuszynski, Michal; Majewski, Jacek A.

    2007-01-01

    We present theoretical studies for the third-order elastic constants $C_{ijk}$ in zinc-blende nitrides AlN, GaN, and InN. Our predictions for these compounds are based on detailed ab initio calculations of strain-energy and strain-stress relations in the framework of the density functional theory. To judge the computational accuracy, we compare the ab initio calculated results for $C_{ijk}$ with experimental data available for Si and GaAs. We also underline the relation of the third-order ela...

  6. Recent achievements in ab initio modelling of liquid water

    CERN Document Server

    Khaliullin, Rustam Z

    2013-01-01

    The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

  7. P-V Relation for Mercuric Calcogenides: Ab Initio Method

    Directory of Open Access Journals (Sweden)

    G. Misra

    2011-01-01

    Full Text Available Mercuric Calcogenides found many applications in electronic and optical devices as semiconducting materials. An equation of state provides useful information about the relationship between pressure (P, volume (V and temperature (T that helps to understand the behaviour of materials under the effect of high pressure and high temperature. The present paper sheds light on the electronic structure of Mercuric Calcogenides by simulating its electronic properties through ab initio method. This ab initio method is extended to derive the equation of state for Mercuric Calcogenides. The present equation of state has also been tested for the prediction of End Point. The computed results compare well with Quantum statistical data.

  8. Ab initio calculation of the potential bubble nucleus 34Si

    Science.gov (United States)

    Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.

    2017-03-01

    Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to

  9. Ab initio study of Mg(AlH4)2

    NARCIS (Netherlands)

    van Setten, M.J.; de Wijs, G.A.; Popa, V.A.; Popa, V.A.; Brocks, G.

    2005-01-01

    Magnesium alanate Mg(AlH4)2 has recently raised interest as a potential material for hydrogen storage. We apply ab initio calculations to characterize structural, electronic and energetic properties of Mg(AlH4)2. Density functional theory calculations within the generalized gradient approximation

  10. Ab initio study of energy-level alignments in polymer-dye blends

    NARCIS (Netherlands)

    Pasveer, W.F.; Bobbert, P.A.; Michels, M.A.J.; Langeveld-Voss, B.M.W.; Schoo, H.F.M.; Bastiaansen, J.J.A.M.

    2003-01-01

    Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/ LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and polyfluorene

  11. Ab initio study of energy-level alignments in polymer-dye blends

    NARCIS (Netherlands)

    Pasveer, W.F.; Bobbert, P.A.; Michels, M.A.J.; Langeveld-Voss, B.M.W.; Schoo, H.F.M.; Bastiaansen, J.J.A.M.

    2003-01-01

    Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/ LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and

  12. Precise Ab-initio prediction of terahertz vibrational modes in crystalline systems

    DEFF Research Database (Denmark)

    Jepsen, Peter Uhd; Clark, Stewart J.

    2007-01-01

    We use a combination of experimental THz time-domain spectroscopy and ab-initio density functional perturbative theory to accurately predict the terahertz vibrational spectrum of molecules in the crystalline phase. Our calculations show that distinct vibrational modes found in solid-state materials...

  13. Ab initio study of Mg(AlH4)2

    NARCIS (Netherlands)

    Setten, van M.J.; Wijs, de G.A.; Popa, V.A.; Brocks, G.

    2005-01-01

    Magnesium alanate Mg(AlH4)2 has recently raised interest as a potential material for hydrogen storage. We apply ab initio calculations to characterize structural, electronic and energetic properties of Mg(AlH4)2. Density functional theory calculations within the generalized gradient approximation (G

  14. Ab initio thermodynamic results for warm dense matter

    Science.gov (United States)

    Bonitz, Michael

    2016-10-01

    Warm dense matter (WDM) - an exotic state where electrons are quantum degenerate and ions may be strongly correlated - is ubiquitous in dense astrophysical plasmas and highly compressed laboratory systems including inertial fusion. Accurate theoretical predictions require precision thermodynamic data for the electron gas at high density and finite temperature around the Fermi temperature. First such data have been obtained by restricted path integral Monte Carlo (restricted PIMC) simulations and transformed into analytical fits for the free energy. Such results are also key input for novel finite temperature density functional theory. However, the RPIMC data of Ref. 1 are limited to moderate densities, and even there turned out to be surprisingly inaccurate, which is a consequence of the fermion sign problem. These problems were recently overcome by the development of alternative QMC approaches in Kiel (configuration PIMC and permutation blocking PIMC) and Imperial College (Density matrix QMC). The three methods have their strengths and limitations in complementary parameter regions and provide highly accurate thermodynamic data for the electronic contributions in WDM. While the original results were obtained for small particle numbers, recently accurate finite size corrections were derived allowing to compute ab initio thermodynamic data with an unprecedented accuracy of better than 0.3 percent. This provides the final step for the use as benchmark data for experiments and models of Warm dense matter. Co-authors: T. Schoof, S. Groth, T. Dornheim, F. D. Malone, M. Foulkes, and T. Sjostroem, Funded by: DFG via SFB-TR24 and project BO1366-10.

  15. Evidence for anisotropic dielectric properties of monoclinic hafnia using valence electron energy-loss spectroscopy in high-resolution transmission electron microscopy and ab initio time-dependent density-functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Guedj, C. [University Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France); Hung, L.; Sottile, F. [LSI, CNRS, CEA, École Polytechnique, F-91128 Palaiseau (France); European Theoretical Spectroscopy Facility (ETSF) (France); Zobelli, A. [LPS, CNRS and University Paris Sud, F-91405 Orsay (France); Blaise, P. [University Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France); European Theoretical Spectroscopy Facility (ETSF) (France); Olevano, V. [University Grenoble Alpes, F-38000 Grenoble (France); European Theoretical Spectroscopy Facility (ETSF) (France); CNRS, Institut Néel, F-38042 Grenoble (France)

    2014-12-01

    The effect of nanocrystal orientation on the energy loss spectra of monoclinic hafnia (m-HfO{sub 2}) is measured by high resolution transmission electron microscopy (HRTEM) and valence energy loss spectroscopy (VEELS) on high quality samples. For the same momentum-transfer directions, the dielectric properties are also calculated ab initio by time-dependent density-functional theory (TDDFT). Experiments and simulations evidence anisotropy in the dielectric properties of m-HfO{sub 2}, most notably with the direction-dependent oscillator strength of the main bulk plasmon. The anisotropic nature of m-HfO{sub 2} may contribute to the differences among VEELS spectra reported in literature. The good agreement between the complex dielectric permittivity extracted from VEELS with nanometer spatial resolution, TDDFT modeling, and past literature demonstrates that the present HRTEM-VEELS device-oriented methodology is a possible solution to the difficult nanocharacterization challenges given in the International Technology Roadmap for Semiconductors.

  16. Evidence for anisotropic dielectric properties of monoclinic hafnia using valence electron energy-loss spectroscopy in high-resolution transmission electron microscopy and ab initio time-dependent density-functional theory

    Science.gov (United States)

    Guedj, C.; Hung, L.; Zobelli, A.; Blaise, P.; Sottile, F.; Olevano, V.

    2014-12-01

    The effect of nanocrystal orientation on the energy loss spectra of monoclinic hafnia (m-HfO2) is measured by high resolution transmission electron microscopy (HRTEM) and valence energy loss spectroscopy (VEELS) on high quality samples. For the same momentum-transfer directions, the dielectric properties are also calculated ab initio by time-dependent density-functional theory (TDDFT). Experiments and simulations evidence anisotropy in the dielectric properties of m-HfO2, most notably with the direction-dependent oscillator strength of the main bulk plasmon. The anisotropic nature of m-HfO2 may contribute to the differences among VEELS spectra reported in literature. The good agreement between the complex dielectric permittivity extracted from VEELS with nanometer spatial resolution, TDDFT modeling, and past literature demonstrates that the present HRTEM-VEELS device-oriented methodology is a possible solution to the difficult nanocharacterization challenges given in the International Technology Roadmap for Semiconductors.

  17. Communication: Unraveling the {sup 4}He droplet-mediated soft-landing from ab initio-assisted and time-resolved density functional simulations: Au@{sup 4}He{sub 300}/TiO{sub 2}(110)

    Energy Technology Data Exchange (ETDEWEB)

    Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es; Aguirre, Néstor F. [Instituto de Física Fundamental (C.S.I.C.), Serrano 123, E-28006 Madrid (Spain); Stoll, Hermann [Institut für Theoretische Chemie, Universität Stuttgart, D-70550 Stuttgart (Germany); Mitrushchenkov, Alexander O. [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France); Mateo, David; Pi, Martí [Department ECM, Facultat de Física, and IN" 2UB, Universitat de Barcelona, Diagonal 645, E-08028 Barcelona (Spain)

    2015-04-07

    An ab-initio-based methodological scheme for He-surface interactions and zero-temperature time-dependent density functional theory for superfluid {sup 4}He droplets motion are combined to follow the short-time collision dynamics of the Au@{sup 4}He{sub 300} system with the TiO{sub 2}(110) surface. This composite approach demonstrates the {sup 4}He droplet-assisted sticking of the metal species to the surface at low landing energy (below 0.15 eV/atom), thus providing the first theoretical evidence of the experimentally observed {sup 4}He droplet-mediated soft-landing deposition of metal nanoparticles on solid surfaces [Mozhayskiy et al., J. Chem. Phys. 127, 094701 (2007) and Loginov et al., J. Phys. Chem. A 115, 7199 (2011)].

  18. Gas phase ion chemistry of coumarins: ab initio calculations used to ...

    African Journals Online (AJOL)

    Gas phase ion chemistry of coumarins: ab initio calculations used to justify ... and quadrupole mass spectrometer (qMS) coupled to a gas chromatograph is ... Ab Initio calculations, Electron ionization, Positive chemical ionization, Negative ...

  19. Melting curves of metals by ab initio calculations

    Science.gov (United States)

    Minakov, Dmitry; Levashov, Pavel

    2015-06-01

    In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).

  20. Resonance and Aromaticity : An Ab Initio Valence Bond Approach

    NARCIS (Netherlands)

    Rashid, Zahid; van Lenthe, Joop H.; Havenith, Remco W. A.

    2012-01-01

    Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wav

  1. Relaxation of Small Molecules: an ab initio Study

    Institute of Scientific and Technical Information of China (English)

    CAO Yi-Gang; JIAO Zheng-Kuan; A. Antons; K. Schroeder; S. Blügel2

    2002-01-01

    Using an ab initio total energy and force method, we have relaxed several group IV and group V elementalclusters, in detail the arsenic and antimony dimers, silicon, phosphorus, arsenic and antimony tetramers. The obtainedbond lengths and cohesive energies are more accurate than other calculating methods, and in excellent agreement withthe experimental results.

  2. Ab initio interatomic potentials and the thermodynamic properties of fluids

    Science.gov (United States)

    Vlasiuk, Maryna; Sadus, Richard J.

    2017-07-01

    Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

  3. Bicanonical ab Initio Molecular Dynamics for Open Systems.

    Science.gov (United States)

    Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

    2017-08-08

    Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

  4. Ab-Initio Theory of Charge Transport in Organic Crystals

    Science.gov (United States)

    Hannewald, K.; Bobbert, P. A.

    2005-06-01

    A theory of charge transport in organic crystals is presented. Using a Holstein-Peierls model, an explicit expression for the charge-carrier mobilities as a function of temperature is obtained. Calculating all material parameters from ab initio calculations, the theory is applied to oligo-acene crystals and a brief comparison to experiment is given.

  5. Structural flexibility of DABCO. Ab initio and DFT benchmark study

    Science.gov (United States)

    Nizovtsev, Anton S.; Ryzhikov, Maxim R.; Kozlova, Svetlana G.

    2017-01-01

    The energy and structural parameters of 1,4-diazabicyclo[2.2.2]octane (DABCO) obtained by various DFT methods are examined versus ab initio and experimental data. The features of twisting potentials of DABCO and closely-related species (1-azabicyclo[2.2.2]octane and bicyclo[2.2.2]octane) are discussed in light of computational schemes applied.

  6. Ab initio simulation of dislocation cores in metals; Simulation ab initio des coeurs de dislocation dans les metaux

    Energy Technology Data Exchange (ETDEWEB)

    Ventelon, L. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN/SRMP), 91 - Gif-sur-Yvette (France)

    2008-07-01

    In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)

  7. An efficient approach to ab initio Monte Carlo simulation.

    Science.gov (United States)

    Leiding, Jeff; Coe, Joshua D

    2014-01-21

    We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β(0)), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where-depending on the quality of the reference system potential-acceptance probabilities were enhanced by factors of 1.2-28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.

  8. Ab initio modelling of boron related defects in amorphous silicon

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Tiago A.; Torres, Vitor J.B. [Department of Physics, University of Aveiro, Campus Santiago, 3810-193 Aveiro (Portugal)

    2012-10-15

    We have modeled boron related point defects in amorphous silicon, using an ab initio method, the Density functional theory-pseudopotential code Aimpro. The boron atoms were embedded in 64 atom amorphous silicon cubic supercells. The calculations were performed using boron defects in 15 different supercells. These supercells were developed using a modified Wooten-Winer-Weaire bond switching mechanism. In average, the properties of the 15 supercells agree with the observed radial and bond angle distributions, as well the electronic and vibrational density of states and Raman spectra. In amorphous silicon it has been very hard to find real self-interstitials, since for almost all the tested configurations, the amorphous lattice relaxes overall. We found that substitutional boron prefers to be 4-fold coordinated. We find also an intrinsic hole-trap in the non-doped amorphous lattice, which may explain the low efficiency of boron doping. The local vibrational modes are, in average, higher than the correspondent crystalline values (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  9. Ab initio calculation of the potential bubble nucleus $^{34}$Si

    CERN Document Server

    Duguet, T; Lecluse, S; Barbieri, C; Navrátil, P

    2016-01-01

    The possibility that an unconventional depletion in the center of the charge density distribution of certain nuclei occurs due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. We report on ab initio self-consistent Green's function calculations of one of such candidates, $^{34}$Si, together with its Z+2 neighbour $^{36}$S. Binding energies, rms radii and density distributions of the two nuclei as well as low-lying spectroscopy of $^{35}$Si, $^{37}$S, $^{33}$Al and $^{35}$P are discussed. The interpretation of one-nucleon removal and addition spectra in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input inter-nucleon interactions. The prediction regarding the (non-)existence of the bubble structure in $^{34}$Si varies significantly with the nuclear Hamiltonian used. However, demandin...

  10. Local Environment Distribution in Ab Initio Liquid Water

    Science.gov (United States)

    Santra, Biswajit; Distasio, Robert A., Jr.; Car, Roberto

    2013-03-01

    We have analyzed the distribution of local environments in liquid water at ambient conditions and its inherent potential energy surface (IPES) based on state-of-the-art ab initio molecular dynamics simulations performed on 128 molecules implementing hybrid PBE0 exchange [PRB 79, 085102 (2009)] and van der Waals (vdW) interactions [PRL 102, 073005 (2009)]. The local environments of molecules are characterized in terms of the local structure index (LSI) [JCP 104, 7671 (1996)] which is able to distinguish high- and low-density molecular environments. In agreement with simulations based on model potentials, we find that the distribution of LSI is unimodal at ambient conditions and bimodal in the IPES, consistent with the existence of polymorphism in amorphous phases of water. At ambient conditions spatial LSI fluctuations extend up to ~7 Å and their dynamical correlation decays on a time scale of ~3 ps, as found for density fluctuations in a recent study [PRL 106, 037801 (2011)]. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500

  11. Ab initio molecular crystal structures, spectra, and phase diagrams.

    Science.gov (United States)

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  12. Ab initio charge-carrier mobility model for amorphous molecular semiconductors

    Science.gov (United States)

    Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.

    2016-05-01

    Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.

  13. Computer simulation of acetonitrile and methanol with ab initio-based pair potentials

    Science.gov (United States)

    Hloucha, M.; Sum, A. K.; Sandler, S. I.

    2000-10-01

    This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.

  14. Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation

    Science.gov (United States)

    Correa, J. D.; Cisternas, E.

    2016-09-01

    By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.

  15. Ab Initio Calculations for the BaTiO3 (001) Surface Structure

    Institute of Scientific and Technical Information of China (English)

    XUE Xu-Yan; WANG Chun-Lei; ZHONG Wei-Lie

    2004-01-01

    @@ The ab initio method within the local density approximation is applied to calculate cubic BaTiO3 (001) surface relaxation and rumpling for two different terminations (BaO and TiO2). Our calculations demonstrate that cubic perovskite BaTiO3 crystals possess surface polarization, accompanied by the presence of the relevant electric field.We analyse their electronic structures (band structure, density of states and the electronic density redistribution with emphasis on the covalency effects). The results are also compared with that of the previous ab initio calculations. Considerable increases of Ti-O chemical bond covalency nearby the surface have been observed.The band gap reduces especially for the TiO2 termination.

  16. Ab initio studies of niobium defects in uranium

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, S; Huang, H; Hsiung, L

    2007-06-01

    Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.

  17. Ab-initio calculations for dilute magnetic semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Belhadji, Brahim

    2008-03-03

    This thesis focusses on ab-initio calculations for the electronic structure and the magnetic properties of dilute magnetic semiconductors (DMS). In particular we aim at the understanding of the complex exchange interactions in these systems. Our calculations are based on density functional theory, being ideally suited for a description of the material specific properties of the considered DMS. Moreover we use the KKR Green function method in connection with the coherent potential approximation (CPA), which allows to include the random substitutional disorder in a mean field-like approximation for the electronic structure. Finally we calculate the exchange coupling constants J{sub ij} between two impurities in a CPA medium by using the Lichtenstein formula and from this calculate the Curie temperature by a numerically exact Monte Carlo method. Based on this analysis we found and investigated four different exchange mechanisms being of importance in DMS systems: Double exchange, p-d exchange, antiferromagnetic superexchanges, and ferromagnetic superexchange. A second topic we have investigated in this thesis is the pressure dependence of the exchange interactions and the Curie temperatures in (Ga,Mn)As and (In,Mn)As, using the LDA and the LDA+U approximations. Exact calculations of T{sub C} by Monte Carlo simulations show a somehow different behavior. (orig.)

  18. Exploring the free energy surface using ab initio molecular dynamics

    Science.gov (United States)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  19. Ab initio predictions of the symmetry energy and recent constraints

    Science.gov (United States)

    Sammarruca, Francesca

    2017-01-01

    The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.

  20. Ab initio transport across bismuth selenide surface barriers

    KAUST Repository

    Narayan, Awadhesh

    2014-11-24

    © 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results demonstrate the suppression of perfect backscattering, while all other scattering processes, which do not entail a complete spin and momentum reversal, are allowed. Furthermore, we find that the spin of the surface state develops an out-of-plane component as it traverses the barrier. Our calculations reveal the existence of quasibound states in the vicinity of the surface barriers, which appear in the form of an enhanced density of states in the energy window corresponding to the topological state. For double barriers we demonstrate the formation of quantum well states. To complement our first-principles results we construct a two-dimensional low-energy effective model and illustrate its shortcomings. Our findings are discussed in the context of a number of recent experimental works.

  1. Ab initio calculations of the absorption spectrum of chalcone

    Science.gov (United States)

    Oumi, Manabu; Maurice, David; Head-Gordon, Martin

    1999-03-01

    The excitation energies and excited states of trans-chalcone ( trans-( s-cis)-1,3-diphenylpropenone), and several related molecules ( trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone, propenal, trans-( s-cis)-1-(4-hydroxyphenyl)-3-phenylpropenone, trans-( s-cis)3-(4-hydroxyphenyl)-1-phenylpropenone) have been calculated using single reference ab initio molecular orbital methods, and characterized by attachment-detachment density analysis. The results suggest assignments for the lowest three electronic transitions observed experimentally for trans-( s-cis)-chalcone in solution. The extent of localization of the electronic transitions is established by calculations on the excited states of trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone and propenal, as well as analysis of the chalcone calculations. Contrary to some previous work, none of these excitations are strongly delocalized over the entire molecule. Calculated substituent shifts for the hydroxy chalcones are in qualitative agreement with experimental data, and support the localized interpretation of the main π→ π* transition.

  2. Serine Proteases an Ab Initio Molecular Dynamics Study

    CERN Document Server

    De Santis, L

    1999-01-01

    In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.

  3. Spin-orbit decomposition of ab initio wavefunctions

    CERN Document Server

    Johnson, Calvin W

    2014-01-01

    Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum $j$, leading to $j$-$j$ coupling, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulting wavefunctions into their component $L$- and $S$-components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly fifty years and six orders of magnitude in basis dimensions. I suggest $L$-$S$ may be a useful tool for analyzing \\textit{ab initio} wavefunctions of light nuclei, for example in the case of rotational bands.

  4. Spin-orbit decomposition of ab initio nuclear wave functions

    Science.gov (United States)

    Johnson, Calvin W.

    2015-03-01

    Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.

  5. High Level Ab Initio Kinetics as a Tool for Astrochemistry

    Science.gov (United States)

    Klippenstein, Stephen

    2015-05-01

    We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.

  6. Toward the Ab-initio Description of Medium Mass Nuclei

    CERN Document Server

    Barbieri, C; Soma, V; Duguet, T; Navratil, P

    2012-01-01

    As ab-initio calculations of atomic nuclei enter the A=40-100 mass range, a great challenge is how to approach the vast majority of open-shell (degenerate) isotopes. We add realistic three-nucleon interactions to the state of the art many-body Green's function theory of closed-shells, and find that physics of neutron driplines is reproduced with very good quality. Further, we introduce the Gorkov formalism to extend ab-initio theory to semi-magic, fully open-shell, isotopes. Proof-of-principle calculations for Ca-44 and Ni-74 confirm that this approach is indeed feasible. Combining these two advances (open-shells and three-nucleon interactions) requires longer, technical, work but it is otherwise within reach.

  7. Ab initio theories for light nuclei and neutron stars

    Science.gov (United States)

    Gezerlis, Alexandros

    2016-09-01

    In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).

  8. Study of Nuclear Clustering from an Ab Initio Perspective

    Science.gov (United States)

    Kravvaris, Konstantinos; Volya, Alexander

    2017-08-01

    We put forward a new ab initio approach that seamlessly bridges the structure, clustering, and reactions aspects of the nuclear quantum many-body problem. The configuration interaction technique combined with the resonating group method based on a harmonic oscillator basis allows us to treat the reaction and multiclustering dynamics in a translationally invariant way and preserve the Pauli principle. Our presentation includes studies of Be,108 and an exploration of 3 α clustering in 12C.

  9. Uniaxial Phase Transition in Si : Ab initio Calculations

    OpenAIRE

    Cheng, C.

    2002-01-01

    Based on a previously proposed thermodynamic analysis, we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, beta-tin, sh, sc, and hcp structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different conributions to the relative pahse stability, we identified the most important factors in reducing t...

  10. Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

    Science.gov (United States)

    2015-07-15

    144306  (2010)]  and  the   cubic -­‐ spline -­‐fitted   PES   reported   by   Xu,   Xie,   Zhang,   Lin,   and   Guo...SUBTITLE 13. SUPPLEMENTARY NOTES 12. DISTRIBUTION AVAILIBILITY STATEMENT 6. AUTHORS 7. PERFORMING ORGANIZATION NAMES AND ADDRESSES 15. SUBJECT TERMS b ...accurate global PESs and for direct dynamics simulations using interpolating moving least squares (IMLS) that guarantee high fidelity to ab initio data. A

  11. GAUSSIAN 76: An ab initio Molecular Orbital Program

    Science.gov (United States)

    Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

    1978-01-01

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

  12. Nuclear forces and ab initio calculations of atomic nuclei

    OpenAIRE

    Meißner, Ulf-G.

    2014-01-01

    Nuclear forces and the nuclear many-body problem have been some of Gerry Brown's main topics in his so productive life as a theoretical physicist. In this talk, I outline how Gerry's work laid the foundations of the modern theory of nuclear forces and ab initio calculations of atomic nuclei. I also present some recent developments obtained in the framework of nuclear lattice simulations.

  13. Thermochemical data for CVD modeling from ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Ho, P. [Sandia National Labs., Albuquerque, NM (United States); Melius, C.F. [Sandia National Labs., Livermore, CA (United States)

    1993-12-31

    Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.

  14. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.

    Science.gov (United States)

    Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  15. Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)

    2014-09-28

    We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).

  16. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Makhov, Dmitry V.; Shalashilin, Dmitrii V. [Department of Chemistry, University of Leeds, Leeds LS2 9JT (United Kingdom); Glover, William J.; Martinez, Todd J. [Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  17. Effects of K doping on electronic structure of Ba{sub 1−x}K{sub x}Fe{sub 2}As{sub 2} superconductor by ab-initio density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Sandoghchi, M. [Advanced Materials Laboratory (AML), Department of Physics, Sharif University of Technology, P.O. Box 11365-9161, Tehran (Iran, Islamic Republic of); Khosroabadi, H., E-mail: khosroabadi@sharif.edu [Advanced Materials Laboratory (AML), Department of Physics, Sharif University of Technology, P.O. Box 11365-9161, Tehran (Iran, Islamic Republic of); Magnet Research Laboratory (MRL), Department of Physics, Sharif University of Technology, P.O. Box 11365-916, Tehran (Iran, Islamic Republic of); Akhavan, M. [Magnet Research Laboratory (MRL), Department of Physics, Sharif University of Technology, P.O. Box 11365-916, Tehran (Iran, Islamic Republic of)

    2014-12-15

    Highlights: • The lattice parameters changes by K doping is explained by ionic charge and the metal–metal bonding scenario. • Creation of a larger peak near the Fermi level and increase the DOS at the Fermi level by K doping. • The effects of K on DOS has been related to the magnetic transition, change of the lattice parameters and FeAs{sub 4} tetrahedron. • Investigation of the number of Fermi level crossed bands by K doping and the band changes near the Fermi level. - Abstract: The crystal and electronic structures of normal phase of Ba{sub 1−x}K{sub x}Fe{sub 2}As{sub 2} for x = 0.0, 0.5 and 1.0 have been studied by using pseudopotential Quantum Espresso code based on ab-initio density functional theory. Effects of K doping on the crystal structure and lattice parameters have been calculated and compared with the experimental and computational reported data for similar compounds. The metal–metal bonding scenario was used to explain the changes of lattice parameters by K doping. The electronic structure of this system including of density of states and band structure have been calculated and investigated by K doping. One of the interesting results is that a larger peak is appeared near the Fermi level by increasing of the K doping. These changes could produce a potential for creation of the superconducting state in this system.

  18. Towards hydrogen metallization: an Ab initio approach; Vers la metallisation de l`hydrogene: approche AB initio

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, St

    1998-12-31

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.

  19. Thermodynamic prediction of glass formation tendency, cluster-in-jellium model for metallic glasses, ab initio tight-binding calculations, and new density functional theory development for systems with strong electron correlation

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Yongxin [Iowa State Univ., Ames, IA (United States)

    2009-01-01

    also plays an important role, as it may directly track the movement of every atom. Simulation time is a major limit for molecular dynamics, not only because of “slow” computer speed, but also because of the accumulation error in the numerical treatment of the motion equations. There is also a great concern about the reliability of the emperical potentials if using classical molecular dynamics. Ab initio methods based on density functional theory(DFT) do not have this problem, however, it suffers from small simulation cells and is more demanding computationally. When crystal phase is involved, size effect of the simulation cell is more pronounced since long-range elastic energy would be established. Simulation methods which are more efficient in computation but yet have similar reliability as the ab initio methods, like tight-binding method, are highly desirable. While the complexity of metallic glasses comes from the atomistic level, there is also a large field which deals with the complexity from electronic level. The only “ab initio” method applicable to solid state systems is density functional theory with local density approximation( LDA) or generalized gradient approximation(GGA) for the exchange-correlation energy. It is very successful for simple sp element, where it reaches an high accuracy for determining the surface reconstruction. However, there is a large class of materials with strong electron correlation, where DFT based on LDA or GGA fails in a fundamental way. An “ab initio” method which can generally apply to correlated materials, as LDA for simple sp element, is still to be developed. The thesis is prepared to address some of the above problems.

  20. Ab initio lattice dynamics of complex structures

    DEFF Research Database (Denmark)

    Voss, Johannes

    2008-01-01

    systems in particular. A more detailed analysis of the phonon spectrum has been performed for the compound Mg(BH4)2, where several crystal symmetries have been proposed theoretically and experimentally. By means of an analysis of the instabilities of these structures, a new, stable phase has been......In this thesis, density functional theory is applied in a study of thermodynamic properties of so-called complex metal hydrides, which are promising materials for hydrogen storage applications. Since the unit cells of these crystals can be relatively large with many symmetrically inequivalent...... determined. Aiming at finding scaling relationships between alloy stabilities and computationally inexpensive properties, the stabilities of cation-alloyed metal aluminum hexahydrides have been studied. The analysis shows that charge density symmetries are correlated to the stability. In addition...

  1. Optical and other material properties of SiO2 from ab initio studies

    Science.gov (United States)

    Warmbier, Robert; Mohammed, Faris; Quandt, Alexander

    2014-07-01

    The optical properties of photonic devices largely depend on the dielectric properties of the underlying materials. We apply modern ab initio methods to study crystalline SiO2 phases, which serve as toy models for amorphous glass. We discuss the dielectric response from the infrared to the VIS/UV, which is crucial for glass based photonic applications. Low density silica, like cristobalite, may provide a good basis for high transmission optical devices.

  2. Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states

    DEFF Research Database (Denmark)

    Kreitmeir, M.; Bertagnolli, H.; Mortensen, Jens Jørgen;

    2003-01-01

    Liquid hydrogen fluoride is a simple but interesting system for studies of the influence of hydrogen bonds on physical properties. We have performed ab initio molecular dynamics simulations of HF at several thermodynamic states, where we examine the microscopic structure of the liquid as well...... as its static and dynamic properties. The results obtained show good agreement with well established data, and, moreover, we were able to show significant changes within the structure depending on the system's temperature and density....

  3. Ab-initio electronic structure method for substitutional disorder applied to iron-based superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Herbig, Alexander

    2016-02-12

    An ab-initio electronic structure method for substitutionally disordered real materials is developed within a pseudopotential density functional theory approach. The method is validated against exact diagonalization and for simple disordered CuZn alloys. The developed method is applied to iron-based superconductors. In particular, band renormalization effects due to various chemical substitutions in BaFe{sub 2}As{sub 2} are investigated and their Cooper pair breaking effects are compared.

  4. Scalar relativistic calculations of hyperfine coupling constants using ab initio density matrix renormalization group method in combination with third-order Douglas-Kroll-Hess transformation: case studies on 4d transition metals.

    Science.gov (United States)

    Nguyen Lan, Tran; Kurashige, Yuki; Yanai, Takeshi

    2015-01-13

    We have developed a new computational scheme for high-accuracy prediction of the isotropic hyperfine coupling constant (HFCC) of heavy molecules, accounting for the high-level electron correlation effects, as well as the scalar-relativistic effects. For electron correlation, we employed the ab initio density matrix renormalization group (DMRG) method in conjunction with a complete active space model. The orbital-optimization procedure was employed to obtain the optimized orbitals required for accurately determining the isotropic HFCC. For the scalar-relativistic effects, we initially derived and implemented the Douglas-Kroll-Hess (DKH) hyperfine coupling operators up to the third order (DKH3) by using the direct transformation scheme. A set of 4d transition-metal radicals consisting of Ag atom, PdH, and RhH2 were chosen as test cases. Good agreement between the isotropic HFCC values obtained from DMRG/DKH3 and experiment was archived. Because there are no available gas-phase values for PdH and RhH2 radicals in the literature, the results from the present high-level theory may serve as benchmark data.

  5. Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}] as model system

    Energy Technology Data Exchange (ETDEWEB)

    Ulian, Gianfranco; Valdrè, Giovanni, E-mail: giovanni.valdre@unibo.it [Dipartimento di Scienze Biologiche e Geologico-Ambientali, Centro di Ricerca Interdisciplinare di Biomineralogia, Cristallografia e Biomateriali, Università di Bologna “Alma Mater Studiorum” Piazza di Porta San Donato 1, 40126 Bologna (Italy); Tosoni, Sergio [Departament de Química Física and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/ Martí i Franquès 1, E-08028 Barcelona (Spain)

    2013-11-28

    The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.

  6. Ab initio vibrations in nonequilibrium nanowires

    DEFF Research Database (Denmark)

    Jauho, Antti-Pekka; Engelund, Mads; Markussen, T

    2010-01-01

    We review recent results on electronic and thermal transport in two different quasi one-dimensional systems: Silicon nanowires (SiNW) and atomic gold chains. For SiNW's we compute the ballistic electronic and thermal transport properties on equal footing, allowing us to make quantitative predicti......We review recent results on electronic and thermal transport in two different quasi one-dimensional systems: Silicon nanowires (SiNW) and atomic gold chains. For SiNW's we compute the ballistic electronic and thermal transport properties on equal footing, allowing us to make quantitative...... predictions for the thermoelectric properties, while for the atomic gold chains we evaluate microscopically the damping of the vibrations, due to the coupling of the chain atoms to the modes in the bulk contacts. Both approaches are based on the combination of density-functional theory, and nonequilibrium...... Green's functions....

  7. Toward ab initio extremely metal poor stars

    CERN Document Server

    Ritter, Jeremy S; Milosavljevic, Milos; Bromm, Volker

    2016-01-01

    Extremely metal poor stars have been the focus of much recent attention owing to the expectation that their chemical abundances can shed light on the metal and dust yields of the earliest supernovae. We present our most realistic simulation to date of the astrophysical pathway to the first metal enriched stars. We simulate the radiative and supernova hydrodynamic feedback of a 60 Msun Population III star starting from cosmological initial conditions realizing Gaussian density fluctuations. We follow the gravitational hydrodynamics of the supernova remnant at high spatial resolution through its freely-expanding, adiabatic, and radiative phases, until gas, now metal-enriched, has resumed runaway gravitational collapse. Our findings are surprising: while the Population III progenitor exploded with a low energy of 10^51 erg and injected an ample metal mass of 6 Msun, the first cloud to collapse after the supernova explosion is a dense surviving primordial cloud on which the supernova blastwave deposited metals on...

  8. Ab initio calculations of ^12C and neutron drops

    Science.gov (United States)

    Pieper, Steven C.

    2009-10-01

    Ab initio calculations of nuclei, which treat a nucleus as a system of A nucleons interacting by realistic two- and three-nucleon forces, have made tremendous progress in the last 15 years. This is a result of better Hamiltonians, rapidly increasing computer power, and new or improved many-body methods. Three methods are principally being used: Green's function Monte Carlo (GFMC), no-core shell model, and coupled cluster. In the limit of large computer resources, all three methods produce exact eigenvalues of a given nuclear Hamiltonian. With DOE SciDAC and INCITE support, all three methods are using the largest computers available today. Under the UNEDF SciDAC grant, the Argonne GFMC program was modified to efficiently use more than 2000 processors. E. Lusk (Argonne), R.M. Butler (Middle Tennessee State U.) and I have developed an Asynchronous Dynamic Load-Balancing (ADLB) library. In addition all the cores in a node are used via OpenMP as one ADLB/MPI client. In this way we obtain very good scalability up to 30,000 processors on Argonne's IBM Blue Gene/P. Two systems of particular interest that require this computer power are ^12C and neutron drops. V.R. Pandharipande (UIUC, deceased), J. Carlson (LANL), R.B. Wiringa (Argonne), and I have developed new trial wave functions that explicitly contain the three-alpha particle structure of ^12C. These are being used with the Argonne V18 and Illinois-7 potentials which reproduce the energies of 51 states in 3energy-density functionals.

  9. Ab Initio Studies of Metal Hexaboride Materials

    Science.gov (United States)

    Schmidt, Kevin M.

    Metal hexaborides are refractory ceramics with several qualities relevant to materials design, such as low work functions, high hardness, low thermal expansion coefficients, and high melting points, among many other properties of interest for industrial applications. Thermal and mechanical stability is a common feature provided by the covalently-bonded network boron atoms, and electronic properties can vary significantly with the resident metal. While these materials are currently employed as electron emitters and abrasives, promising uses of these materials also include catalytic applications for chemical dissociation reactions of various molecules such as hydrogen, water and carbon monoxide, for example. However, these extensions require a thorough understanding of particular mechanical and electronic properties. This dissertation is a collection of studies focused on understanding the behavior of metal hexaboride materials using computational modeling methods to investigate materials properties of these from both classical and quantum mechanical points of view. Classical modeling is performed using molecular dynamics methods with interatomic potentials obtained from density functional theory (DFT) calculations. Atomic mean-square displacements from the quasi-harmonic approximation and lattice energetic data are produced with DFT for developing the potentials. A generalized method was also developed for the inversion of cohesive energy curves of crystalline materials; pairwise interatomic potentials are extracted using detailed geometrical descriptions of the atomic interactions and a list of atomic displacements and degeneracies. The surface structure of metal hexaborides is studied with DFT using several model geometries to describe the terminal cation layouts, and these provide a basis for further studies on metal hexaboride interactions with hydrogen. The surface electronic structure calculations show that segregated regions of metal and boron

  10. AB-INITIO STUDY OF BULK MODULUS AND CHARGE DENSITY OF CUBIC SrMO3 PEROVSKITES (M = Ti, Zr, Mo, Rh, Ru

    Directory of Open Access Journals (Sweden)

    AVINASH DAGA

    2012-03-01

    Full Text Available Bulk modulus & charge density of cubic SrMO3 perovskites (M = Ti, Zr, Mo, Rh & Ru have been investigated systematically using the first principle density functional calculations. Local density approximation (LDAmethod has been used to compute the two quantities for five perovskites. It is found that the calculated bulk modulus for all the transition metal oxides are in good agreement with the available experimental data and with other theoretical results previously reported in the literature. ABINIT computer code is used to carry out all the calculations. Charge density plots for all the five cubic SrMO3 perovskites have been drawn using MATLAB. The maximum and minimum values of charge density along with the corresponding reduced coordinates are reported for all the perovskites.

  11. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

    Science.gov (United States)

    Whitfield, T. W.; Crain, J.; Martyna, G. J.

    2006-03-01

    In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.

  12. Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Rio, B. G. del; González, L. E. [Departamento de Física Teórica, Atómica y Óptica, Universidad de Valladolid, 47011 Valladolid (Spain)

    2015-08-17

    Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.

  13. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Zen, Andrea, E-mail: a.zen@ucl.ac.uk [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); London Centre for Nanotechnology, University College London, London WC1E 6BT (United Kingdom); Luo, Ye, E-mail: xw111luoye@gmail.com; Mazzola, Guglielmo, E-mail: gmazzola@phys.ethz.ch; Sorella, Sandro, E-mail: sorella@sissa.it [SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste (Italy); Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila (Italy)

    2015-04-14

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

  14. Melting of sodium under high pressure. An ab-initio study

    Energy Technology Data Exchange (ETDEWEB)

    González, D. J.; González, L. E. [Departamento de Física Teórica, Atómica y Optica, Universidad de Valladolid, 47011 Valladolid (Spain)

    2015-08-17

    We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.

  15. Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo

    CERN Document Server

    Zen, Andrea; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro

    2014-01-01

    Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in excellent agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous Density Functional Theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab-initio simulations of complex chemical systems.

  16. Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon

    Science.gov (United States)

    Drumm, Daniel W.; Budi, Akin; Per, Manolo C.; Russo, Salvy P.; L Hollenberg, Lloyd C.

    2013-02-01

    The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%.

  17. Properties of metals during the heating by intense laser irradiation using ab initio simulations

    Science.gov (United States)

    Holst, Bastian; Recoules, Vanina; Torrent, Marc; Mazevet, Stephane

    2011-10-01

    Ultrashort laser pulses irradiating a target heat the electrons to very high temperatures. In contrast, the ionic lattice is unaffected on the time scale of the laser pulse since the heat capacity of electrons is much smaller than that of the lattice. This non-equilibrium system can be described as a composition of two subsystems: one consisting of hot electrons and the other of an ionic lattice at low temperature. We studied the effect of this intense electronic excitations on the optical properties of gold using ab initio simulations. We additionally use ab initio linear response to compute the phonon spectrum and the electron-phonon coupling constant within Density Functional Theory for several electronic temperatures of few eV. LULI, Ecole Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau, France.

  18. Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon.

    Science.gov (United States)

    Drumm, Daniel W; Budi, Akin; Per, Manolo C; Russo, Salvy P; L Hollenberg, Lloyd C

    2013-02-27

    : The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%.

  19. X-ray Crystal Structure, Raman Spectroscopy and Ab Initio Density Functional Theory Calculations on 1,1,3,3-Tetramethylguanidinium Bromide

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Riisager, Anders; Nguyen van Buu, Olivier

    2010-01-01

    = 104.31(3)°, Z = 2, based on 11769 reflections, measured from θ = 2.71-28.00° on a small colorless needle crystal. Raman and IR spectra are presented and assigned. When heated, both the chloride and the bromide salts form vapor phases. The Raman spectra of the vapors are surprisingly alike, showing......, for example, a characteristic strong band at 2229 cm-1. This band was interpreted by some of us to show that the [tmgH]Cl gas phase should consist of monomeric ion pair “molecules” held together by a single N-H+ · · · Cl- hydrogen bond, the stretching vibration of which should be causing the band, based on ab...

  20. Benchmarks of the ab initio FCI, MCSM and NCFC methods

    CERN Document Server

    Abe, T; Otsuka, T; Shimizu, N; Utsuno, Y; Vary, J P

    2012-01-01

    We report ab initio no-core solutions for properties of light nuclei with three different approaches in order to assess the accuracy and convergence rates of each method. Full Configuration Interaction (FCI), Monte Carlo Shell Model (MCSM) and No Core Full Configuration (NCFC) approaches are solved separately for the ground state energy and other properties of seven light nuclei using the realistic JISP16 nucleon-nucleon interaction. The results are consistent among the different approaches. The methods differ significantly in how the required computational resources scale with increasing particle number for a given accuracy.

  1. Ab initio modeling of small proteins by iterative TASSER simulations

    Directory of Open Access Journals (Sweden)

    Zhang Yang

    2007-05-01

    Full Text Available Abstract Background Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins. Results We developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (α-root mean square deviation (RMSD of 3.8Å, with 6 of them having a Cα-RMSD α-RMSD α-RMSD of the I-TASSER models was 3.9Å, whereas it was 5.9Å using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (α-RMSD of 3.9Å was obtained for the third benchmark, with seven cases having a Cα-RMSD Conclusion Our simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.

  2. Ab initio study of phase equilibria in TiCx

    DEFF Research Database (Denmark)

    Korzhavyi, P.A.; Pourovskii, L.V.; Hugosson, H.W.

    2002-01-01

    The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti2C, Ti......3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures....

  3. Accelerating Ab Initio Nuclear Physics Calculations with GPUs

    CERN Document Server

    Potter, Hugh; Maris, Pieter; Sosonkina, Masha; Vary, James; Binder, Sven; Calci, Angelo; Langhammer, Joachim; Roth, Robert; Çatalyürek, Ümit; Saule, Erik

    2014-01-01

    This paper describes some applications of GPU acceleration in ab initio nuclear structure calculations. Specifically, we discuss GPU acceleration of the software package MFDn, a parallel nuclear structure eigensolver. We modify the matrix construction stage to run partly on the GPU. On the Titan supercomputer at the Oak Ridge Leadership Computing Facility, this produces a speedup of approximately 2.2x - 2.7x for the matrix construction stage and 1.2x - 1.4x for the entire run.

  4. Spin-orbit decomposition of ab initio wavefunctions

    OpenAIRE

    Johnson, Calvin W.

    2014-01-01

    Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum $j$, leading to $j$-$j$ coupling, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulti...

  5. Tailoring magnetoresistance at the atomic level: An ab initio study

    KAUST Repository

    Tao, Kun

    2012-01-05

    The possibility of manipulating the tunneling magnetoresistance (TMR) of antiferromagnetic nanostructures is predicted in the framework of ab initio calculations. By the example of a junction composed of an antiferromagnetic dimer and a spin-polarized scanning tunneling microscopy tip we show that the TMR can be tuned and even reversed in sign by lateral and vertical movements of the tip. Moreover, our finite-bias calculations demonstrate that the magnitude and the sign of the TMR can also be tuned by an external voltage. © 2012 American Physical Society.

  6. Ab initio structure determination via powder X-ray diffraction

    Indian Academy of Sciences (India)

    Digamber G Porob; T N Guru Row

    2001-10-01

    Structure determination by powder X-ray diffraction data has gone through a recent surge since it has become important to get to the structural information of materials which do not yield good quality single crystals. Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination of -NaBi3V2O10.

  7. Hydrogen Desorption from Mg Hydride: An Ab Initio Study

    Directory of Open Access Journals (Sweden)

    Simone Giusepponi

    2012-07-01

    Full Text Available Hydrogen desorption from hydride matrix is still an open field of research. By means of accurate first-principle molecular dynamics (MD simulations an Mg–MgH2 interface is selected, studied and characterized. Electronic structure calculations are used to determine the equilibrium properties and the behavior of the surfaces in terms of structural deformations and total energy considerations. Furthermore, extensive ab-initio molecular dynamics simulations are performed at several temperatures to characterize the desorption process at the interface. The numerical model successfully reproduces the experimental desorption temperature for the hydride.

  8. Morphing ab initio potential energy curve of beryllium monohydride

    Science.gov (United States)

    Špirko, Vladimír

    2016-12-01

    Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.

  9. An ab initio study of plutonium oxides surfaces; Etude ab initio des surfaces d'oxydes de Pu

    Energy Technology Data Exchange (ETDEWEB)

    Jomard, G.; Bottin, F.; Amadon, B

    2007-07-01

    By means of first-principles calculations, we have studied the atomic structure as well as the thermodynamic stability of various plutonium dioxide surfaces in function of their environment (in terms of oxygen partial pressure and temperature). All these simulations have been performed with the ABINIT code. It is well known that DFT fails to describe correctly plutonium-based materials since 5f electrons in such systems are strongly correlated. In order to go beyond DFT, we have treated PuO{sub 2} and {beta}-Pu{sub 2}O{sub 3} in a DFT+U framework. We show that the couple of parameters (U,J) that works well for pure Pu is also well designed for describing ground state (GS) properties of these two oxides. The major improvement with respect with DFT is that we are able to predict an insulating GS in agreement with experiments. The presence of a gap in the DOS (Density of States) of plutonium oxides should play a significant role in the predicted surface reactivity. However, performing DFT+U calculations on surfaces of plutonium oxide from scratch was too ambitious. That is why we decided, as a first step, to study the stability of the (100), (110) and (111) surfaces of PuO{sub 2} in a DFT-GGA framework. For each of these orientations, we considered various terminations. These ab initio results have been introduced in a thermodynamic model which allows us to predict the relative stability of the different terminations as a function of temperature and oxygen partial pressure (p{sub O{sub 2}}). We conclude that at room temperature and for p{sub O{sub 2}}{approx}10 atm., the polar O{sub 2}-(100) termination is favoured. The stabilization of such a polar stoichiometric surface is surprising and should be confirmed by DFT+U calculations before any final conclusion. (authors)

  10. Serious Gaming for Test & Evaluation of Clean-Slate (Ab Initio) National Airspace System (NAS) Designs

    Science.gov (United States)

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

    Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that

  11. Ab initio full charge-density study of the atomic volume of α-phase Fr, Ra, Ac, Th, Pa, U, Np, and Pu

    DEFF Research Database (Denmark)

    Vitos, Levente; Kollár, J.; Skriver, Hans Lomholt

    1997-01-01

    We have used a full charge-density technique based on the linear muffin-tin orbitals method in first-principles calculations of the atomic volumes of the light actinides including Fr, Ra, and Ac in their low-temperature crystallographic phases. The good agreement between the theoretical and exper...... and experimental values along the series support the picture of itinerant 5f electronic states in Th to Pu. The increased deviation between theory and experiment found in Np and Pu may be an indication of correlation effects not included in the local density approximation....

  12. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chung-De [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); National Tsing Hua University, Hsinchu, Taiwan (China); Huang, Yen-Chieh [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); Chiang, Hsin-Lin [National Tsing Hua University, Hsinchu, Taiwan (China); Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); Chen, Chun-Jung, E-mail: cjchen@nsrrc.org.tw [National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan (China); National Tsing Hua University, Hsinchu, Taiwan (China); National Cheng Kung University, Tainan City 701, Taiwan (China); National Cheng Kung University, Tainan City 701, Taiwan (China)

    2014-09-01

    A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ{sub 1} and ϕ{sub 2}) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ{sub DS} list as a criterion to select optimized phases ϕ{sub am} from ϕ{sub 1} or ϕ{sub 2} of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ{sub SAD} has been developed. Based on this work, reflections with an angle θ{sub DS} in the range 35–145° are selected for an optimized improvement, where θ{sub DS} is the angle between the initial phase ϕ{sub SAD} and a preliminary density-modification (DM) phase ϕ{sub DM}{sup NHL}. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.

  13. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    Energy Technology Data Exchange (ETDEWEB)

    Elenewski, Justin E.; Hackett, John C, E-mail: jchackett@vcu.edu [Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540 (United States)

    2015-02-14

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

  14. Unified ab initio approaches to nuclear structure and reactions

    CERN Document Server

    Navratil, Petr; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo

    2016-01-01

    The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in {\\em ab initio} nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches - built upon the No-Core Shell Model - that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the $^6$He halo nucleus, of five- and six...

  15. Ab initio calculations of reactions of light nuclei

    Science.gov (United States)

    Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr

    2017-09-01

    An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable as a support tool for accurate evaluations of crucial reaction data for nuclear astrophysics, fusion-energy research, and other applications. We present an efficient many-body approach to nuclear bound and scattering states alike, known as the ab initio no-core shell model with continuum. In this approach, square-integrable energy eigenstates of the A-nucleon system are coupled to (A-A)+A target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges. We show that predictive results for nucleon and deuterium scattering on 4He nuclei can be obtained from the direct solution of the Schröedinger equation with modern nuclear potentials.

  16. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Hua Y., E-mail: huay.geng@gmail.com [National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, CAEP, P.O. Box 919-102, Mianyang, Sichuan, 621900 (China); Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853 (United States)

    2015-02-15

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.

  17. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    Science.gov (United States)

    Geng, Hua Y.

    2015-02-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.

  18. Ab initio density functional theory investigation of the structural, electronic and optical properties of Ca3Sb2 in hexagonal and cubic phases

    Science.gov (United States)

    Arghavani Nia, Borhan; Sedighi, Matin; Shahrokhi, Masoud; Moradian, Rostam

    2013-11-01

    A density functional theory study of structural, electronical and optical properties of Ca3Sb2 compound in hexagonal and cubic phases is presented. In the exchange-correlation potential, generalized gradient approximation (PBE-GGA) has been used to calculate lattice parameters, bulk modulus, cohesive energy, dielectric function and energy loss spectra. The electronic band structure of this compound has been calculated using the above two approximations as well as another form of PBE-GGA, proposed by Engle and Vosko (EV-GGA). It is found that the hexagonal phase of Ca3Sb2 has an indirect gap in the Γ→N direction; while in the cubic phase there is a direct-gap at the Γ point in the PBE-GGA and EV-GGA. Effects of applying pressure on the band structure of the system studied and optical properties of these systems were calculated.

  19. The Crystal Structure of Impurity Centers Tm^{2+} and Eu^{2+} in SrCl2: Ab Initio Calculations

    Science.gov (United States)

    Chernyshev, V. A.; Serdcev, A. V.; Petrov, V. P.; Nikiforov, A. E.

    2016-12-01

    Ab initio calculations of the impurity centers Tm^{2+} thulium and europium Eu^{2+} in SrCl2 and MeF2 (Me = Ca, Sr, Ba) were carried out at low (zero) temperature. The crystal structure of impurity centers was investigated. Charge density maps show that the bonds formed by the rare-earth ions have an ionic character. The crystal structures, lattice dynamics, and band structures of MeF2 and SrCl2 were calculated at low temperature. Ab initio calculations were performed in periodic CRYSTAL code within the framework of the MO LCAO approach by using hybrid DFT functionals.

  20. Multiscale modeling of femtosecond laser irradiation on copper film with electron thermal conductivity from ab initio calculation

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    By combining ab initio quantum mechanics calculation and Drude model, electron temperature and lattice temperature dependent electron thermal conductivity is calculated and implemented into a multiscale model of laser material interaction, which couples the classical molecular dynamics and two-temperature model. The results indicated that the electron thermal conductivity obtained from ab initio calculation leads to faster thermal diffusion than that using the electron thermal conductivity from empirical determination, which further induces deeper melting region, larger number of density waves travelling inside the copper film and more various speeds of atomic clusters ablated from the irradiated film surface.

  1. Ab initio density functional theory investigation of the structural, electronic and optical properties of Ca{sub 3}Sb{sub 2} in hexagonal and cubic phases

    Energy Technology Data Exchange (ETDEWEB)

    Arghavani Nia, Borhan, E-mail: b.arghavani@gmail.com [Department of Physics, Kermanshah Branch, Islamic Azad University, Kermanshah (Iran, Islamic Republic of); Sedighi, Matin [Department of Physics, Kermanshah Branch, Islamic Azad University, Kermanshah (Iran, Islamic Republic of); Shahrokhi, Masoud [Young Researchers and Elite Club, Kermanshah Branch, Islamic Azad University, Kermanshah (Iran, Islamic Republic of); Moradian, Rostam [Nano-Science and Nano-Technology Research Center, Razi University, Kermanshah (Iran, Islamic Republic of); Computational Physics Science Research Laboratory, Department of Nano-Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), P.O. Box 19395-1795, Tehran (Iran, Islamic Republic of)

    2013-11-15

    A density functional theory study of structural, electronical and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. In the exchange–correlation potential, generalized gradient approximation (PBE-GGA) has been used to calculate lattice parameters, bulk modulus, cohesive energy, dielectric function and energy loss spectra. The electronic band structure of this compound has been calculated using the above two approximations as well as another form of PBE-GGA, proposed by Engle and Vosko (EV-GGA). It is found that the hexagonal phase of Ca{sub 3}Sb{sub 2} has an indirect gap in the Γ→N direction; while in the cubic phase there is a direct-gap at the Γ point in the PBE-GGA and EV-GGA. Effects of applying pressure on the band structure of the system studied and optical properties of these systems were calculated. - Graphical abstract: A density functional theory study of structural, electronic and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. Display Omitted - Highlights: • Physical properties of Ca{sub 3}Sb{sub 2} in hexagonal and cubic phases are investigated. • It is found that the hexagonal phase is an indirect gap semiconductor. • Ca{sub 3}Sb{sub 2} is a direct-gap semiconductor at the Γ point in the cubic phase. • By increasing pressure the semiconducting band gap and anti-symmetry gap are decreased.

  2. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies.

    Science.gov (United States)

    Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W

    2015-01-28

    X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.

  3. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    Science.gov (United States)

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

  4. An ab-initio density functional theory investigation of fullerene/Zn-phthalocyanine (C60/ZnPc) interface with face-on orientation

    Energy Technology Data Exchange (ETDEWEB)

    Javaid, Saqib [EMMG, Physics Division, PINSTECH, P.O. Nilore, Islamabad (Pakistan); National Centre of Physics, Islamabad (Pakistan); Javed Akhtar, M., E-mail: javedakhtar6@gmail.com [EMMG, Physics Division, PINSTECH, P.O. Nilore, Islamabad (Pakistan)

    2015-07-28

    We have employed density functional theory to study the C60/ZnPc interface with face-on orientation, which has recently been tailored experimentally. For this purpose, adsorption of ZnPc on C60 has been studied, while taking into account different orientations of C60. Out of various adsorption sites investigated, 6:6 C-C bridge position in apex configuration of C60 has been found energetically the most favourable one with C60-ZnPc adsorption distance of ∼2.77 Å. The adsorption of ZnPc on C60 ensues both charge re-organization and charge transfer at the interface, resulting in the formation of interface dipole. Moreover, by comparing results with that of C60/CuPc interface, we show that the direction of interface dipole can be tuned by the change of the central atom of the phthalocyanine molecule. These results highlight the complexity of electronic interactions present at the C60/Phthalocyanine interface.

  5. Magnetic properties and pairing tendencies of the iron-based superconducting ladder BaFe2S3 : Combined ab initio and density matrix renormalization group study

    Science.gov (United States)

    Patel, Niravkumar D.; Nocera, Alberto; Alvarez, Gonzalo; Arita, Ryotaro; Moreo, Adriana; Dagotto, Elbio

    2016-08-01

    The recent discovery of superconductivity under high pressure in the two-leg ladder compound BaFe2S3 [H. Takahashi et al., Nat. Mater. 14, 1008 (2015), 10.1038/nmat4351] opens a broad avenue of research, because it represents the first report of pairing tendencies in a quasi-one-dimensional iron-based high-critical-temperature superconductor. Similarly, as in the case of the cuprates, ladders and chains can be far more accurately studied using many-body techniques and model Hamiltonians than their layered counterparts, particularly if several orbitals are active. In this publication, we derive a two-orbital Hubbard model from first principles that describes individual ladders of BaFe2S3 . The model is studied with the density matrix renormalization group. These first reported results are exciting for two reasons: (i) at half-filling, ferromagnetic order emerges as the dominant magnetic pattern along the rungs of the ladder, and antiferromagnetic order along the legs, in excellent agreement with neutron experiments; and (ii) with hole doping, pairs form in the strong coupling regime, as found by studying the binding energy of two holes doped on the half-filled system. In addition, orbital selective Mott phase characteristics develop with doping, with only one Wannier orbital receiving the hole carriers while the other remains half-filled. These results suggest that the analysis of models for iron-based two-leg ladders could clarify the origin of pairing tendencies and other exotic properties of iron-based high-critical-temperature superconductors in general.

  6. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, Gianluca; Brocks, Geert; Brink, van den Jeroen

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic mome

  7. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, G.; Brocks, G.; van den Brink, J.

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic

  8. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, G.; Brocks, G.; van den Brink, J.

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic mome

  9. Ab-initio study of magnetic properties and phase transitions in Ga (Mn) N with Monte Carlo approach

    Energy Technology Data Exchange (ETDEWEB)

    Sbai, Y.; Ait Raiss, A.; Salmani, E. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Bahmad, L., E-mail: Bahmad@fsr.ac.ma [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Benyoussef, A. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco); Hassan II Academy of Science and Technology, Rabat (Morocco)

    2015-12-15

    On the basis of ab-initio calculations and Monte Carlo simulations the magnetic and electronic properties of Gallium nitride (GaN) doped with the transition metal Manganese (Mn) were studied. The ab initio calculations were done using the AKAI–KKR–CPA method within the Local Density Approximation (LDA) approximation. We doped our Diluted Magnetic Semiconductor (DMS), with different concentrations of magnetic impurities Mn and plotted the density of state (DOS) for each one. Showing a half-metallic behavior and ferromagnetic state especially for Ga{sub 0.95}Mn{sub 0.05}N making this DMS a strong candidate for spintronic applications. Moreover, the magnetization and susceptibility of our system as a function of the temperature has been calculated and give for various system size L to study the size effect. In addition, the transition temperature was deduced from the peak of the susceptibility. The Ab initio results are in good agreement with literature especially for (x=0.05) of Mn which gives the most interesting results. - Highlights: • The AKAI–KKR–CPA method has been applied to study the doped compound GaN:Mn. • The local density approximation (LDA) has been applied. • The ab-initio calculations have been performed. • The density of states (DOS) have been plotted for differents doping concentrations, using Monte Carlo simulations.

  10. Structural, dynamical, electronic, and bonding properties of laser-heated silicon: An ab initio molecular-dynamics study

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1997-01-01

    The method of ab initio molecular dynamics, based on finite-temperature density-functional theory, is used to simulate laser heating of crystalline silicon. We found that a high concentration of excited electrons dramatically weakens the covalent bonding. As a result the system undergoes a melting t

  11. Electronic and optical properties of the SiB{sub 2}O{sub 4} (B=Mg, Zn, and Cd) spinel oxides: An ab initio study with the Tran–Blaha-modified Becke–Johnson density functional

    Energy Technology Data Exchange (ETDEWEB)

    Allali, D. [Laboratory for Developing New Materials and their Characterization, University of Setif 1, 19000 Setif (Algeria); Bouhemadou, A., E-mail: a_bouhemadou@yahoo.fr [Laboratory for Developing New Materials and their Characterization, University of Setif 1, 19000 Setif (Algeria); Safi, E. Muhammad Abud Al [Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Bin-Omran, S. [Department of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Department of Physics, Faculty of Science and Humanitarian Studies, Salman Bin Abdalaziz University, Alkharj 11942 (Saudi Arabia); Chegaar, M. [Department of Physics, Faculty of Science, University of Setif 1, 19000 Setif (Algeria); Khenata, R. [Laboratoire de Physique Quantique et de Modélisation Mathématique (LPQ3M), Département de Technologie, Université de Mascara, 29000 Mascara (Algeria); Reshak, A.H. [New Technologies-Research Center, University of West Bohemia, Univerzitni 8, 306 14 Pilson (Czech Republic); Center of Excellence Geopolymer and Green Technology, School of Material Engineering, University Malaysia Perlis, 01007 Kangar, Perlis (Malaysia)

    2014-06-15

    We report ab initio density functional theory calculations of the structural, electronic and optical properties of the spinel oxides SiMg{sub 2}O{sub 4}, SiZng{sub 2}O{sub 4}, and SiCd{sub 2}O{sub 4} using the full-potential linearized augmented plane-wave method. The structural parameters calculated using both the local density and generalized gradient approximations to the exchange-correlation potential are consistent with the literature data. To calculate the electronic properties, the exchange-correlation potential is treated with various functionals, and we find that the newly developed Tran–Blaha-modified Becke–Johnson functional significantly improves the band gap. We predict a direct band gap in all of the considered SiB{sub 2}O{sub 4} compounds, and the band gaps continuously decrease as the atomic size of the B element increases. The decrease in the fundamental direct band gap (Γ–Γ) from SiMg{sub 2}O{sub 4} to SiZn{sub 2}O{sub 4} to SiCd{sub 2}O{sub 4} can be attributed to p–d mixing in the upper valence bands of SiZn{sub 2}O{sub 4} and SiCd{sub 2}O{sub 4}. The lowest conduction band is well dispersive, similar to that found for transparent conducting oxides such as ZnO. This band is mainly defined by the s and p electrons of the Si and B (B=Mg, Zn, Cd) atoms. The topmost valence band is considerably less dispersive and is defined by O-2p and B–d electrons. The charge-carrier effective masses are evaluated at the topmost valence band and at the bottommost conduction band that were calculated. The frequency-dependent complex dielectric function, absorption coefficient, refractive index, extinction coefficient, reflectivity and electron energy loss function were estimated. We find that the value of the zero-frequency limit of the dielectric function ε(0) increases as the band gap decreases. The origins of the peaks and structures in the optical spectra are determined in terms of the calculated energy band structures.

  12. A Review on Ab Initio Approaches for Multielectron Dynamics

    CERN Document Server

    Ishikawa, Kenichi L

    2015-01-01

    In parallel with the evolution of femtosecond and attosecond laser as well as free-electron laser technology, a variety of theoretical methods have been developed to describe the behavior of atoms, molecules, clusters, and solids under the action of those laser pulses. Here we review major ab initio wave-function-based numerical approaches to simulate multielectron dynamics in atoms and molecules driven by intense long-wavelength and/or ultrashort short-wavelength laser pulses. Direct solution of the time-dependent Schr\\"odinger equation (TDSE), though its applicability is limited to He, ${\\rm H}_2$, and Li, can provide an exact description and has been greatly contributing to the understanding of dynamical electron-electron correlation. Multiconfiguration self-consistent-field (MCSCF) approach offers a flexible framework from which a variety of methods can be derived to treat both atoms and molecules, with possibility to systematically control the accuracy. The equations of motion of configuration interactio...

  13. Ab initio Molecular Dynamics Study on Small Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    叶林晖; 刘邦贵; 王鼎盛

    2001-01-01

    Ab initio molecular dynamics simulations are performed on small single wall nanotubes. By structural relaxation,the equilibrium C-C bond lengths and bond angles are determined. Our result shows that for both zigzag and armchair nanotubes there are two nonequivalent bond lengths. One bond stretches from that of the graphene sheet, while the other shrinks. Small variations on bond angles are also shown. Energy bands are calculated for the optimized structures. It is found that the intrinsic curvature of the very small nanotube greatly modifies the energy band which can no longer be well described in the tight-binding zone-folding picture. In our calculation very small nanotubes are metallic. The energy per atom fits quite well with the relation of E(R) = E0 + f/R2 even for the extreme small radius. The implications of the results on the properties of small nanotubes are discussed.

  14. Ab initio quantum dynamics using coupled-cluster.

    Science.gov (United States)

    Kvaal, Simen

    2012-05-21

    The curse of dimensionality (COD) limits the current state-of-the-art ab initio propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schrödinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster, and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given.

  15. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Kolorenč, Přemysl, E-mail: kolorenc@mbox.troja.mff.cuni.cz [Charles University in Prague, Faculty of Mathematics and Physics, Institute of Theoretical Physics, V Holešovičkách 2, 180 00 Prague (Czech Republic); Sisourat, Nicolas [Sorbonne Universités, UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France)

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.

  16. Ab initio and kinetic modeling studies of formic acid oxidation

    DEFF Research Database (Denmark)

    Marshall, Paul; Glarborg, Peter

    2015-01-01

    A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism...... as the fate of HOCO, determines the oxidation rate of formic acid. At lower temperatures HO2, formed from HOCO + O2, is an important chain carrier and modeling predictions become sensitive to the HOCHO + HO2 reaction. © 2014 The Combustion Institute....... on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well...

  17. Ab initio study of II-(VI){sub 2} dichalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, P; Vidal, J; Lincot, D, E-mail: polsson@kth.se [Institut de R and D sur l' energie photovoltaique (IRDEP), UMR 7174-EDF-CNRS-ENSCP, 6 quai Watier, 78401 Chatou Cedex (France)

    2011-10-12

    The structural stabilities of the (Zn,Cd)(S,Se,Te){sub 2} dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe{sub 2} pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications. (paper)

  18. Ab initio quantum dynamics using coupled-cluster

    CERN Document Server

    Kvaal, Simen

    2012-01-01

    The curse of dimensionality (COD) limits the current state-of-the-art {\\it ab initio} propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schr\\"odinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster (OATDCC), and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given.

  19. Ab initio study of the transition-metal carbene cations

    Institute of Scientific and Technical Information of China (English)

    李吉海; 冯大诚; 冯圣玉

    1999-01-01

    The geometries and bonding characteristics of the first-row transition-metal carbene cations MCH2+ were investigated by ab initio molecular orbital theory (HF/LANL2DZ). All of MCH2+ are coplanar. In the closed shell structures the C bonds to M with double bonds; while in the open shell structures the partial double bonds are formed, because one of the σ and π orbitals is singly occupied. It is mainly the π-type overlap between the 2px orbital of C and 4px, 3dxz, orbitals of M+ that forms the π orbitals. The dissociation energies of C—M bond appear in periodic trend from Sc to Cu. Most of the calculated bond dissociation energies are close to the experimental ones.

  20. Ab initio study of structural, electronic, and thermal properties of Ir1-xRhx alloys

    Directory of Open Access Journals (Sweden)

    Sh. Ahmed

    2015-06-01

    Full Text Available The structural, electronic, mechanical and thermal properties of Ir1-xRhx alloys was studied systematically using ab initio density functional theory at different concentration (x = 0.00, 0.25, 0.50, 0.75, 1.00. The Special Quasirandom Structure method was used to make the alloys with FCC structure with four atoms per unit cell. The ground state properties such as lattice constant and bulk modulus were calculated to find the equilibrium atomic position for stable alloys. The calculated ground state properties are in good agreement with the experimental and previously presented other theoretical data. The electronic band structure and density of states were calculated to study the electronic properties for these alloys at different concentration. The electronic properties substantiate metallic behavior of alloys. The first principle density functional perturbation theory as implemented in quasiharmonic approximation was used for the calculation of thermal properties. We have calculated the thermal properties such the Debye temperatures, vibration energy, entropy, constant-volume specific heat and internal energy. The ab initio linear-response method was used for phonon densities of states calculations.

  1. Improved Ab Initio Molecular Dynamics by Minimal Biasing with Experimental Data

    CERN Document Server

    White, Andrew D; Hocky, Glen M; Voth, Gregory A

    2016-01-01

    Accounting for electrons and nuclei simultaneously is a key goal of computer simulation via ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce the properties of systems such as water due to inaccuracies in the underlying electronic density functionals, shortcomings that are often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy-based approach to directly incorporate limited experimental data via a minimal bias. The biased AIMD simulations of both water and of an excess proton in water are shown to give significantly improved properties for both the biased and unbiased observables.

  2. Structural Features of Boron-Doped Si(113) Surfaces Simulated by ab initio Calculations

    Institute of Scientific and Technical Information of China (English)

    LIAO Long-Zhong; LIU Zheng-Hui; ZHANG Zhao-Hui

    2008-01-01

    Based on ab initio calculations, boron-doped Si(113) surfaces have been simulated and atomic structures of the surfaces have been proposed. It has been determined that surface features of empty and filled states that are separately localized at pentamers and adatoms indicates a low surface density of B atoms, while it is attributed to heavy doping of B atoms at the second layer that pentamers and adatoms are both present in an image of scanning tunnelling microscopy. B doping at the second layer should be balanced by adsorbed B or Si atoms beside the adatoms and inserted B interstitials below the adatoms.

  3. Novel silicon allotropes for photovoltaic applications from ab initio structure prediction

    Science.gov (United States)

    Amsler, Maximilian; Goedecker, Stefan; Botti, Silvana; Marques, Miguel A. L.

    2015-03-01

    Sophisticated structure prediction methods have been developed and become essential tools when theoretically designing new materials with desired properties. Their successful applications to many systems at various conditions and increasing computational power have strongly contributed to their popularity. However, an accurate prediction from ab initio calculations still remains an extremely challenging task. The Minima Hopping Method is a powerful tool to find low energy structures given only the chemical composition of a system and allows the prediction of structures at any boundary condition. I will present the results of our studies on low density silicon phases with potential use in photovoltaic applications.

  4. Ab initio studies on the mechanic and magnetic properties of PdHx

    Institute of Scientific and Technical Information of China (English)

    Cui Xin; Liang Xi-Xia; Wang Jian-Tao; Zhao Guo-Zhong

    2011-01-01

    Based on ab initio total energy calculations, the structural, electronic, mechanic, and magnetic properties of PdHx are investigated. It is found that bulk modulus of PdHx is larger than the metal Pd with the hydrogen storage except Pd4H2. The calculated results for the magnetic moments show that the hydrogen addition weakens the magnetic properties of the PdHx systems. A strong magneto-volume effect is found in PdHx structures as well as Pd. The transition from paramagnetism to ferromagnetism is discussed. The corresponding densities of states for both structures are also shown to understand the magnetic behaviour.

  5. Ab initio study of the EFG at the N sites in imidazole

    Energy Technology Data Exchange (ETDEWEB)

    Brown Goncalves, Marcos, E-mail: browngon@if.usp.br [Universidade de Sao Paulo, Instituto de Fisica (Brazil); Di Felice, R. [National Center on Nanostructures and Biosystems at Surfaces (S3) of INFM-CNR (Italy); Poleshchuk, O. Kh. [Tomsk State Pedagogical University (Russian Federation); Petrilli, H. M. [Universidade de Sao Paulo, Instituto de Fisica (Brazil)

    2008-01-15

    We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

  6. Orbital free ab initio study of static and dynamic properties of some liquid transition metals

    Directory of Open Access Journals (Sweden)

    Bhuiyan G. M.

    2017-01-01

    Full Text Available Several static and dynamic properties of liquid transition metals Cr, Mn and Co are studied for the first time using the orbital free ab-initio molecular dynamics simulation (OF-AIMD. This method is based on the density functional theory (DFT which accounts for the electronic energy of the system whereas the interionic forces are derived from the electronic energy via the Hellman-Feynman theorem. The external energy functional is treated with a local pseudopotential. Results are reported for static structure factors, isothermal compressibility, diffusion coeffcients, sound velocity and viscosity and comparison is performed with the available experimental data and other theoretical calculations.

  7. Ab initio quasiparticle energies in 2H, 4H, and 6H SiC

    Science.gov (United States)

    Ummels, R. T. M.; Bobbert, P. A.; van Haeringen, W.

    1998-09-01

    Ab initio quasiparticle energies are calculated for the 2H, 4H, and 6H polytypes of SiC within the GW approximation for the self-energy. The starting point is a calculation within the pseudopotential local-density approximation framework. The calculated fundamental gaps of 3.15, 3.35, and 3.24 eV for 2H, 4H, and 6H SiC, respectively, show very good agreement with experimental data. The energy dependence of the screened interaction is modeled by a plasmon pole model from which the plasmon band structures are obtained.

  8. Ab initio study of energy-level alignments in polymer-dye blends

    Science.gov (United States)

    Pasveer, W. F.; Bobbert, P. A.; Michels, M. A. J.; Langeveld-Voss, B. M. W.; Schoo, H. F. M.; Bastiaansen, J. J. A. M.

    2003-11-01

    Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and polyfluorene. Special attention is paid to the trends in these energies with variation of the sidegroups of the dyes as observed in cyclic-voltammetry measurements. From the energy-level alignments between dye and polymer we can understand and predict electron and hole trapping, crucial processes for the functioning of light-emitting devices based on these blends.

  9. Ab initio study of spin-dependent transport in carbon nanotubes with iron and vanadium adatoms

    DEFF Research Database (Denmark)

    Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka

    2008-01-01

    We present an ab initio study of spin-dependent transport in armchair carbon nanotubes with transition metal adsorbates: iron or vanadium. The method based on density functional theory and nonequilibrium Green's functions is used to compute the electronic structure and zero-bias conductance...... (majority or minority) being scattered depends on the adsorbate and is explained in terms of d-state filling. We contrast the single-walled carbon nanotube results to the simpler case of the adsorbate on a flat graphene sheet with periodic boundary conditions and corresponding width in the zigzag direction...

  10. Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

    We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

  11. From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia

    CERN Document Server

    Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik

    2003-01-01

    The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...

  12. Emergence of rotational bands in ab initio no-core configuration interaction calculations

    CERN Document Server

    Caprio, M A; Vary, J P; Smith, R

    2015-01-01

    Rotational bands have been observed to emerge in ab initio no-core configuration interaction (NCCI) calculations for p-shell nuclei, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. We investigate the ab initio emergence of nuclear rotation in the Be isotopes, focusing on 9Be for illustration, and make use of basis extrapolation methods to obtain ab initio predictions of rotational band parameters for comparison with experiment. We find robust signatures for rotational motion, which reproduce both qualitative and quantitative features of the experimentally observed bands.

  13. Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules

    Science.gov (United States)

    Shiga, Motoyuki; Nakayama, Akira

    2008-01-01

    The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.

  14. Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

    Science.gov (United States)

    Good, Brian S.

    2004-01-01

    We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

  15. Novel zinc(II) and copper(II) complexes of a Mannich base derived from lawsone: Synthesis, single crystal X-ray analysis, ab initio density functional theory calculations and vibrational analysis.

    Science.gov (United States)

    Neves, Amanda P; Vargas, Maria D; Téllez Soto, Claudio A; Ramos, Joanna M; Visentin, Lorenzo do C; Pinheiro, Carlos B; Mangrich, Antônio S; de Rezende, Edivaltrys I P

    2012-08-01

    Zinc(II) and copper(II) complexes of a tridentate Mannich base L1 derived from 2-hydroxy-1,4-naphthoquinone, pyridinecarboxyaldehyde and 2-aminomethylpyridine, [ZnL1Cl(2)]·H(2)O 1 and [CuL1Cl(2)]·2H(2)O 2, have been synthesized and fully characterized. The structure of complex 1 has been elucidated by a single crystal X-ray diffraction study: the zinc atom is pentacoordinate and the coordination geometry is a distorted square base pyramid, with a geometric structural parameter τ equal to 0.149. Vibrational spectroscopy and ab initio DFT calculations of both compounds have confirmed that the two complexes exhibit similar structures. Full assignment of the vibrational spectra was also supported by careful analysis of the distorted geometries generated by the normal modes. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Experimental and ab initio investigations on textured Li–Mn–O spinel thin film cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, J., E-mail: Julian.Fischer@kit.edu [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Music, D. [RWTH Aachen University, Materials Chemistry, Kopernikusstrasse 10, 52074 Aachen (Germany); Bergfeldt, T.; Ziebert, C.; Ulrich, S.; Seifert, H.J. [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany)

    2014-12-01

    This paper describes the tailored preparation of nearly identical lithium–manganese–oxide thin film cathodes with different global grain orientations. The thin films were synthesized by rf magnetron sputtering from a LiMn{sub 2}O{sub 4}-target in a pure argon plasma. Under appropriate processing conditions, thin films with a cubic spinel structure and a nearly similar density and surface topography but different grain orientation, i.e. (111)- and (440)-textured films, were achieved. The chemical composition was determined by inductively coupled plasma optical emission spectroscopy and carrier gas hot extraction. The constitution- and microstructure were evaluated by X-ray diffraction and Raman spectroscopy. The surface morphology and roughness were investigated by scanning electron and atomic force microscopy. The differently textured films represent an ideal model system for studying potential effects of grain orientation on the lithium ion diffusion and electrochemical behavior in LiMn{sub 2}O{sub 4}-based thin films. They are nearly identical in their chemical composition, atomic bonding behavior, surface-roughness, morphology and thickness. Our initial ab initio molecular dynamics data indicate that Li ion transport is faster in (111)-textured structure than in (440)-textured one. - Highlights: • Thin film model system of differently textured cubic Li–Mn–O spinels. • Investigation of the Li–Mn–O thin film mass density by X-ray reflectivity. • Ab initio molecular dynamics simulation on Li ion diffusion in LiMn{sub 2}O{sub 4}.

  17. Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

    Science.gov (United States)

    Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

    2017-02-01

    The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

  18. A New Generation of Cool White Dwarf Atmosphere Models Using Ab Initio Calculations

    Science.gov (United States)

    Blouin, S.; Dufour, P.; Kowalski, P. M.

    2017-03-01

    Due to their high photospheric density, cool helium-rich white dwarfs (particularly DZ, DQpec and ultracool) are often poorly described by current atmosphere models. As part of our ongoing efforts to design atmosphere models suitable for all cool white dwarfs, we investigate how the ionization ratio of heavy elements and the H2-He collision-induced absorption (CIA) spectrum are altered under fluid-like densities. For the conditions encountered at the photosphere of cool helium-rich white dwarfs, our ab initio calculations show that the ionization of most metals is inhibited and that the H2-He CIA spectrum is significantly distorted for densities higher than 0.1 g/cm3.

  19. A New Generation of Cool White Dwarf Atmosphere Models Using Ab Initio Calculations

    CERN Document Server

    Blouin, Simon; Kowalski, Piotr M

    2016-01-01

    Due to their high photospheric density, cool helium-rich white dwarfs (particularly DZ, DQpec and ultracool) are often poorly described by current atmosphere models. As part of our ongoing efforts to design atmosphere models suitable for all cool white dwarfs, we investigate how the ionization ratio of heavy elements and the H$_2$-He collision-induced absorption (CIA) spectrum are altered under fluid-like densities. For the conditions encountered at the photosphere of cool helium-rich white dwarfs, our ab initio calculations show that the ionization of most metals is inhibited and that the H$_2$-He CIA spectrum is significantly distorted for densities higher than 0.1 g/cm$^3$.

  20. Ab initio study of heterojunction discontinuities in the ZnO/Cu2O system

    Science.gov (United States)

    Zemzemi, M.; Alaya, S.; Ben Ayadi, Z.

    2014-06-01

    Solar cells based on transparent conductive oxides such as ZnO/Cu2O constitute a very advanced way to build high-performance cells. In this work, we are interested in the characterization of the interface through nanoscale modeling based on ab initio approaches (density functional theory, local density approximation, and pseudopotential). This work aims to build a supercell containing a heterojunction ZnO/Cu2O and study the structural properties and the discontinuity of the valence band (band offset) from a semiconducting to another phase. We build a zinc oxide in the wurtzite structure along [0001] on which we place the copper oxide in the hexagonal (CdI2-type) structure. We choose the method of Van de Walle and Martin to calculate the energy offset. This approach fits well the density functional theory. Our calculation of the band offset gives a value that corresponds to other experimental and theoretical values.

  1. Time-resolved photoelectron spectroscopy and ab initio multiple spawning studies of hexamethylcyclopentadiene

    DEFF Research Database (Denmark)

    Wolf, T. J. A.; Kuhlman, Thomas Scheby; Schalk, O.

    2014-01-01

    Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom....

  2. Hydrogen adsorption on boron doped graphene: an {\\it ab initio} study

    OpenAIRE

    Miwa, R. H.; Martins, T B; Fazzio, A.

    2007-01-01

    The electronic and structural properties of (i) boron doped graphene sheets, and (ii) the chemisorption processes of hydrogen adatoms on the boron doped graphene sheets have been examined by {\\it ab initio} total energy calculations.

  3. Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures

    Science.gov (United States)

    Debernardi, Alberto; Marchetti, Luigi

    2016-06-01

    Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.

  4. Engineering Room-temperature Superconductors Via ab-initio Calculations

    Science.gov (United States)

    Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen

    The BCS, or bosonic model of superconductivity, as Little and Ginzburg have first argued, can bring in superconductivity at room temperatures in the case of high-enough frequency of bosonic mode. It was further elucidated by Kirzhnitset al., that the condition for existence of high-temperature superconductivity is closely related to negative values of the real part of the dielectric function at finite values of the reciprocal lattice vectors. In view of these findings, the task is to calculate the dielectric function for real materials. Then the poles of this function will indicate the existence of bosonic excitations which can serve as a "glue" for Cooper pairing, and if the frequency is high enough, and the dielectric matrix is simultaneously negative, this material is a good candidate for very high-Tc superconductivity. Thus, our approach is to elaborate a methodology of ab-initio calculation of the dielectric function of various materials, and then point out appropriate candidates. We used the powerful codes (TDDF with the DP package in conjunction with ABINIT) for computing dielectric responses at finite values of the wave vectors in the reciprocal lattice space. Though our report is concerned with the particular problem of superconductivity, the application range of the data processing methodology is much wider. The ability to compute the dielectric function of existing and still non-existing (though being predicted!) materials will have many more repercussions not only in fundamental sciences but also in technology and industry.

  5. Rational design of electrolyte components by ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Johansson, Patrik; Jacobsson, Per [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)

    2006-02-28

    This paper is a small review of the use of computer simulations and especially the use of standard quantum-mechanical ab initio electronic structure calculations to rationally design and investigate different choices of chemicals/systems for lithium battery electrolytes. Covered systems and strategies to enhance the performance of electrolytes will range from assisting the interpretation of vibrational spectroscopy experiments over development of potentials for molecular dynamics simulations, to the design of new lithium salts and the lithium ion coordination in liquid, polymer, and gel polymer electrolytes. Examples of studied properties include the vibrational spectra of anions and ion pairs to characterize the nature and extent of the interactions present, the lithium ion affinities of anions, important for the salt solvation and the ability to provide a high concentration of charge carriers, the HOMO energies of the anions to estimate the stability versus oxidation, the anion volumes that correlate to the anion mobility, the lithium ion coordination and dynamics to reveal the limiting steps of lithium ion transport, etc. (author)

  6. Ab initio evaluations of the He solubility in liquid Li

    Energy Technology Data Exchange (ETDEWEB)

    Sedano, Luis A. [EURATOM-CIEMAT Assoc., Materials for Fusion Program, Bd. 43 P0.04, Avda. Complutense 22, 28040 Madrid (Spain)]. E-mail: luis.sedano@ciemat.es; Hassanein, Ahmed [Argonne Nat. Lab, 9700 South Class Av., Argonne, IL (United States)]. E-mail: hassanein@anl.gov; Sanz, Javier [ETSII-UNED, c/Juan del Rosal, 12, 28040 Madrid (E) (Spain)]. E-mail: jsanz@ind.UNED.es

    2005-11-15

    Modified embedding atom methods (MEAM) are developed to have predictions of the partial molar heat of solution (-H{sub s}) by direct simulation of metal cohesion, He-metal and He-He interaction. Transitions from crystalline Li to configurations, having the liquid Li structure's factors (h-bar (q)), are simulated ab initio. Once h-bar (q) reproduced, He atoms are added, one by one, to the Li system. Parallel lines for each case, with slopes clearly independent on the number of He atoms in the system, are obtained for energy versus pressure at given temperatures. Average differences between two adjacent parallels at zero pressure, once kinetic energy of the system discounted, represents the energy gained by an He atom when added to the Li system, related to the solution energy -H{sub s}. The molar excess entropy of gas in solution (S-bar {sub l}{sup ex}) is previously evaluated following diverse fundamental approaches: a 'thermodynamic liquid-hole' (TL-H) model for alkali liquids and a statistical-mechanics (Neff and McQuarrie's) model (SMM). Between 600 and 900 deg. C, a typical range of interest for the use of Li in fusion technology, the computed values for the (He) Henry's constant in Li range from 8x10{sup -14} to 10{sup -13} at. fr. Pa{sup -1}.

  7. Ab initio modeling of decomposition in iron based alloys

    Science.gov (United States)

    Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.

    2016-12-01

    This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.

  8. The Hydration Structure of Carbon Monoxide by Ab Initio Methods

    CERN Document Server

    Awoonor-Williams, Ernest

    2016-01-01

    The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO--H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface it incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration is in good agreement with experiment (9.3 kJ/mol calc. vs 10.7 kJ/mol exptl.). The calculated diffusivity of CO(aq) in TIP3P-model water was 5.19 x 10-5 cm2/s ...

  9. An ab initio Non-Equilibrium Green Function Approach to Charge Transport: Dithiolethine

    Institute of Scientific and Technical Information of China (English)

    Alexander Schnurpfeil; SONG Bo; Martin Albrecht

    2006-01-01

    @@ We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wavefunction-based full ab initio description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green function formalism. Our procedure is demonstrated for a dithiolethine molecule located between silver electrodes. The main conducting channel is identified and the full current-voltage characteristic is calculated.

  10. Efficient Ab-Initio Electron Transport Calculations for Heterostructures by the Nonequilibrium Green’s Function Method

    Directory of Open Access Journals (Sweden)

    Hirokazu Takaki

    2014-01-01

    Full Text Available We present an efficient computation technique for ab-initio electron transport calculations based on density functional theory and the nonequilibrium Green’s function formalism for application to heterostructures with two-dimensional (2D interfaces. The computational load for constructing the Green’s functions, which depends not only on the energy but also on the 2D Bloch wave vector along the interfaces and is thus catastrophically heavy, is circumvented by parallel computational techniques with the message passing interface, which divides the calculations of the Green’s functions with respect to energy and wave vectors. To demonstrate the computational efficiency of the present code, we perform ab-initio electron transport calculations of Al(100-Si(100-Al(100 heterostructures, one of the most typical metal-semiconductor-metal systems, and show their transmission spectra, density of states (DOSs, and dependence on the thickness of the Si layers.

  11. Ab-initio vibrational properties of transition metal chalcopyrite alloys determined as high-efficiency intermediate-band photovoltaic materials

    Energy Technology Data Exchange (ETDEWEB)

    Palacios, P. [Instituto de Energia Solar and Dpt. de Tecnologias Especiales, ETSI de Telecomunicacion, UPM. Ciudad Universitaria s/n, 28040 Madrid (Spain); Instituto de Catalisis y Petroleoquimica, CSIC. Marie Curie 2, Cantoblanco, 28049 Madrid (Spain)], E-mail: pablop@etsit.upm.es; Aguilera, I.; Wahnon, P. [Instituto de Energia Solar and Dpt. de Tecnologias Especiales, ETSI de Telecomunicacion, UPM. Ciudad Universitaria s/n, 28040 Madrid (Spain)

    2008-08-30

    In this work, we present frozen phonon and linear response ab-initio research into the vibrational properties of the CuGaS{sub 2} chalcopyrite and transition metal substituted (CuGaS{sub 2})M alloys. These systems are potential candidates for developing a novel solar-cell material with enhanced optoelectronic properties based in the implementation of the intermediate-band concept. We have previously carried out ab-initio calculations of the electronic properties of these kinds of chalcopyrite metal alloys showing a narrow transition metal band isolated in the semiconductor band gap. The substitutes used in the present work are the 3d metal elements, Titanium and Chromium. For the theoretical calculations we use standard density functional theory at local density and generalized gradient approximation levels. We found that the optical phonon branches of the transition metal chalcopyrite, are very sensitive to the specific bonding geometry and small changes in the transition metal environment.

  12. Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides

    Science.gov (United States)

    Sharma, Vinit; Krogel, Jaron T.; Kent, P. R. C.; Reboredo, Fernando A.

    One of the critical scientific challenges of contemporary research is to obtain an accurate theoretical description of the electronic properties of strongly correlated systems such as transition metal oxides and rare-earth compounds, since state-of-art ab-initio methods based on approximate density functionals are not always sufficiently accurate. Quantum Monte Carlo (QMC) methods, which use statistical sampling to evaluate many-body wave functions, have the potential to answer this challenge. Owing to the few fundamental approximations made and the direct treatment of electron correlation, QMC methods are among the most accurate electronic structure methods available to date. We assess the accuracy of the diffusion Monte Carlo method in the case of rocksalt manganese oxide (MnO). We study the electronic properties of this strongly-correlated oxide, which has been identified as a suitable candidate for many applications ranging from catalysts to electronic devices. ``This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.'' Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides.

  13. Ab initio study of the structural properties of acetonitrile-water mixtures

    Science.gov (United States)

    Chen, Jinfan; Sit, Patrick H.-L.

    2015-08-01

    Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.

  14. Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces

    Science.gov (United States)

    Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos

    2016-08-01

    Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.

  15. Thermodynamic assessment of the Ho–Te system supported by ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Ghamri, H.; Belgacem-Bouzida, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Djaballah, Y., E-mail: ydjaballah@yahoo.fr [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Hidoussi, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria)

    2013-03-05

    Highlights: ► We calculated enthalpies of formation of the HoTe and Ho{sub 2}Te{sub 5} compounds by using ab initio method. ► We modeled the Gibbs energy of the HoTe intermediate phase for the first time. ► The thermodynamic parameters of the all phases existing in the system were determined. ► The complete phase diagram of the system (Ho–Te) is calculated. -- Abstract: The phase diagram of the Ho–Te binary system has been assessed by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data of the phase equilibria and enthalpies of formation from ab initio electronic-structure calculations within the framework of density-functional theory. Reasonable models were constructed for all the phases of the system. The liquid phase was described as the substitutional solution model with excess energy expressed by Redlich–Kister polynomial. The compounds Ho{sub 2}Te{sub 5} and HoTe{sub 3} were expressed as stoichiometric phases. The (HoTe) phase was modeled by two-sublattices; (Ho,Va){sub 1}(Te){sub 1}. A consistent set of thermodynamic parameters has been derived, and calculated phase diagram was compared with the experimental data. A good agreement between the calculated results and experimental data was obtained.

  16. Ab initio calculations of the optical properties of crystalline and liquid InSb

    Energy Technology Data Exchange (ETDEWEB)

    Sano, Haruyuki, E-mail: h-sano@ishikawa-nct.ac.jp [National Institute of Technology, Ishikawa College, Kitacyujo, Tsubata, Ishikawa 929-0392 (Japan); Mizutani, Goro [School of Materials Science, Japan Advanced Institute of Science and Technology, Tatsunokuchi, Ishikawa 923-1292 (Japan)

    2015-11-15

    Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.

  17. Ab initio study of pressure induced structural and electronic properties in TmPo

    Energy Technology Data Exchange (ETDEWEB)

    Makode, Chandrabhan, E-mail: cbmakode@gmail.com; Pataiya, Jagdish; Sanyal, Sankar P. [Department of Physics, Barkatullah University, Bhopal-462026 (India); Panwar, Y. S.; Aynyas, Mahendra [Department of Physics, C.S.A. Govt. P.G. College, Sehore-466001 (India)

    2015-06-24

    We report an ab initio calculation of pressure induced structural phase transition and electronic properties of Thulium Polonide (TmPo).The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). It is found that TmPo is stable in NaCl-type (B{sub 1}-phase) structure to CsCl-type (B{sub 2}-phase) structure of this compound in the pressure range of 7.0 GPa. We also calculate the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure and density of states. From energy diagram it is observed that TmPo exhibit metallic behavior. The calculated values of equilibrium lattice parameter and bulk modulus are in general good agreement.

  18. Ab initio electronic structure, magnetism, and magnetocrystalline anisotropy of UGa2

    Science.gov (United States)

    Diviš, Martin; Richter, Manuel; Eschrig, Helmut; Steinbeck, Lutz

    1996-04-01

    Ab initio electronic structure calculations for the intermetallic compound UGa2 were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5f states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5f states, which have been treated by self-interaction corrected local-density theory. This approach with 5f2 occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant.

  19. {ital Ab initio} electronic structure, magnetism, and magnetocrystalline anisotropy of UGa{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Divis, M. [Department of Metal Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2 (Czech Republic)]|[Max-Planck-Gesellschaft, Research Group ``Electron Systems,`` University of Technology, D-01062 Dresden (Germany); Richter, M.; Eschrig, H.; Steinbeck, L. [Max-Planck-Gesellschaft, Research Group ``Electron Systems,`` University of Technology, D-01062 Dresden (Germany)

    1996-04-01

    {ital Ab} {ital initio} electronic structure calculations for the intermetallic compound UGa{sub 2} were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5{ital f} states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5{ital f} states, which have been treated by self-interaction corrected local-density theory. This approach with 5{ital f}{sup 2} occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant. {copyright} {ital 1996 The American Physical Society.}

  20. High-pressure elastic properties of cubic Ir2P from ab initio calculations

    Science.gov (United States)

    Sun, Xiao-Wei; Bioud, Nadhira; Fu, Zhi-Jian; Wei, Xiao-Ping; Song, Ting; Li, Zheng-Wei

    2016-10-01

    A study of the high-pressure elastic properties of new synthetic Ir2P in the anti-fluorite structure is conducted using ab initio calculations based on density functional theory. The elastic constants C11, C12 and C44 for the cubic Ir2P are obtained by the stress-strain method and the elastic stability calculations under pressure indicate that it is stable at least 100 GPa. Additionally, the electronic density of states, the aggregate elastic moduli, that is bulk modulus, shear modulus, and Young's modulus along with the Debye temperature, Poisson's ratio, and elastic anisotropy factor are all successfully obtained. Moreover, the pressure dependence of the longitudinal and shear wave velocities in three different directions [100], [110], and [111] for Ir2P are also predicted for the first time.

  1. A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data

    CERN Document Server

    Eckl, Bernhard; Hasse, Hans

    2009-01-01

    A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e. vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl...

  2. Ab initio research of stopping power for energetic ions in solids

    Energy Technology Data Exchange (ETDEWEB)

    He, Bin, E-mail: hebin-rc@163.com; Meng, Xu-Jun; Wang, Jian-Guo

    2017-03-01

    A new physical scenario is suggested to estimate the stopping power of energetic α particles in solid-density Be, Na, and Al at room temperature in an ab initio way based on the average atom model. In the scenario the stopping power is caused by the transition of free electrons to higher energy states and the ionization of bound electrons of the atom. Our results are found generally in good agreement with the recommended data in Al, Be and Na as well as the experimental data in Al. A comparison of energy loss with the recent experiment of protons in Be indicates that the scenario is more reasonable than the local density approximation in this case.

  3. Ab initio research of stopping power for energetic ions in solids

    Science.gov (United States)

    He, Bin; Meng, Xu-Jun; Wang, Jian-Guo

    2017-03-01

    A new physical scenario is suggested to estimate the stopping power of energetic α particles in solid-density Be, Na, and Al at room temperature in an ab initio way based on the average atom model. In the scenario the stopping power is caused by the transition of free electrons to higher energy states and the ionization of bound electrons of the atom. Our results are found generally in good agreement with the recommended data in Al, Be and Na as well as the experimental data in Al. A comparison of energy loss with the recent experiment of protons in Be indicates that the scenario is more reasonable than the local density approximation in this case.

  4. Ab initio approach to the ion stopping power at the plasma-solid interface

    Science.gov (United States)

    Bonitz, Michael; Schlünzen, Niclas; Wulff, Lasse; Joost, Jan-Philip; Balzer, Karsten

    2016-10-01

    The energy loss of ions in solids is of key relevance for many applications of plasmas, ranging from plasma technology to fusion. Standard approaches are based on density functional theory or SRIM simulations, however, the applicability range and accuracy of these results are difficult to assess, in particular, for low energies. Here we present an independent approach that is based on ab initio nonequilibrium Green functions theory, e.g. that allows to incorporate electronic correlations effects of the solid. We present the first application of this method to low-temperature plasmas, concentrating on proton and alpha-particle stopping in a graphene layer. In addition to the stopping power we present time-dependent results for the local electron density, the spectral function and the photoemission spectrum that is directly accessible in optical, UV or x-ray diagnostics. http://www.itap.uni-kiel.de/theo-physik/bonitz/.

  5. Femtosecond Laser Processing of Germanium: An Ab Initio Molecular Dynamics Study

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    An ab initio molecular dynamics study of femtosecond laser processing of germanium is presented in this paper. The method based on the finite temperature density functional theory is adopted to probe the structural change, thermal motion of the atoms, dynamic property of the velocity autocorrelation, and the vibrational density of states. Starting from a cubic system at room temperature (300 K) containing 64 germanium atoms with an ordered arrangement of 1.132 nm in each dimension, the femtosecond laser processing is simulated by imposing the Nose Hoover thermostat to the electronic subsystem lasting for ~100 fs and continuing with microcanonical ensemble simulation of ~200 fs. The simulation results show solid, liquid and gas phases of germanium under adjusted intensities of the femtosecond laser irradiation. We find the irradiated germanium distinguishes from the usual germanium crystal by analyzing their melting and dynamic properties.

  6. Minimal parameter implicit solvent model for ab initio electronic structure calculations

    CERN Document Server

    Dziedzic, Jacek; Skylaris, Chris-Kriton; Mostofi, Arash A; Payne, Mike C

    2011-01-01

    We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersion-repulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules show dramatic improvement compared to existing models. Our approach is implemented in, but not restricted to, a linear-scaling density functional theory (DFT) framework, opening the path for self-consistent implicit solvent DFT calculations on systems of unprecedented size, which we demonstrate with calculations on a 2615-atom protein-ligand complex.

  7. Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data

    Science.gov (United States)

    White, Andrew D.; Knight, Chris; Hocky, Glen M.; Voth, Gregory A.

    2017-01-01

    Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD.

  8. Cosmic-Ray Modulation: an Ab Initio Approach

    Science.gov (United States)

    Engelbrecht, N. E.; Burger, R. A.

    2014-10-01

    A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three-dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented.

  9. Lithium Insertion In Silicon Nanowires: An ab Initio Study

    KAUST Repository

    Zhang, Qianfan

    2010-09-08

    The ultrahigh specific lithium ion storage capacity of Si nanowires (SiNWs) has been demonstrated recently and has opened up exciting opportunities for energy storage. However, a systematic theoretical study on lithium insertion in SiNWs remains a challenge, and as a result, understanding of the fundamental interaction and microscopic dynamics during lithium insertion is still lacking. This paper focuses on the study of single Li atom insertion into SiNWs with different sizes and axis orientations by using full ab initio calculations. We show that the binding energy of interstitial Li increases as the SiNW diameter grows. The binding energies at different insertion sites, which can be classified as surface, intermediate, and core sites, are quite different. We find that surface sites are energetically the most favorable insertion positions and that intermediate sites are the most unfavorable insertion positions. Compared with the other growth directions, the [110] SiNWs with different diameters always present the highest binding energies on various insertion locations, which indicates that [110] SiNWs are more favorable by Li doping. Furthermore, we study Li diffusion inside SiNWs. The results show that the Li surface diffusion has a much higher chance to occur than the surface to core diffusion, which is consistent with the experimental observation that the Li insertion in SiNWs is layer by layer from surface to inner region. After overcoming a large barrier crossing surface-to-intermediate region, the diffusion toward center has a higher possibility to occur than the inverse process. © 2010 American Chemical Society.

  10. Efficient conformational space exploration in ab initio protein folding simulation.

    Science.gov (United States)

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel

    2015-08-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.

  11. Resonance and aromaticity: an ab initio valence bond approach.

    Science.gov (United States)

    Rashid, Zahid; van Lenthe, Joop H; Havenith, Remco W A

    2012-05-17

    Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randić's conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.

  12. An investigation of ab initio shell-model interactions derived by no-core shell model

    Science.gov (United States)

    Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing

    2016-09-01

    The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.

  13. Vibrational spectral investigation, NBO, first hyperpolarizability and UV-Vis spectral analysis of 3,5-dichlorobenzonitrile and m-bromobenzonitrile by ab initio and density functional theory methods.

    Science.gov (United States)

    Senthil kumar, J; Jeyavijayan, S; Arivazhagan, M

    2015-02-05

    The FT-IR and FT-Raman spectra of 3,5-dichlorobenzonitrile and m-bromobenzonitrile have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The optimized geometry, wave numbers and intensity of vibrational bonds of title molecules are obtained by ab initio and DFT level of theory with complete relaxation in the potential energy surface using 6-311++G(d, p) basis set. A complete vibrational assignments aided by the theoretical harmonic frequency, analysis have been proposed. The harmonic vibrational frequencies calculated have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The UV-Vis spectral analysis of the molecules has also been done which confirms the charge transfer of the molecules. Furthermore, the first hyperpolarizability and total dipole moment of the molecules have been calculated.

  14. Two-step spin-switchable tetranuclear Fe(II) molecular solid: Ab initio theory and predictions

    Science.gov (United States)

    Maldonado, Pablo; Kanungo, Sudipta; Saha-Dasgupta, Tanusri; Oppeneer, Peter M.

    2013-07-01

    Using density functional theory supplemented with on-site Coulomb U interaction in combination with ab initio molecular dynamics simulations, we investigate the spin-crossover (SCO) properties of a Fe(II) based cyanide-bridged square molecular system, [FeII4(μ-CN)4(bpy)4(tpa)2](PF6)4 (where bpy = 2,2'-bipyridine and tpa = tris(2-pyridylmethyl)amine], exhibiting a two-step SCO transition. The ab initio calculated SCO temperatures are found to show remarkably good agreement with experimentally measured spin conversion temperatures [M. Nihei , Angew. Chem., Int. Ed.1433-785110.1002/anie.200502216 44, 6484 (2005)]. Our theoretical study predicts further chemo switching of the spin state by introduction of guest molecules such as CO2, CS2, and H2O into the porous topology of the system, which would add another dimensionality to this interesting material.

  15. Structure and dynamics of liquid Zn: an analysis of ab-initio simulations

    Directory of Open Access Journals (Sweden)

    del Rio B. G.

    2017-01-01

    Full Text Available The static and dynamic properties of liquid Zn have been studied using an ab initio molecular dynamics method. Results are reported for the thermodynamic states at 723K near which inelastic neutron and x-ray scattering data are available. The calculated static structure shows very good agreement with experimental measurements, including an asymmetric main peak. The dynamic structure reveals the existence of propagating density fluctuations, and the associated dispersion relation has also been calculated. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, qp, as suggested by the recently reported appearance of high frequency transverse waves in several liquid metals under high pressures; the second region is around qp/2, as suggested by inelastic scattering experiments for liquid Zn and other metals.

  16. Structural phase transition of CdTe: an ab initio study.

    Science.gov (United States)

    Alptekin, Sebahaddin

    2013-01-01

    A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in zinc-blende CdTe. We found that CdTe undergoes a structural first-order phase transition to [Formula: see text] (binary β-tin) tetragonal structure in the constant pressure molecular dynamics simulation at 20 GPa. When the pressure was increased to 50 GPa, the phase of tetragonal structure converted to a new Imm2 orthorhombic structure. These phase transformations were also calculated by using the enthalpy calculations. Transition phases, lattice parameters and bulk properties we attained are comparable with experimental and theoretical data.

  17. Pressure-induced phase transition in wurtzite ZnTe: an ab initio study.

    Science.gov (United States)

    Alptekin, Sebahaddin

    2012-03-01

    A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in wurtzite ZnTe. A first-order phase transition from the wurtzite structure to a Cmcm structure was successfully observed in a constant-pressure molecular dynamics simulation. This phase transformation was also analyzed using enthalpy calculations. We also investigated the stability of wurtzite (WZ) and zinc-blende (ZB) phases from energy-volume calculations, and found that both structures show quite similar equations of state and transform into a Cmcm structure at 16 GPa using enthalpy calculations, in agreement with experimental observations. The transition phase, lattice parameters and bulk properties we obtained are comparable with experimental and theoretical data.

  18. High-pressure physical properties of magnesium silicate post-perovskite from ab initio calculations

    Indian Academy of Sciences (India)

    Zi-Jiang Liu; Xiao-Wei Sun; Cai-Rong Zhang; Jian-Bu Hu; Ling-Cang Cai; Qi-Feng Chen

    2012-08-01

    The structure, thermodynamic and elastic properties of magnesium silicate (MgSiO3) post-perovskite at high pressure are investigated with quasi-harmonic Debye model and ab initio method based on the density functional theory (DFT). The calculated structural parameters of MgSiO3 post-perovskite are consistent with the available experimental results and the recent theoretical results. The Debye temperature, heat capacity and thermal expansion coefficient at high pressures and temperatures are predicted using the quasi-harmonic Debye model. The elastic constants are calculated using stress–strain relations. A complete elastic tensor of MgSiO3 post-perovskite is determined in the wide pressure range. The calculated elastic anisotropic factors and directional bulk modulus show that MgSiO3 post-perovskite possesses high elastic anisotropy.

  19. Voltage and capacity control of polyaniline based organic cathodes: An ab initio study

    Science.gov (United States)

    Chen, Yingqian; Manzhos, Sergei

    2016-12-01

    Polyaniline (PANI) is a promising organic cathode material for electrochemical batteries. Its specific capacity is limited by irreversible formation of pernigraniline base, and its energy density is limited by the voltage which could be improved. We present an ab initio study of PANI and PANI functionalized with functional groups which lead to increased voltage and stabilization of the pernigraniline salt. Specifically, the oxidation potential achieved by functionalization with CN on the nitrogen is computed to be 1.3 V higher than that of pristine PANI oligomer, leading to a higher voltage, and the formation of the pernigraniline base is predicted to be simultaneously suppressed, leading to a higher reversible capacity. Therefore, functionalized PANI could be a promising candidate organic cathode for Li-ion batteries.

  20. Ab initio calculation of structure and thermodynamic properties of Zintl aluminide SrAl{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Zhi-Jian [Chongqing Key Laboratory of Micro/Nano Materials Engineering and Technology, Chongqing (China); Chongqing Univ. of Arts and Sciences (China). School of Electrical and Electronic Engineering; China Academy of Engineering Physics (CAEP), Mianyang, Sichuan (China). National Key Lab. of Shock Wave and Detonation Physics; Jia, Li-Jun [Chongqing Univ. of Arts and Sciences Library (China); Xia, Ji-Hong; Tang, Ke; Li, Zhao-Hong [Chongqing Univ. of Arts and Sciences (China). School of Electrical and Electronic Engineering; Sun, Xiao-Wei [Lanzhou Jiaotong Univ. (China). School of Mathematics and Physics; Chen, Qi-Feng [China Academy of Engineering Physics (CAEP), Mianyang, Sichuan (China). National Key Lab. of Shock Wave and Detonation Physics

    2015-07-01

    The structural and thermodynamic properties of the orthorhombic and cubic structure SrAl{sub 2} at pressure and temperature are investigated by using the ab initio plane-wave pseudopotential density functional theory method within the generalised gradient approximation (GGA). The calculated lattice parameters are in agreement with the available experimental data and other theoretical results. The phase transition predicted takes place at 0.5 GPa from the orthorhombic to the cubic structure at zero temperature. The thermodynamic properties of the zinc-blende structure SrAl{sub 2} are calculated by the quasi-harmonic Debye model. The pressure-volume relationship and the variations in the thermal expansion a are obtained systematically in the pressure and temperature ranges of 0-5 GPa and 0-500 K, respectively.

  1. Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.

    Science.gov (United States)

    Šipr, O; Ebert, H; Minár, J

    2015-02-11

    A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.

  2. Ab-initio study of magnetism behavior in TiO2 semiconductor with structural defects

    Science.gov (United States)

    Zarhri, Z.; Houmad, M.; Ziat, Y.; El Rhazouani, O.; Slassi, A.; Benyoussef, A.; El Kenz, A.

    2016-05-01

    Magnetic, electronic and structural properties of titanium dioxide material with different structural defects are studied using the first-principles ab-initio calculations and the Korringa-Kohn-Rostoker method (KKR) combined with the coherent potential approximation (CPA) method in connection with the local density approximation (LDA). We investigated all structural defects in rutile TiO2 such as Titanium interstitial (Tii), Titanium anti-sites (Tio), Titanium vacancies (VTi), Oxygen interstitial (Oi), Oxygen anti-sites (OTi) and oxygen vacancies (Vo). Mechanisms of hybridization and interaction between magnetic atoms are investigated. The transition temperature is computed using the Mean Field Approximation (MFA).Magnetic stability energy of ferromagnetic and disordered local moment states is calculated to determine the most stable state. Titanium anti-sites have a half-metallic aspect. We also studied the change type caused by structural defects in this material.

  3. Ab initio and DFT studies on vibrational spectra of some halides of group IIIB elements

    Science.gov (United States)

    Zhang, Yu; Zhao, Jianying; Tang, Guodong; Zhu, Longgen

    2005-11-01

    The vibrational spectra of some group IIIB elements halides MX 3 and their dimmers, M 2X 6 (M = Sc(III), Y(III), La(III); X = F, Cl, Br, I), have been systematically investigated by ab initio restricted Hartree-Fock (RHF) and density functional B3LYP methods with LanL2DZ and SDD basis sets. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational frequencies, calculated by two methods with different basis sets, are compared to each other. The effect of the methods and the basis sets used on the calculated vibrational frequencies are discussed. Some vibrational frequencies of these complexes are also predicted.

  4. Change in Inertial Confinement Fusion Implosions upon Using an Ab Initio Multiphase DT Equation of State

    Science.gov (United States)

    Caillabet, L.; Canaud, B.; Salin, G.; Mazevet, S.; Loubeyre, P.

    2011-09-01

    Improving the description of the equation of state (EOS) of deuterium-tritium (DT) has recently been shown to change significantly the gain of an inertial confinement fusion target [S. X. Hu , Phys. Rev. Lett. 104, 235003 (2010)PRLTAO0031-900710.1103/PhysRevLett.104.235003]. Here we use an advanced multiphase EOS, based on ab initio calculations, to perform a full optimization of the laser pulse shape with hydrodynamic simulations starting from 19 K in DT ice. The thermonuclear gain is shown to be a robust estimate over possible uncertainties of the EOS. Two different target designs are discussed, for shock ignition and self-ignition. In the first case, the areal density and thermonuclear energy can be recovered by slightly increasing the laser energy. In the second case, a lower in-flight adiabat is needed, leading to a significant delay (3 ns) in the shock timing of the implosion.

  5. EFFECT OF SCANDIUM ON HIDROGEN DISSOCIATION ENERGY AT MAGNESIUM SURFACE: AB INITIO DFT STUDY

    Directory of Open Access Journals (Sweden)

    I Wayan Sutapa

    2010-07-01

    Full Text Available The dissociative chemisorption of hydrogen on both pure and Sc-incorporated Mg(0001 surfaces have been studied by ab initio density functional theory (DFT calculation. The calculated dissociation energy of hydrogen molecule on a pure Mg(0001 surface (1.200 eV is in good agreement with comparable theoretical studies. For the Sc-incorporated Mg(0001 surface, the activated barrier decreases to 0.780 eV due to the strong interaction between the molecular orbital of hydrogen and the d metal state of Sc. This could explain the experimentally observed improvement in absorption kinetics of hydrogen when transition metals have been introduced into the magnesium materials.   Keywords: Dissociation, Adsorption, Chemisorptions, DFT, Magnesium

  6. Ab initio determination of coarse-grained interactions in double stranded DNA

    Science.gov (United States)

    Hsu, Chia Wei; Fyta, Maria; Lakatos, Greg; Melchionna, Simone; Kaxiras, Efthimios

    2012-02-01

    We derive the coarse-grained interactions between DNA nucleotides from ab initio calculations using density functional theory (DFT). The interactions take into account the base and sequence specificity, and are decomposed into physically distinct contributions. The interactions energies calculated from DFT for a wide range of configurations are fitted to simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This non-empirical model accurately yields structural properties of B-DNA even in extreme conditions, and predicts persistence length in excellent agreement with experiments. The model enables quantitative an efficient investigations of the dynamics of long DNA strands in various environments, making it possible to reach microsecond time scales and beyond.

  7. Ab initio determination of coarse-grained interactions in double-stranded DNA

    Science.gov (United States)

    Hsu, Chia Wei; Fyta, Maria; Lakatos, Greg; Melchionna, Simone; Kaxiras, Efthimios

    2012-09-01

    We derive the coarse-grained interactions between DNA nucleotides from ab initio total-energy calculations based on density functional theory (DFT). The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that include hydrogen bonding, stacking interactions, backbone, and backbone-base interactions. The interaction energies of each contribution are calculated from DFT for a wide range of configurations and are fitted by simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This model is not derived from experimental data, yet it successfully reproduces the stable B-DNA structure and gives good predictions for the persistence length. It may be used to realistically probe dynamics of DNA strands in various environments at the μs time scale and the μm length scale.

  8. Estudo ab-initio da a-alanina em meio aquoso

    Directory of Open Access Journals (Sweden)

    Sambrano Júlio Ricardo

    1999-01-01

    Full Text Available Ab initio Hartree-Fock (HF, Density Functional (B3LYP and electron correlation (MP2 methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z. The Z structure is a stationary point at the HF/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.

  9. Ab initio contribution to the study of complexes formed during dilute FeCu alloys radiation

    CERN Document Server

    Becquart, C S

    2003-01-01

    Cu plays an important role in the embrittlement of pressure vessel steels under radiation and entities containing both Cu atoms and vacancies seem to appear as a consequence of displacement cascades. The characterisation of the stability as well as the migration of small Cu-vacancy complexes is thus necessary to understand and simulate the formation of these entities. For instance, cascade ageing studied by kinetic Monte Carlo or by rate theory models requires a good characterisation of such complexes which are parameters for these methods. We have investigated, by ab initio calculations based on the density functional theory, point defects and small defects in dilute FeCu alloys. The structure of small Cu clusters and Cu-vacancy complexes has been determined, as well as their formation and binding energies. Their relative stability is discussed. Vacancy migration energies in the presence of Cu atoms have been calculated and analysed. All the results are compared to the figures obtained with empirical interat...

  10. Ab-initio Study of the Diffusion Mechanisms of Gallium in a Silicon Matrix

    Science.gov (United States)

    Levasseur-Smith, Kevin; Mousseau, Normand

    2007-03-01

    We present the results of a study into the diffusion mechanisms of Ga defects in crystalline Si. The dominant neutral configurations for single and multi-atom defects are established by ab-initio calculations using the density functional theory in the LDA approximation, with a LCAO basis as implemented in the SIESTA package. We find formation energies of 0.7 eV and 2.9 eV, respectively, for the substitutional and tetrahedral interstitial defects, while the diatomic substitutional-tetrahedral complex has a formation energy of 2.2 eV. Subsequent calculations using this same DFT package in conjunction with the activation relaxation technique (ART nouveau) allow us to determine possible diffusion pathways as well as their corresponding saddle points and energy barriers.

  11. Tunneling of electrons via rotor-stator molecular interfaces: combined ab initio and model study

    CERN Document Server

    Petreska, Irina; Pejov, Ljupco; Kocarev, Ljupco

    2015-01-01

    Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that confirmation dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previ...

  12. Ab initio determination of effective electron-phonon coupling factor in copper

    Science.gov (United States)

    Ji, Pengfei; Zhang, Yuwen

    2016-04-01

    The electron temperature Te dependent electron density of states g (ε), Fermi-Dirac distribution f (ε), and electron-phonon spectral function α2 F (Ω) are computed as prerequisites before achieving effective electron-phonon coupling factor Ge-ph. The obtained Ge-ph is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing Ge-ph from ab initio calculation shows a faster decrease of Te and increase of Tl than those using Ge-ph from phenomenological treatment. The approach of calculating Ge-ph and its implementation into MD-TTM simulation is applicable to other metals.

  13. Ab initio determination of effective electron-phonon coupling factor in copper

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    The electron temperature T_e dependent electron density of states g({\\epsilon}), Fermi-Dirac distribution f({\\epsilon}), and electron-phonon spectral function {\\alpha}^2 F({\\Omega}) are computed as prerequisites before achieving effective electron-phonon coupling factor. The obtained is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing G_(e-ph) from ab initio calculation, shows a faster decrease of T_e and increase of T_l than those using G_(e-ph) from phenomenological treatment. The approach of calculating G_(e-ph) and its implementation into MD-TTM simulation is applicable to other metals.

  14. Ab-initio calculations on two-electron ions in strongly coupled plasma environment

    CERN Document Server

    Bhattacharyya, S; Mukherjee, T K

    2015-01-01

    In this work, the controversy between the interpretations of recent measurements on dense aluminum plasma created with Linac coherent light sources (LCLS) X-ray free electron laser (FEL) and Orion laser has been addressed. In both kind of experiments, helium-like and hydrogen-like spectral lines are used for plasma diagnostics . However, there exist no precise theoretical calculations for He-like ions within dense plasma environment. The strong need for an accurate theoretical estimates for spectral properties of He-like ions in strongly coupled plasma environment leads us to perform ab initio calculations in the framework of Rayleigh-Ritz variation principle in Hylleraas coordinates where ion-sphere potential is used. An approach to resolve the long-drawn problem of numerical instability for evaluating two-electron integrals with extended basis inside a finite domain is presented here. The present values of electron densities corresponding to disappearance of different spectral lines obtained within the fram...

  15. Structure and lattice dynamics of rare-earth ferroborate crystals: Ab initio calculation

    Science.gov (United States)

    Chernyshev, V. A.; Nikiforov, A. E.; Petrov, V. P.; Serdtsev, A. V.; Kashchenko, M. A.; Klimin, S. A.

    2016-08-01

    The ab initio calculation of the crystal structure and the phonon spectrum of crystals RFe3(BO3)4 ( R = Pr, Nd, Sm) has been performed in the framework of the density functional theory. The ion coordinates in the unit cell, the lattice parameters, the frequencies and the types of fundamental vibrations, and also the intensities of lines in the Raman spectrum and infrared reflection spectra have been found. The elastic constants of the crystals have been calculated. For low-frequency A 2 mode in PrFe3(BO3)4, a "seed" vibration frequency that strongly interacts with the electronic excitation on a praseodymium ion was found. The calculation results satisfactory agree with the experimental data.

  16. Ab initio study of the phononic origin of negative thermal expansion

    Science.gov (United States)

    Argaman, Uri; Eidelstein, Eitan; Levy, Ohad; Makov, Guy

    2016-11-01

    Negative thermal expansion is an uncommon phenomenon of theoretical interest. Multiple hypotheses regarding its microscopic origins have been suggested. In this paper, the thermal expansion of a representative semiconductor, Si, and a representative metal, Ti, are calculated ab initio using density-functional perturbation theory. The phonon modes' contributions to the thermal expansion are analyzed and the negative thermal expansion is shown to be dominated by negative mode Grüneisen parameters at specific points on the Brillouin zone boundaries. Thus, the elastic (Debye) theory for negative thermal expansion is shown to be irrelevant for these phenomena. The anomalous behavior of these modes in Ti is shown to be unaffected by an electronic topological transition as previously suggested, instead it arises from complex interplay of atomic displacements of the anomalous mode.

  17. Extend of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    CERN Document Server

    Rosenow, Phil

    2016-01-01

    The extent of hydrogen coverage of the Si(001)c(4x2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computationa...

  18. A correlation study of quinoline derivatives and their pharmaceutical behavior by ab initio calculated NQR parameters.

    Science.gov (United States)

    Rafiee, Marjan A; Hadipour, Nasser L; Naderi-manesh, Hossein

    2004-03-01

    In this paper, ab initio calculated NQR parameters for some quinoline-containing derivatives are presented. The calculations are carried out in a search for the relationships between the charge distribution of these compounds and their ability to interact with haematin. On the basis of NQR parameters, pi-electron density on the nitrogen atom of the quinoline ring plays a dominant role in determining the ability of quinolines to interact with haematin. This point was confirmed with investigation of Fe+3 cation-pi quinoline ring interactions in 2- and 4-aminoquinoline. However, our results do not show any preference for those carbon atoms of the quinoline ring which previous reports have noted. In order to calculate the NQR parameters, the electric field gradient (EFG) should be evaluated at the site of a quadrupolar nucleus in each compound. EFGs are calculated by the Gaussian 98 program using the B3LYP/6-31 G* level of theory.

  19. Ab initio modeling of radiation damage in MgF{sub 2} crystals

    Energy Technology Data Exchange (ETDEWEB)

    Abuova, F.U. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Kotomin, E.A., E-mail: kotomin@latnet.lv [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia); Lisitsyn, V.M. [Tomsk Polytechnical University, Tomsk 634003 (Russian Federation); Akilbekov, A.T. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Piskunov, S. [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia)

    2014-05-01

    MgF{sub 2} with a rutile structure is important radiation-resistant material with numerous applications due to its transparency from vacuum ultraviolet to infrared range of photon energies. We present and discuss the results of calculations for basic radiation defects in this crystal. The study is based on the large scale ab initio DFT calculations using hybrid B3PW exchange–correlation functional and atomic basis set. We analyzed the electronic structure, atomic displacements, charge density distribution as well as defect formation energies using large supercells. We compared properties of close and well separated F−H (Frenkel) defect pairs as well as individual defects. We simulated also formation and energetic preference of inert F{sub 2} interstitial molecules as sinks of mobile interstitial fluorine atoms which is relevant for material radiation stability. We discussed also diffusion of the primary electronic defects—F centers.

  20. Ab Initio Theory of Coherent Laser-Induced Magnetization in Metals

    Science.gov (United States)

    Berritta, Marco; Mondal, Ritwik; Carva, Karel; Oppeneer, Peter M.

    2016-09-01

    We present the first materials specific ab initio theory of the magnetization induced by circularly polarized laser light in metals. Our calculations are based on nonlinear density matrix theory and include the effect of absorption. We show that the induced magnetization, commonly referred to as inverse Faraday effect, is strongly materials and frequency dependent, and demonstrate the existence of both spin and orbital induced magnetizations which exhibit a surprisingly different behavior. We show that for nonmagnetic metals (such as Cu, Au, Pd, Pt) and antiferromagnetic metals the induced magnetization is antisymmetric in the light's helicity, whereas for ferromagnetic metals (Fe, Co, Ni, FePt) the imparted magnetization is only asymmetric in the helicity. We compute effective optomagnetic fields that correspond to the induced magnetizations and provide guidelines for achieving all-optical helicity-dependent switching.

  1. The ideal strength of gold under uniaxial stress: an ab initio study.

    Science.gov (United States)

    Wang, Hao; Li, Mo

    2010-07-28

    We employ an ab initio calculation based on density functional theory to investigate the ideal strength of face-centered cubic crystal Au under uniaxial stress along the [100] direction. We show that the stability of the perfect Au crystal under tensile stress is determined by the tetragonal shear stiffness modulus, with an ideal tensile strength of 4.2 GPa and the corresponding Lagrangian tensile strain of ∼ 0.07. The potential bifurcation from the primary uniaxial loading path is along the tetragonal shear. Under compressive stress, there is a stress-free body-centered cubic phase, which is unstable and ready to transform to a stress-free body-centered tetragonal phase with lower internal energy. The stable region is from - 1.6 to 4.2 GPa in the ideal strength, or from - 0.07 to 0.07 in the Lagrangian strain.

  2. Ab initio study of adsorption of molecular hydrogen on microporous metal-organic frameworks.

    Science.gov (United States)

    Hamel, Sébastien; Côté, Michel

    2004-03-01

    In the ongoing search for promising compounds for hydrogen storage, novel porous metal-organic frameworks (MOF) have been discovered recently [1]. Well defined binding sites were deduced from inelastic neutron scattering (INS) spectroscopy of the rotational transitions of the adsorbed molecular hydrogen. In light of this discovery we performed ab initio density functional theory (DFT) calculations of the adsorption of molecular hydrogen on this class of microporous MOF to compare different adsorption sites. Different approximations for the exchange-correlation potentials were accessed for a set of relevant properties such as binding energy, energetically favored configuration and distance between the adsorbents and adsorbates. In particular, theoretical rotational spectra of the adsorbed H2 were obtained that could be compared to the experimental INS spectra. [1] Rosi et al., Science Vol. 300, 1127 (2003)

  3. An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics.

    Science.gov (United States)

    Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki

    2014-05-14

    We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.

  4. Ab Initio Simulation of Electrical Currents Induced by Ultrafast Laser Excitation of Dielectric Materials

    Science.gov (United States)

    Wachter, Georg; Lemell, Christoph; Burgdörfer, Joachim; Sato, Shunsuke A.; Tong, Xiao-Min; Yabana, Kazuhiro

    2014-08-01

    We theoretically investigate the generation of ultrafast currents in insulators induced by strong few-cycle laser pulses. Ab initio simulations based on time-dependent density functional theory give insight into the atomic-scale properties of the induced current signifying a femtosecond-scale insulator-metal transition. We observe the transition from nonlinear polarization currents during the laser pulse at low intensities to tunnelinglike excitation into the conduction band at higher laser intensities. At high intensities, the current persists after the conclusion of the laser pulse considered to be the precursor of the dielectric breakdown on the femtosecond scale. We show that the transferred charge sensitively depends on the orientation of the polarization axis relative to the crystal axis, suggesting that the induced charge separation reflects the anisotropic electronic structure. We find good agreement with very recent experimental data on the intensity and carrier-envelope phase dependence [A. Schiffrin et al., Nature (London) 493, 70 (2013)].

  5. Ab initio theory for current-induced molecular switching: Melamine on Cu(001)

    KAUST Repository

    Ohto, Tatsuhiko

    2013-05-28

    Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green\\'s function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current. © 2013 American Physical Society.

  6. Benchmarking ab initio binding energies of hydrogen-bonded molecular clusters based on FTIR spectroscopy

    DEFF Research Database (Denmark)

    Bork, Nicolai Christian; Du, Lin; Reiman, Heidi;

    2014-01-01

    Models of formation and growth of atmospheric aerosols are highly dependent on accurate cluster binding energies. These are most often calculated by ab initio electronic structure methods but remain associated with significant uncertainties. We present a computational benchmarking study......) and compare this range to predictions from several widely used electronic structure methods, including five density functionals, Møller-Plesset perturbation theory, and five coupled cluster methods up to CCSDT quality, considering also the D3 dispersion correctional scheme. With some exceptions, we find...... that most electronic structure methods overestimate ΔG°295 K. The effects of vibrational anharmonicity is approximated using scaling factors, reducing ΔG°295 K by ca. 1.8 kJ mol(-1), whereby ΔG°295 K predictions well within the experimental range can be obtained....

  7. Realization of prediction of materials properties by ab initio computer simulation

    Indian Academy of Sciences (India)

    Yoshiyuki Kawazoe

    2003-01-01

    Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical properties of academically and industrially interesting materials. There is, however, some limitation in size and time of the system up to the order of several hundred atoms and ∼ 1 pico second, even if we use the fastest supercomputer efficiently. Therefore, it is very difficult to simulate realistic materials with grain boundaries and important reactions like diffusion in materials. To improve this situation, two ways have been invented. One way is to upgrade approximations to match the necessary levels according to inhomogeneous electron gas theory beyond the present day standard, i.e. local density approximation (LDA). The reason is simply that the system we are interested in is composed of many particles interacting with Coulomb forces governed by quantum mechanics. (Complete knowledge is available, and only what we should do is to make better approximations to explain the phenomena!). Another is to extract the necessary parameters from the ab initio calculations on systems with limited number of atoms, and apply these results into cluster variation, direct, or any other sophisticated methods based on classical concepts such as statistical mechanics. In this paper, several typical examples recently worked out by our research group are introduced to indicate that these methodologies are actually possible to be successfully used to predict materials properties before experiments based on the present day state-of-art supercomputing systems. It includes scientific visualization of the results of ab initio molecular dynamics simulation on atom insertion process to C60 and to carbon nanotube, tight-binding calculation of single electron conductance properties in nanotube to create nano-scale diode virtually by computer, which will be a base of future nanoscale electric device in nanometer size, Li + H reaction without Born–Oppenheimer approximation, structural phase

  8. Ab initio study of perovskite type oxide materials for solid oxide fuel cells

    Science.gov (United States)

    Lee, Yueh-Lin

    2011-12-01

    Perovskite type oxides form a family of materials of significant interest for cathodes and electrolytes of solid oxide fuel cells (SOFCs). These perovskites not only are active catalysts for surface oxygen reduction (OR) reactions but also allow incorporating the spilt oxygen monomers into their bulk, an unusual and poorly understood catalytic mechanism that couples surface and bulk properties. The OR mechanisms can be influenced strongly by defects in perovskite oxides, composition, and surface defect structures. This thesis work initiates a first step in developing a general strategy based on first-principles calculations for detailed control of oxygen vacancy content, transport rates of surface and bulk oxygen species, and surface/interfacial reaction kinetics. Ab initio density functional theory methods are used to model properties relevant for the OR reactions on SOFC cathodes. Three main research thrusts, which focus on bulk defect chemistry, surface defect structures and surface energetics, and surface catalytic properties, are carried to investigate different level of material chemistry for improved understanding of key physics/factors that govern SOFC cathode OR activity. In the study of bulk defect chemistry, an ab initio based defect model is developed for modeling defect chemistry of LaMnO 3 under SOFC conditions. The model suggests an important role for defect interactions, which are typically excluded in previous defect models. In the study of surface defect structures and surface energetics, it is shown that defect energies change dramatically (1˜2 eV lower) from bulk values near surfaces. Based on the existing bulk defect model with the calculated ab initio surface defect energetics, we predict the (001) MnO 2 surface oxygen vacancy concentration of (La0.9Sr0.1 )MnO3 is about 5˜6 order magnitude higher than that of the bulk under typical SOFC conditions. Finally, for surface catalytic properties, we show that area specific resistance, oxygen

  9. Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization

    Science.gov (United States)

    Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng

    With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.

  10. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

    Energy Technology Data Exchange (ETDEWEB)

    Keegan, Ronan M. [STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Bibby, Jaclyn; Thomas, Jens [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Xu, Dong [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037 (United States); Zhang, Yang [University of Michigan, Ann Arbor, MI 48109 (United States); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom); STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom)

    2015-02-01

    Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

  11. Electrical resistivity of NaPb compound-forming liquid alloy using ab initio pseudopotentials

    Indian Academy of Sciences (India)

    Anil Thakur; N S Negi; P K Ahluwalla

    2005-08-01

    The study of electrical resistivity of compound-forming liquid alloy, NaPb, is presented as a function of concentration. Hard sphere diameters of Na and Pb are obtained through the interionic pair potentials evaluated using Troullier and Martins ab initio pseudopotential, which have been used to calculate the partial structure factors (). Considering the liquid alloy to be a ternary mixture, Ziman formula, modified for complex formation has been used for calculating resistivity of binary liquid alloys. Form factors are calculated using ab initio pseudopotentials. The results suggest that Ziman formalism, when used with ab initio pseudopotentials, are quite successful in explaining the electrical resistivity data of compound-forming binary liquid alloys.

  12. Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

    Science.gov (United States)

    Mishra, S. B.; Nanda, B. R. K.

    2017-05-01

    Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

  13. Ab-Initio-Based Approach to Study Complete Metalloproteins: Divide and Conquer Geometry Optimization of Nitric-Oxide Reductase

    Science.gov (United States)

    Yue, Yutao; Chachiyo, Teepanis; Rodriguez, Jorge H.

    2007-03-01

    The direct application of ab-initio methods (Hartree-Fock or density functional theory) to study complete biomolecules has been impossible due to the huge computational cost of fully quantum mechanical calculations. As an initial step towards overcoming this problem, we implemented an ab-initio-based method to predict geometric structures of large metalloproteins using the principle of ``divide and conquer.'' The method has been applied to small test systems showing satisfactory agreement with all-atom ab initio calculations. We have successfully applied the divide and conquer approach to partially optimize the geometry of a ligand-enzyme system, namely NO binding to nitric-oxide reductases (NOR, P450nor). NOR is a metalloenzyme that catalyzes the reduction of NO to N2O. To compare our results with all atom calculations we studied a biochemically relevant subsystem (375 atoms) of the ligand-enzyme complex. The deviation between the divide and conquer geometry and the all atom partial geometry optimization is minor, on order of 10-1 å for bond lengths. The computational cost of the method is moderately expensive making its application to large (bio) molecules plausible. Supported by NSF CAREER Award CHE-0349189 (JHR).

  14. Intramolecular SN2 reaction caused by photoionization of benzene chloride-NH3 complex: direct ab initio molecular dynamics study.

    Science.gov (United States)

    Tachikawa, Hiroto

    2006-01-12

    Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.

  15. Transport and optical properties of warm dense aluminum in the two-temperature regime: Ab initio calculation and semiempirical approximation

    CERN Document Server

    Knyazev, D V

    2014-01-01

    This work is devoted to the investigation of transport and optical properties of liquid aluminum in the two-temperature case. At first optical properties, static electrical and thermal conductivities were obtained in the \\textit{ab initio} calculation. The \\textit{ab initio} calculation is based on the quantum molecular dynamics, density functional theory and the Kubo-Greenwood formula. The semiempirical approximation was constructed based on the results of the \\textit{ab initio} caculation. The approximation yields the dependences $\\sigma_{1_\\mathrm{DC}}\\propto1/T_i^{0.25}$ and $K\\propto T_e/T_i^{0.25}$ for the static electrical conductivity and thermal conductivity, respectively. The approximation is valid for liquid aluminum at $\\rho=2.70$~g/cm$^3$, 3~kK~$\\leq T_i\\leq T_e\\leq20$~kK. Our results are well described by the Drude model with the effective relaxation time $\\tau\\propto T_i^{-0.25}$. We have compared our results with a number of other models. They are all reduced in the low-temperature limit to th...

  16. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

    Science.gov (United States)

    John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

    2016-04-01

    We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

  17. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

    Science.gov (United States)

    Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

    2015-02-01

    AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

  18. Ab Initio Calculation on Self-Assembled Base-Functionalized Single-Walled Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    SONG Chen; XIA Yue-Yuan; ZHAO Ming-Wen; LIU Xiang-Dong; LI Ji-Ling; LI Li-Juan; LI Feng; HUANG Bo-Da

    2006-01-01

    @@ We perform ab initio calculations on the self-assembled base-functionalized single-walled carbon nanotubes (SWNTs) which exhibit the quasi-1D ‘ladder’ structure. The optimized configuration in the ab initio calculation is very similar to that obtainedfrom molecular dynamics simulation. We also calculate the electronic structures of the self-assembled base-functionalized SWNTs that exhibit distinct difference from the single-branch base-functionalized SWNT with a localized state lying just below the Fermi level, which may result from the coupling interaction between the bases accompanied by the self-assembly behaviour.

  19. Atomic carbon chains as spin-transmitters: An ab initio transport study

    DEFF Research Database (Denmark)

    Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka

    2010-01-01

    An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin-polarization of the transmi......An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin...

  20. Ab initio quantum-enhanced optical phase estimation using real-time feedback control

    DEFF Research Database (Denmark)

    Berni, Adriano; Gehring, Tobias; Nielsen, Bo Melholt

    2015-01-01

    as demonstrated in a variety of different optical systems(3-8). Most of these accounts, however, deal with the measurement of a very small shift of an already known phase, which is in stark contrast to ab initio phase estimation where the initial phase is unknown(9-12). Here, we report on the realization...... of a quantum-enhanced and fully deterministic ab initio phase estimation protocol based on real-time feedback control. Using robust squeezed states of light combined with a real-time Bayesian adaptive estimation algorithm, we demonstrate deterministic phase estimation with a precision beyond the quantum shot...

  1. Ab initio I-V characteristics of short C-20 chains

    DEFF Research Database (Denmark)

    Roland, C.; Larade, B.; Taylor, Jeremy Philip

    2002-01-01

    We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both on the orien......We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both...

  2. An ab initio study on single electron transfer between ClO2 and phenol

    Institute of Scientific and Technical Information of China (English)

    崔崇威; 黄君礼

    2004-01-01

    The SET mechanism between chlorine dioxide (ClO2 ) and phenol was studied by using ab initio method at 4-31G* level. Geometries of the reactants, intermediate and products of the reaction were optimized and the single point energy calculations of the species were performed. The relative structure data of the reactants, intermediate and products are given. The SET mechanism between ClO2 and phenol was confirmed by ab initio calculations. The reaction is exothermic about 200. 88 k J/mol.

  3. Ab initio theory of charge-carrier conduction in ultrapure organic crystals

    Science.gov (United States)

    Hannewald, K.; Bobbert, P. A.

    2004-08-01

    We present an ab initio description of charge-carrier mobilities in organic molecular crystals of high purity. Our approach is based on Holstein's original concept of small-polaron bands but generalized with respect to the inclusion of nonlocal electron-phonon coupling. By means of an explicit expression for the mobilities as a function of temperature in combination with ab initio calculations of the material parameters, we demonstrate the predictive power of our theory by applying it to naphthalene. The results show a good qualitative agreement with experiment and provide insight into the difference between electron and hole mobilities as well as their peculiar algebraic and anisotropic temperature dependencies.

  4. The keto-enol equilibrium in substituted acetaldehydes: focal-point analysis and ab initio limit

    Science.gov (United States)

    Balabin, Roman M.

    2011-10-01

    High-level ab initio electronic structure calculations up to the CCSD(T) theory level, including extrapolations to the complete basis set (CBS) limit, resulted in high precision energetics of the tautomeric equilibrium in 2-substituted acetaldehydes (XH2C-CHO). The CCSD(T)/CBS relative energies of the tautomers were estimated using CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z calculations with MP2/aug-cc-pVTZ geometries. The relative enol (XHC = CHOH) stabilities (ΔE e,CCSD(T)/CBS) were found to be 5.98 ± 0.17, -1.67 ± 0.82, 7.64 ± 0.21, 8.39 ± 0.31, 2.82 ± 0.52, 10.27 ± 0.39, 9.12 ± 0.18, 5.47 ± 0.53, 7.50 ± 0.43, 10.12 ± 0.51, 8.49 ± 0.33, and 6.19 ± 0.18 kcal mol-1 for X = BeH, BH2, CH3, Cl, CN, F, H, NC, NH2, OCH3, OH, and SH, respectively. Inconsistencies between the results of complex/composite energy computations methods Gn/CBS (G2, G3, CBS-4M, and CBS-QB3) and high-level ab initio methods (CCSD(T)/CBS and MP2/CBS) were found. DFT/aug-cc-pVTZ results with B3LYP, PBE0 (PBE1PBE), TPSS, and BMK density functionals were close to the CCSD(T)/CBS levels (MAD = 1.04 kcal mol-1).

  5. Modelling of nuclear glasses by classical and ab initio molecular dynamics; Modelisation de verres intervenant dans le conditionnement des dechets radioactifs par dynamiques moleculaires classique et ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Ganster, P

    2004-10-15

    A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

  6. Ab initio and DFT Studies of Be(BH42

    Directory of Open Access Journals (Sweden)

    J. S. Al-Otaibi

    2016-03-01

    Full Text Available In this study, the Ab inito and DFT calculations of optimized geometries, energy and vibrational spectra for the Beryllium borohydride Be(BH42 at different levels are achieved by Hartre – Fock (HF, perturbation theory (MP2 and density functional theory (B3LYP methods. They utilize the 6-31G(d, 6-311G(d,p, 6-311+G(d,p and 6-311++G(d,p basis sets. The theoretical results showed that Beryllium borohydride with the D2d structure which contains two identical groups of double bridging hydrogen has the lowest energy at all levels. Consequently, this compound is considered as the most stable one and the results of IR and Raman Spectra at all levels support that. We found that both structures Cs, C3v have the structure of D2d kind at all levels. The values of bond lengths for these two structures are identical for the bond lengths to the structure D2d kind which confirms this theory.

  7. Local Structure in Ab Initio Liquid Water: Signatures of Amorphous Phases

    Science.gov (United States)

    Santra, Biswajit; Distasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyze the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I), was unimodal with most water molecules characterized by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water This work was supported by the DOE: DE-SC0008626, DE-SC0005180.

  8. Ab-initio Electronic, Transport and Related Properties of Zinc Blende Boron Arsenide (zb-BAs)

    Science.gov (United States)

    Nwigboji, Ifeanyi H.; Malozovsky, Yuriy; Bagayoko, Diola

    We present results from ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of zinc blende boron arsenide (zb-BAs). We utilized a local density approximation (LDA) potential and the linear combination of atomic orbital (LCAO) formalism. Our computational technique follows the Bagayoko, Zhao, and Williams method, as enhanced by Ekuma and Franklin. Our results include electronic energy bands, densities of states, and effective masses. We explain the agreement between these findings, including the indirect band gap, and available, corresponding, experimental ones. This work confirms the capability of DFT to describe accurately properties of materials, provided the computations adhere to the conditions of validity of DFT [AIP Advances, 4, 127104 (2014)]. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE- NA0002630), LaSPACE, and LONI-SUBR.

  9. Ab-initio Calculation of Optoelectronic and Structural Properties of Cubic Lithium Oxide (Li2O)

    Science.gov (United States)

    Ziegler, Joshua; Polin, Daniel; Malozovsky, Yuriy; Bagayoko, Diola

    Using the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), we performed ab-initio, density functional theory (DFT) calculations of optoelectronic, transport, and bulk properties of Li2S. In so doing, we avoid ``band gap'' and problems plaguing many DET calculations [AIP Advances 4, 127104 (2014)]. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). With the BZW-EF method, our results possess the full, physical content of DFT and agree with available, corresponding experimental ones. In particular, we found a room temperature indirect band gap of 6.659 eV that compares favorably with experimental values ranging from 5 to 7.99 eV. We also calculated total and partial density of states (DOS and PDOS), effective masses of charge carriers, the equilibrium lattice constant, and the bulk modulus. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.

  10. Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics

    Science.gov (United States)

    Marcolongo, Aris; Umari, Paolo; Baroni, Stefano

    2014-03-01

    The Green-Kubo approach to thermal transport is often considered to be incompatible with ab-initio molecular dynamics (AIMD) because a suitable quantum-mechanical definition of the heat current is not readily available, due to the ill-definedness of the microscopic energy density to which it is related by the continuity equation. We argue that a similar difficulty actually exists in classical mechanics as well, and we address the conditions that have to be fulfilled in order for the physically well defined transport coefficients to be independent of the ill defined microscopic energy density from which they derive. We then provide two alternative approaches to calculating thermal conductivites from equilibrium AIMD. The first is based on the Green-Kubo formula, supplemented with an expression for the energy current, which is a generalization of Thouless' expression for the adiabatic charge current. The second approach, which avoids the recourse to an energy current altogether, rests on an efficient and accurate extrapolation to infinite wavelengths of the energy-density time correlation functions. The two methods are compared on a simple classical test bed, and their implementation in AIMD is demonstrated with the calculation of the thermal conductivity of simple fluids.

  11. Ab initio study of structural, electronic, and thermal properties of Pt1-xPdx alloys

    Science.gov (United States)

    Ahmed, Shabbir; Zafar, Muhammad; Shakil, M.; Choudhary, M. A.; Hashmi, Muhammad Raza-Ur-Rehman

    2017-01-01

    We report a systematic theoretical study of Pt1-xPdx alloys using ab initio density functional theory (DFT) by pseudo potential method. We have used super cell approach to investigate structural, electronic and thermal properties of Platinum (Pt), Palladium (Pd) and their alloys Pt1-xPdx(x = 0.00, 0.25, 0.50, 0.75, 1.00). The calculated lattice constants and bulk moduli are in good agreement with available literature data. The results of electronic properties revealed that the alloys are metallic in nature. The thermal properties were investigated through density functional perturbation theory (DFPT) and quasi-harmonic approximation. The contribution to the free energy from the lattice vibration was calculated using the phonon densities of states (DOS) derived by means of the linear-response theory. The DFPT with quasi-harmonic approximation methods was applied to determine the phonon DOS and thermal quantities i.e., the Debye temperatures, vibration energy, entropy and constant-volume specific heat.

  12. Ab initio Defect Energetics in LaBO3 Perovskite Solid Oxide Fuel Cell Materials

    DEFF Research Database (Denmark)

    Lee, Yueh-Lin; Morgan, Dane; Kleis, Jesper;

    2009-01-01

    Perovskite materials of the form ABO3 are a promising family of compounds for use in solid oxide fuel cell (SOFC) cathodes. Study of the physics of these compounds under SOFC conditions with ab initio methods is particularly challenging due to high temperatures, exchange of oxygen with O2 gas...

  13. Ab initio and work function and surface energy anisotropy of LaB6

    NARCIS (Netherlands)

    Uijttewaal, M. A.; de Wijs, G. A.; de Groot, R. A.

    2006-01-01

    Lanthanum hexaboride is one of the cathode materials most used in high-power electronics technology, but the many experimental results do not provide a consistent picture of the surface properties. Therefore, we report the first ab initio calculations of the work functions and surface energies of

  14. Ab initio ground state phenylacetylene-argon intermolecular potential energy surface and rovibrational spectrum

    DEFF Research Database (Denmark)

    Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian

    2012-01-01

    We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set ...

  15. Ab Initio Investigations of the C2F4S Isomers and of Their Interconversions

    DEFF Research Database (Denmark)

    Shim, Irene; Vallano-Lorenzo, Sandra; Lisbona-Martin, Pilar

    2003-01-01

    The transition states and the activation energies for the unobserved isomerization reactions between the three possible C2F4S isomers with divalent sulfur, trifluorothioacetyl fluoride 1, tetrafluorothiirane 2, and trifluoroethenesulfenyl fluoride 3, have been determined by ab initio Hartree-Fock...

  16. Ab initio electronic-structure calculations on the Nb/Zr multilayer system

    NARCIS (Netherlands)

    Leuken, H. v.; Czyżyk, M.T.; Springelkamp, F.; Groot, R.A. de

    1990-01-01

    Ab initio electronic-structure calculations are performed for the Nb/Zr metallic multilayer system in the coherent bcc structure and in the incoherent bcc/hcp structure, observed for small and larger modulation wavelengths, respectively. A new calculational scheme, the localized-spherical-wave

  17. Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

    Science.gov (United States)

    Halpern, Arthur M.

    2011-01-01

    A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

  18. An ab initio Valence Bond Study on Cyclopenta-Fused Naphthalenes and Fluoranthenes

    NARCIS (Netherlands)

    Havenith, R.W.A.; van Lenthe, J.H.; Jenneskens, L.W.

    2005-01-01

    To probe the effect of external cyclopenta-fusion on a naphthalene core, ab initio valence bond (VB) calculations have been performed, using strictly atomic benzene p-orbitals and p-orbitals that are allowed to delocalize, on naphthalene (1), acenaphthylene (2), pyracylene (3), cyclopenta[b,c]-acena

  19. POLY-ANIONS IN LIQUID CSPB - AN AB-INITIO MOLECULAR-DYNAMICS SIMULATION

    NARCIS (Netherlands)

    DEWIJS, GA; PASTORE, G; SELLONI, A; VANDERLUGT, W

    1994-01-01

    Most alkali-group-IV liquid alloys exhibit strong chemical effects leading to well-defined equiatomic compounds. This is generally explained by the survival of particular clusters of lead-''Zintl'' ions-in the liquid state. We report on an ab initio simulation of liquid CsPb, for which the chemical

  20. The Pu–U–Am system: An ab initio informed CALPHAD thermodynamic study

    Energy Technology Data Exchange (ETDEWEB)

    Perron, A., E-mail: perron1@llnl.gov [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Turchi, P.E.A.; Landa, A.; Söderlind, P. [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Ravat, B.; Oudot, B.; Delaunay, F. [CEA-Centre de Valduc, 21120 Is sur Tille (France)

    2015-03-15

    Highlights: • The ab initio informed CALPHAD assessment of the Am–U system has been realized. • A strong tendency toward phase separation across the whole composition range is predicted. • The ab initio informed Pu–U–Am thermodynamic database has been developed. • The solubility of Am and U in the liquid phase is improved by adding Pu. • The δ-Pu (fcc) phase is strongly stabilized by Am, on the contrary to the bcc phase. - Abstract: Phase diagram and thermodynamic properties of the Am–U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu–U and Am–Pu thermodynamic assessments are combined to build a Pu–U–Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies.

  1. Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)

    Science.gov (United States)

    Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang

    2001-01-01

    Semiempirical PM3, ab initio HF/3-21g ∗, and DFT B3LYP/6-31g ∗ calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.

  2. Ab initio study of long-period superstructures in close-packed A3B compounds

    DEFF Research Database (Denmark)

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1994-01-01

    We have performed ab initio calculations of the stability of one-dimensional long-period superstructures in Cu3Pd, Cu3Al, and Ag3Mg by means of an interface Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations. The ene...

  3. Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

    DEFF Research Database (Denmark)

    Zhang, Hao; Lund, Ole; Nielsen, Morten

    2010-01-01

    potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data...

  4. Relativistic ab initio spectroscopy study of forbidden lines of singly ionized zinc

    NARCIS (Netherlands)

    Dixit, Gopal; Sahoo, Bijaya K.; Chaudhuri, Rajat K.; Majumder, Sonjoy

    2009-01-01

    The ab initio calculation has been carried out to study the astrophysically important forbidden electromagnetic transition rates of singly ionized zinc (Zn II). Electron correlations are considered to all orders using coupled-cluster theory in the relativistic framework. Calculated excitation energi

  5. Relativistic ab initio spectroscopy study of forbidden lines of singly ionized zinc

    NARCIS (Netherlands)

    Dixit, Gopal; Sahoo, Bijaya K.; Chaudhuri, Rajat K.; Majumder, Sonjoy

    2009-01-01

    The ab initio calculation has been carried out to study the astrophysically important forbidden electromagnetic transition rates of singly ionized zinc (Zn II). Electron correlations are considered to all orders using coupled-cluster theory in the relativistic framework. Calculated excitation

  6. Mechanical properties of carbynes investigated by ab initio total-energy calculations

    DEFF Research Database (Denmark)

    Castelli, Ivano E.; Salvestrini, Paolo; Manini, Nicola

    2012-01-01

    As sp carbon chains (carbynes) are relatively rigid molecular objects, can we exploit them as construction elements in nanomechanics? To answer this question, we investigate their remarkable mechanical properties by ab initio total-energy simulations. In particular, we evaluate their linear...

  7. Ab-initio modeling of an anion $C_{60}^-$ pseudopotential for fullerene-based compounds

    CERN Document Server

    Vrubel, I I; Ivanov, V K

    2015-01-01

    A pseudopotential of $C_{60}^-$ has been constructed from ab-initio quantum-mechanical calculations. Since the obtained pseudopotential can be easily fitted by rather simple analytical approximation it can be effectively used both in classical and quantum molecular dynamics of fullerene-based compounds.

  8. Ab initio calculations on the structure of pyridine in its lowest triplet state

    NARCIS (Netherlands)

    Buma, W.J.; Groenen, E.J.J.; Schmidt, J.

    1990-01-01

    Recently we have experimentally shown that pyridine-d5, as a guest in a single crystal of benzene-d6, adopts a boatlike structure upon excitation into the lowest triplet state T0. Here MRDCI ab initio calculations are presented that reveal that the observed nonplanarity of the molecule is not caused

  9. New ab initio based pair potential for accurate simulation of phase transitions in ZnO

    NARCIS (Netherlands)

    Wang, Shuaiwei; Fan, Zhaochuan; Koster, Rik S.; Fang, Changming; Van Huis, Marijn A.; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; Vlugt, Thijs J H

    2014-01-01

    A set of interatomic pair potentials is developed for ZnO based on the partially charged rigid ion model (PCRIM). The derivation of the potentials combines lattice inversion, empirical fitting, and ab initio energy surface fitting. We show that, despite the low number of parameters in this model (8)

  10. Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Nørbygaard, Thomas; White, Peter C.

    2011-01-01

    . The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization...

  11. Ab initio and work function and surface energy anisotropy of LaB6

    NARCIS (Netherlands)

    Uijttewaal, M. A.; de Wijs, G. A.; de Groot, R. A.

    2006-01-01

    Lanthanum hexaboride is one of the cathode materials most used in high-power electronics technology, but the many experimental results do not provide a consistent picture of the surface properties. Therefore, we report the first ab initio calculations of the work functions and surface energies of th

  12. Ab initio study of structural, electronic, and thermal properties of Ir_{1-x}Rh_{x} alloys

    Directory of Open Access Journals (Sweden)

    Sh. Ahmed

    2015-06-01

    Full Text Available The structural, electronic, mechanical and thermal properties of Ir_{1-x}Rh_{x} alloys was studied systematically using ab initio density functional theory at different concentration (x = 0.00, 0.25, 0.50, 0.75, 1.00. The Special Quasirandom Structure method was used to make the alloys with FCC structure with four atoms per unit cell. The ground state properties such as lattice constant and bulk modulus were calculated to find the equilibrium atomic position for stable alloys. The calculated ground state properties are in good agreement with the experimental and previously presented other theoretical data. The electronic band structure and density of states were calculated to study the electronic properties for these alloys at different concentration. The electronic properties substantiate metallic behavior of alloys. The first principle density functional perturbation theory as implemented in quasiharmonic approximation was used for the calculation of thermal properties. We have calculated the thermal properties such the Debye temperatures, vibration energy, entropy, constant-volume specific heat and internal energy. The ab initio linear-response method was used for phonon densities of states calculations.

  13. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  14. Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

    Directory of Open Access Journals (Sweden)

    G.M. Bhuiyan

    2012-10-01

    Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

  15. Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

    CERN Document Server

    Bhuiyan, G M; González, D J; 10.5488/CMP.15.33604

    2012-01-01

    Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

  16. Path integral molecular dynamics calculations of the H6+ and D6+ clusters on an ab initio potential energy surface

    Science.gov (United States)

    Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki

    2007-11-01

    Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.

  17. Ab initio study of ferromagnetic La0.5Ba0.5CoO3

    Indian Academy of Sciences (India)

    Umesh V Waghmare

    2003-10-01

    We study structure and magnetic properties of La0.5Ba0.5CoO3 (LBCO) using ab initio density functional theory (DFT) method based on pseudopotentials and a plane-wave basis. We find the cubic structure of LBCO is ferromagnetic and lower in energy than the nonmagnetic rhombohedral structure. Through the calculation of -point phonons of LBCO in the cubic structure, we determine its structural instabilities and find that they correspond to the structural phase transition accompanying a para-ferromagnetic transition observed recently.

  18. Data files for ab initio calculations of the lattice parameter and elastic stiffness coefficients of bcc Fe with solutes.

    Science.gov (United States)

    Fellinger, Michael R; Hector, Louis G; Trinkle, Dallas R

    2017-02-01

    We present computed datasets on changes in the lattice parameter and elastic stiffness coefficients of bcc Fe due to substitutional Al, B, Cu, Mn, and Si solutes, and octahedral interstitial C and N solutes. The data is calculated using the methodology based on density functional theory (DFT) presented in Ref. (M.R. Fellinger, L.G. Hector Jr., D.R. Trinkle, 2017) [1]. All the DFT calculations were performed using the Vienna Ab initio Simulations Package (VASP) (G. Kresse, J. Furthmüller, 1996) [2]. The data is stored in the NIST dSpace repository (http://hdl.handle.net/11256/671).

  19. Ab initio calculations of the electronic structure and bonding characteristics of LaB6

    Science.gov (United States)

    Hossain, Faruque M.; Riley, Daniel P.; Murch, Graeme E.

    2005-12-01

    Lanthanum hexaboride ( LaB6 , NIST SRM-660a) is widely used as a standard reference material for calibrating the line position and line shape parameters of powder diffraction instruments. The accuracy of this calibration technique is highly dependent on how completely the reference material is characterized. Critical to x-ray diffraction, this understanding must include the valence of the La atomic position, which in turn will influence the x-ray form factor (f) and hence the diffracted intensities. The electronic structure and bonding properties of LaB6 have been investigated using ab initio plane-wave pseudopotential total energy calculations. The electronic properties and atomic bonding characteristics were analyzed by estimating the energy band structure and the density of states around the Fermi energy level. The calculated energy band structure is consistent with previously reported experimental findings; de Haas-van Alphen and two-dimensional angular correlation of electron-positron annihilation radiation. In addition, the bond strengths and types of atomic bonds in the LaB6 compound were estimated by analyzing the Mulliken charge density population. The calculated result revealed the coexistence of covalent, ionic, and metallic bonding in the LaB6 system and partially explains its high efficiency as a thermionic emitter.

  20. Characterization of Elastic Properties of Porous Graphene Using an Ab Initio Study

    Directory of Open Access Journals (Sweden)

    Reza Ansari

    2016-12-01

    Full Text Available Importance of covalent bonded two-dimensional monolayer nanostructures and also hydrocarbons is undeniably responsible for creation of new fascinating materials like polyphenylene polymer, a hydrocarbon super honeycomb network, so-called porous graphene. The mechanical properties of porous graphene such as its Young’s modulus, Poisson’s ratio and the bulk modulus as the determinative properties are calculated in this paper using ab initio calculations. To accomplish this aim, the density functional theory on the basis of generalized gradient approximation and the Perdew–Burke–Ernzerhof exchange correlation is employed. Density functional theory calculations are used to calculate strain energy of porous graphene with respect to applied strain. Selected numerical results are then presented to study the properties of porous graphene. Comparisons are made between the properties of porous graphene and those of other analogous nanostructures. The results demonstrated lower stiffness of porous graphene than those of graphene and graphyne, and higher stiffness than that of graphdyine and other graphyne families. Unlikely, Poisson’s ratio is observed to be more than that of graphene and also less than that of graphyne. It is further observed that the presence of porosity and also formation of C-H bond in the pore sites is responsible for these discrepancies. Porous graphene is found to behave as the isotropic material.

  1. Yttrium aluminium garnet under pressure: Structural, elastic, and vibrational properties from ab initio studies

    Energy Technology Data Exchange (ETDEWEB)

    Monteseguro, V. [Departamento de Física and MALTA Consolider Team, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain); Rodríguez-Hernández, P.; Muñoz, A., E-mail: amunoz@ull.es [Departamento de Física and MALTA Consolider Team, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain); Instituto de Materiales y Nanotecnología. Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain)

    2015-12-28

    The structural, elastic, and vibrational properties of yttrium aluminum garnet Y{sub 3}Al{sub 5}O{sub 12} are studied under high pressure by ab initio calculations in the framework of the density functional theory. The calculated ground state properties are in good agreement with the available experimental data. Pressure dependences of bond length and bulk moduli of the constituent polyhedra are reported. The evolution of the elastic constants and the major elastic properties, Young and shear modulus, Poisson's ratios, and Zener anisotropy ratio, are described. The mechanical stability is analyzed, on the light of “Born generalized stability criteria,” showing that the garnet is mechanically unstable above 116 GPa. Symmetries, frequencies, and pressure coefficients of the Raman-active modes are discussed on the basis of the calculated total and partial phonon density of states, which reflect the dynamical contribution of each atom. The relations between the phonon modes of Y{sub 3}Al{sub 5}O{sub 12} and the internal and external molecular modes of the different polyhedra are discussed. Infrared-active modes, as well as the silent modes, and their pressure dependence are also investigated. No dynamical instabilities were found below 116 GPa.

  2. Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

    CERN Document Server

    Van Vleet, Mary J; Stone, Anthony J; Schmidt, J R

    2016-01-01

    Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones (${A}/{r^{12}}$) or Born-Mayer ($A\\exp(-Br)$) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional for...

  3. Electronic Structure of Hydrogenated and Surface-Modified GaAs Nanocrystals: Ab Initio Calculations

    Directory of Open Access Journals (Sweden)

    Hamsa Naji Nasir

    2012-01-01

    Full Text Available Two methods are used to simulate electronic structure of gallium arsenide nanocrystals. The cluster full geometrical optimization procedure which is suitable for small nanocrystals and large unit cell that simulates specific parts of larger nanocrystals preferably core part as in the present work. Because of symmetry consideration, large unit cells can reach sizes that are beyond the capabilities of first method. The two methods use ab initio Hartree-Fock and density functional theory, respectively. The results show that both energy gap and lattice constant decrease in their value as the nanocrystals grow in size. The inclusion of surface part in the first method makes valence band width wider than in large unit cell method that simulates the core part only. This is attributed to the broken symmetry and surface passivating atoms that split surface degenerate states and adds new levels inside and around the valence band. Bond length and tetrahedral angle result from full geometrical optimization indicate good convergence to the ideal zincblende structure at the centre of hydrogenated nanocrystal. This convergence supports large unit cell methodology. Existence of oxygen atoms at nanocrystal surface melts down density of states and reduces energy gap.

  4. Ab Initio study of the diffusion mechanisms of gallium in a silicon matrix

    Science.gov (United States)

    Levasseur-Smith, K.; Mousseau, N.

    2008-07-01

    We present the results of a study into the diffusion mechanisms of Ga defects in crystalline Si using ab initio techniques. Five stable neutral configurations for single and multi-atom defects are identified by density-functional theory (DFT) calculations within the local density approximation and using a localized basis set as implemented in the SIESTA package. Formation energy (E_F) calculations on these stable structures show the most likely neutral single-atom defect to be the Ga substitutional, with an EF of 0.7 eV in good agreement with previous work. Charge state studies show the Ga tetrahedral interstitial defect to be in a +1 state for most doping conditions. They also indicate the possibility for a gallium substitutional-tetrahedral interstitial complex to act as a deactivating center for the Ga dopants except in n-doped regime, where the complex adopts a -1 charge state. Migration pathway calculations using SIESTA coupled with the activation relaxation technique (ART nouveau) allow us to determine possible migration paths from the stable configurations found, under various charge states. In general, diffusion barriers decrease as the charge state becomes more negative, suggesting that the presence of Si self-interstitials can enhance diffusion through the kicking out of substitutional Si and by adding negative charge carriers to the system. An overall picture of a possible Ga diffusion and complex formation mechanism is presented based on these results.

  5. Band offset of the ZnO/Cu2O heterojunction from ab initio calculations

    Science.gov (United States)

    Zemzemi, M.; Alaya, S.

    2013-12-01

    The ZnO/Cu2O system has known a recent revival of interest in solar cells for its potential use as a heterojunction able to highly perform under visible light. In this work, we are interested on the characterization of the interface through nanoscale modelization based on ab initio (Density Functional Theory (DFT), Local Density Approximation (LDA), Generalized Gradient Approximation (GGA-PBE), and Pseudopotential (PP)). This work aims to build a supercell containing a heterojunction ZnO/Cu2O and study the structural properties and the discontinuity of the valence band (band offset) from a semiconductor to another. We built a zinc oxide in the wurtzite structure along the [0 0 0 1] on which we placed the copper oxide in the hexagonal structure (CdI2-type). We choose the method of Van de Walle and Martin to calculate the energy offset. This approach fits well with the DFT. Our calculations of the band offset gave us a value that corresponds to other experimental and theoretical values.

  6. High-level ab initio computations of the absorption spectra of organic iridium complexes.

    Science.gov (United States)

    Plasser, Felix; Dreuw, Andreas

    2015-02-12

    The excited states of fac-tris(phenylpyridinato)iridium [Ir(ppy)3] and the smaller model complex Ir(C3H4N)3 are computed using a number of high-level ab initio methods, including the recently implemented algebraic diagrammatic construction method to third-order ADC(3). A detailed description of the states is provided through advanced analysis methods, which allow a quantification of different charge transfer and orbital relaxation effects and give extended insight into the many-body wave functions. Compared to the ADC(3) benchmark an unexpected striking difference of ADC(2) is found for Ir(C3H4N)3, which derives from an overstabilization of charge transfer effects. Time-dependent density functional theory (TDDFT) using the B3LYP functional shows an analogous but less severe error for charge transfer states, whereas the ωB97 results are in good agreement with ADC(3). Multireference configuration interaction computations, which are in reasonable agreement with ADC(3), reveal that static correlation does not play a significant role. In the case of the larger Ir(ppy)3 complex, results at the TDDFT/B3LYP and TDDFT/ωB97 levels of theory are presented. Strong discrepancies between the two functionals, which are found with respect to the energies, characters, as well as the density of the low lying states, are discussed in detail and compared to experiment.

  7. ab initio Studies on Molecular Conductor (BEDSe-TTF)2[Fe(CN)5NO

    Institute of Scientific and Technical Information of China (English)

    YAO Kai-Lun; TU Hai-Bo; WANG Wei-Zhong

    2001-01-01

    In this paper the ab initio study using pseudopotential plane wave method with the local spin density functional approximation is presented for the molecular conductor (BEDSe-TTF)2[Fe(CN)5NO]. The mean electronic density distributions are obtained, and we find that the extended π orbital of the selenium does not affect the properties of material as assumed in other papers and the "side-by-side" type S...S interaction is the primary interaction between donors. From band structure calculations we analyze the influence of the NO groups on the electronic structure and magnetic properties of molecule. It is shown that the itinerant electrons important to electronic properties in these types of hybrids are delocalized electrons contributed by NO groups, instead of by the 3d electrons of Fe. Additionally, we have found that the localized magnetic moment is also contributed by the NO groups in this molecular conductor. From total energy calculations the molecular structure with the lowest energy is found due to the interaction between split spins, and the particular positions of the NO groups are obtained.

  8. Relaxation of Small Molecules:an ab initio Study

    Institute of Scientific and Technical Information of China (English)

    CAOYi-Gang; A.Antons; 等

    2002-01-01

    Using an ab inito total energy and force method,we have relaxed several group IV and group V elemental clusters,in detail the arsenic and antimony dimers,silicon,phosphorus,arsenic and antimony tetraners,The obtained bond lengths and cohesive energies are more accurate than other calculating methods,and in excellent agreement with the experimental results.

  9. Structure and lattice dynamics of GaN and AlN. Ab-initio investigations of strained polytypes and superlattices

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, Jan-Martin

    2004-10-14

    In this dissertation, ab-initio investigations of the strain influence on vibrational properties of GaN and AlN as well as of short-period GaN/AlN superlattices are presented. Based on densityfunctional theory and density-functional perturbation theory, for differently strained structures complete phonon spectra and related properties are calculated using the local-density approximation and norm-conserving pseudopotentials. (orig.)

  10. Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations

    Science.gov (United States)

    Brandt, Erik G.; Agosta, Lorenzo; Lyubartsev, Alexander P.

    2016-07-01

    Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. Electronic supplementary information (ESI) available: Simulation data on equilibration of energies and structures (root-mean-square-deviations and

  11. Structural, Conformational and Vibrational Studies of Isocyanocyclopentane from Infrared, Raman Spectra and AB Initio Calculations

    Science.gov (United States)

    Sawant, Dattatray K.; Klaassen, Joshua J.; Durig, James R.

    2013-06-01

    The infrared and Raman spectra (3200 to 50 cm^{-1}) of the gas, liquid or solution, and solid have been recorded of isocyanocyclopentane, _{c}-C_{5}H_{9}NC. FT-microwave studies have also been carried out and 23 transitions were recorded for the envelope-axial (Ax) conformer. Variable temperature (-55 to -100°C) studies of the infrared spectra (3200 to 400 cm^{-1}) dissolved in liquid xenon have been carried out. From these data, both the Ax and envelope-equatorial (Eq) conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 102 ± 10 cm^{-1} (1.21 ± 0.03 kJ mol^{-1}) with the Ax conformer the more stable form. The percentage of the Eq conformer is estimated to be 38 ± 1% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been made for the observed bands for both conformers with initial predictions by MP2(full)/6-31G(d) ab initio calculations to obtain harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The heavy atom distances (Å): C≡N = 1.176 ; C_{α}-N≡C= 1.432; C_{α}-C_{β},C_{β}' = 1.534; C_{β}-C_{γ}, C_{γ}' = 1.542; C_{γ}-C_{γ}' = 1.554 and angles (°:angleC_{α}-N≡C = 177.8; angleC_{β}C_{α}-N≡C = 110.4; angleC_{β}C_{α}C_{β}'= 102.9; angleC_{α}C_{β}C_{γ} = 103.6; angleC_{β}C_{γ}C_{γ}' = 105.9. The results are discussed and compared to the corresponding properties of some related molecules.

  12. Molecular tailoring approach: a route for ab initio treatment of large clusters.

    Science.gov (United States)

    Sahu, Nityananda; Gadre, Shridhar R

    2014-09-16

    Conspectus Chemistry on the scale of molecular clusters may be dramatically different from that in the macroscopic bulk. Greater understanding of chemistry in this size regime could greatly influence fields such as materials science and atmospheric and environmental chemistry. Recent advances in experimental techniques and computational resources have led to accurate investigations of the energies and spectral properties of weakly bonded molecular clusters. These have enabled researchers to learn how the physicochemical properties evolve from individual molecules to bulk materials and to understand the growth patterns of clusters. Experimental techniques such as infrared, microwave, and photoelectron spectroscopy are the most popular and powerful tools for probing molecular clusters. In general, these experimental techniques do not directly reveal the atomistic details of the clusters but provide data from which the structural details need to be unearthed. Furthermore, the resolution of the spectral properties of energetically close cluster conformers can be prohibitively difficult. Thus, these investigations of molecular aggregates require a combination of experiments and theory. On the theoretical front, researchers have been actively engaged in quantum chemical ab initio calculations as well as simulation-based studies for the last few decades. To obtain reliable results, there is a need to use correlated methods such as Møller-Plesset second order method, coupled cluster theory, or dispersion corrected density functional theory. However, due to nonlinear scaling of these methods, optimizing the geometry of large clusters still remains a formidable quantum chemistry challenge. Fragment-based methods, such as divide-and-conquer, molecular tailoring approach (MTA), fragment molecular orbitals, and generalized energy-based fragmentation approach, provide alternatives for overcoming the scaling problem for spatially extended molecular systems. Within MTA, a large

  13. Ab initio Computations of the Electronic, Mechanical, and Thermal Properties of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2

    Science.gov (United States)

    Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray

    2011-01-01

    Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.

  14. 360⁰ -View of Quantum Theory and Ab Initio Simulation at Extreme Conditions: 2014 Sanibel Symposium

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Hai-Ping [Univ. of Florida, Gainesville, FL (United States)

    2016-09-02

    The Sanibel Symposium 2014 was held February 16-21, 2014, at the King and Prince, St. Simons Island, GA. It was successful in bringing condensed-matter physicists and quantum chemists together productively to drive the emergence of those specialties. The Symposium had a significant role in preparing a whole generation of quantum theorists. The 54th Sanibel meeting looked to the future in two ways. We had 360⁰-View sessions to honor the exceptional contributions of Rodney Bartlett (70), Bill Butler (70), Yngve Öhrn (80), Fritz Schaefer (70), and Malcolm Stocks (70). The work of these five has greatly impacted several generations of quantum chemists and condensed matter physicists. The “360⁰” is the sum of their ages. More significantly, it symbolizes a panoramic view of critical developments and accomplishments in theoretical and computational chemistry and physics oriented toward the future. Thus, two of the eight 360⁰-View sessions focused specifically on younger scientists. The 360⁰-View program was the major component of the 2014 Sanibel meeting. Another four sessions included a sub-symposium on ab initio Simulations at Extreme Conditions, with focus on getting past the barriers of present-day Born-Oppenheimer molecular dynamics by advances in finite-temperature density functional theory, orbital-free DFT, and new all-numerical approaches.

  15. Systematic ab initio study of half-Heusler materials for optoelectronic applications

    Energy Technology Data Exchange (ETDEWEB)

    Gruhn, Thomas; Felser, Claudia [Institute of Inorganic and Analytical Chemistry, Johannes Gutenberg University, Mainz (Germany)

    2010-07-01

    The development of new, optimized optoelectronic devices depends crucially on the availability of semiconductors with taylored electronic and structural properties. At the moment, the majority of applications is based on a rather small set of semiconducting materials, while many more semiconductors exist in the huge class of ternary compounds. Especially, the class of 8-electron half-Heusler materials comprises a large number semiconducters with various properties. With the help of ab initio density functional theory we have studied essentially all 8-electron half-Heusler compounds that are of technological relevance. For more than 650 compounds we have determined the optimum configuration by varying the lattice constant and permuting the elements over the sublattices. Within this exceptionally large data set we have studied the band structure and the lattice constants as a function of the electronegativities of the elements, the arrangement of the atoms, and the atomic radii. The results are used to select suitable materials for the buffer layer in thin-film solar cells with a Cu(In,Ga)Se{sub 2} (CIGS) absorber layer. Considering the bandgap and the geometrical matching with the CIGS film, we have obtained a set of 29 compounds that are promissing materials for cadmium-free CIGS buffer layer.

  16. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    Science.gov (United States)

    Lespade, Laure

    2016-08-01

    Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car-Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  17. Experimental and ab initio DFT calculated Raman Spectrum of Sudan I, a Red Dye

    DEFF Research Database (Denmark)

    Kunov-Kruse, Andreas Jonas; Kristensen, Steffen Buus; Liu, Chuan

    2011-01-01

    The red dye Sudan I was investigated by Raman spectroscopy using different excitation wavelengths (1064, 532 and 244 nm). A calculation of the Raman spectrum based on quantum mechanical ab initio density functional theory (DFT) was made using the RB3LYP method with the 3-21G and 6-311+G(d,p) basis....... Comparison was made with other azo dyes in the literature on natural, abundant plant pigments. The results show that there is a possibility in foodstuff analysis to distinguish Sudan I from other dyes by using Raman spectroscopy with more than one laser wavelength for resonance enhancement of the different...... of the Sudan I molecule was involved in the majority of the vibrations through N N and C–N stretching and various bending modes. Low-intensity bands in the lower wavenumber range (at about 721, 616, 463 and 218 cm−1) were selectively enhanced by the resonance Raman effect when using the 532 nm excitation line...

  18. Matching a surface complexation model with ab initio molecular dynamics: montmorillonite case

    Energy Technology Data Exchange (ETDEWEB)

    Kulik, D.A.; Churakov, S.V. [Paul Scherrer Institute, Nuclear Energy and Safety Dpt., Lab. for Waste Management, CH-5232 Villigen PSI (Switzerland)

    2005-07-01

    Speciation modelling of sorption on mineral-water interfaces is performed with help of surface complexation models (SCM), suitable for diluted suspensions that seem to reach adsorption equilibrium within laboratory times. Electrostatic SCMs need several input parameters even for a relatively simple oxide mineral surface. Moreover, the electrolyte ion adsorption constants in triple layer (TL) or basic Stern (BS) models depend on the inner layer capacitance density Cl, but clear physical understanding of this parameter is missing so far. SCMs can fit acidimetric or metal titration data well at quite different combinations of input parameters, and this fact casts doubt on any interpretation of fitted parameter values in terms of microscopic physicochemical mechanisms. The problem is even deeper in SCMs for clay minerals like montmorillonite having at least two surface types: the edges exposing different (aluminol and silanol) functional groups, and the basal siloxane planes with permanent charge and ion exchange. A feasible way to overcome the caveat of SCMs is seen nowadays in relying on crystallographic data and ab initio calculations to restrict the EDL setup, species stoichiometries, and input parameter values when constructing the adsorption model. The aim of this contribution is to discuss how recent advances in sample surface characterization an d in quantum-chemistry calculations for pyrophyllite can help in putting together a multi-site-surface electrostatic SCM for montmorillonite implemented in GEM approach. The quality of macroscopic model fits is checked against the titration data. (authors)

  19. SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

    Science.gov (United States)

    Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

    2017-10-01

    As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

  20. Ab initio calculation of the crystalline structure and IR spectrum of polymers: nylon 6 polymorphs.

    Science.gov (United States)

    Quarti, Claudio; Milani, Alberto; Civalleri, Bartolomeo; Orlando, Roberto; Castiglioni, Chiara

    2012-07-19

    State-of-the-art computational methods in solid-state chemistry were applied to predict the structural and spectroscopic properties of the α and γ crystalline polymorphs of nylon 6. Density functional theory calculations augmented with an empirical dispersion correction (DFT-D) were used for the optimization of the two different crystal structures and of the isolated chains, characterized by a different regular conformation and described as one-dimensional infinite chains. The structural parameters of both crystalline polymorphs were correctly predicted, and new insight into the interplay of conformational effects, hydrogen bonding, and van der Waals interactions in affecting the properties of the crystal structures of polyamides was obtained. The calculated infrared spectra were compared to experimental data; based on computed vibrational eigenvectors, assignment of the infrared absorptions of the two nylon 6 polymorphs was carried out and critically analyzed in light of previous investigations. On the basis of a comparison of the computed and experimental IR spectra, a set of marker bands was identified and proposed as a tool for detecting and quantifying the presence of a given polymorph in a real sample: several marker bands employed in the past were confirmed, whereas some of the previous assignments are criticized. In addition, some new marker bands are proposed. The results obtained demonstrate that accurate computational techniques are now affordable for polymers characterization, opening the way to several applications of ab initio modeling to the study of many families of polymeric materials.

  1. Ab initio energetic study of oxide ceramics with rare-earth elements

    Institute of Scientific and Technical Information of China (English)

    WU Bo; Matvei Zinkevich; WANG Chong; Fritz Aldinger

    2006-01-01

    Ab initio energetic calculations based on the density functional theory (DFT) and the projector augmented wave method (PAW) for determining the polymorphisms of lanthanide sesquioxides Ln2O3 (where Ln = rare-earth element. Y,and Sc), LnMO3 perovskites (where M = Al and Ga), and Ln2B2O7 pyrochlores (where B = Ti, Zr, and Hf) were reported. The relative lattice stabilities agreed well with the critically assessed results or the experimental results except the C-type Ln2O3 with a cubic structure, for which the calculated total energies were considerably more negative. With the increase of the Ln3+-cation radius, the polymorphic structures showed a degenerative tendency. The tendencies and quantities of the enthalpies of formation of the ternary oxide ceramics synthesized from their constituent binary oxides reasonably agreed with the available experimental results, and valuable thermodynamic properties were afforded to the compound, for which no experimental data is available. The enthalpies of formation of both perovskites and pyrochlores tend to become more negative with the increase of the Ln3+-cation radius.

  2. Synthesis, FTIR, FT-Raman, UV-visible, ab initio and DFT studies on benzohydrazide.

    Science.gov (United States)

    Arjunan, V; Rani, T; Mythili, C V; Mohan, S

    2011-08-01

    A systematic vibrational spectroscopic assignment and analysis of benzohydrazide (BH) has been carried out by using FTIR and FT-Raman spectral data. The vibrational analysis were aided by electronic structure calculations--ab initio (RHF) and hybrid density functional methods (B3LYP and B3PW91) performed with 6-31G(d,p) and 6-311++G(d,p) basis sets. Molecular equilibrium geometries, electronic energies, IR intensities, harmonic vibrational frequencies, depolarization ratios and Raman activities have been computed. Potential energy distribution (PED) and normal mode analysis have also been performed. The assignments proposed based on the experimental IR and Raman spectra have been reviewed and complete assignment of the observed spectra have been proposed. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λ(max) were determined by time-dependent DFT (TD-DFT) method. The geometrical, thermodynamical parameters and absorption wavelengths were compared with the experimental data. The interactions of carbonyl and hydrazide groups on the benzene ring skeletal modes were investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Ab initio atomistic thermodynamics study on the oxidation mechanism of binary and ternary alloy surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Shi-Yu, E-mail: buaasyliu@gmail.com [College of Physics and Electronic Information Science, Tianjin Normal University, Tianjin 300387 (China); Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, Shiyang [Institute of Information Optics, Zhejiang Normal University, Jinhua, Zhejiang 321004 (China); Li, De-Jun [College of Physics and Electronic Information Science, Tianjin Normal University, Tianjin 300387 (China); Wang, Sanwu, E-mail: sanwu-wang@utulsa.edu [Department of Physics and Engineering Physics, The University of Tulsa, Tulsa, Oklahoma 74104 (United States); Guo, Jing; Shen, Yaogen, E-mail: meshen@cityu.edu.hk [Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong (China)

    2015-02-14

    Utilizing a combination of ab initio density-functional theory and thermodynamics formalism, we have established the microscopic mechanisms for oxidation of the binary and ternary alloy surfaces and provided a clear explanation for the experimental results of the oxidation. We construct three-dimensional surface phase diagrams (SPDs) for oxygen adsorption on three different Nb-X(110) (X = Ti, Al or Si) binary alloy surfaces. On the basis of the obtained SPDs, we conclude a general microscopic mechanism for the thermodynamic oxidation, that is, under O-rich conditions, a uniform single-phase SPD (type I) and a nonuniform double-phase SPD (type II) correspond to the sustained complete selective oxidation and the non-sustained partial selective oxidation by adding the X element, respectively. Furthermore, by revealing the framework of thermodynamics for the oxidation mechanism of ternary alloys through the comparison of the surface energies of two separated binary alloys, we provide an understanding for the selective oxidation behavior of the Nb ternary alloy surfaces. Using these general microscopic mechanisms, one could predict the oxidation behavior of any binary and multi-component alloy surfaces based on thermodynamics considerations.

  4. Ab Initio Study of Thermodynamic Properties of Lithium, Sodium, and Potassium Sulfates

    Science.gov (United States)

    Zhuravlev, Yu. N.; Bugaeva, I. A.; Zhuravleva, L. V.

    2013-11-01

    The thermodynamic parameters of lithium, sodium, and potassium single and double sulfate crystals are determined by the method of ab initio calculation of a linear combination of atomic orbitals in the gradient approximation of density functional theory using the software package CRYSTAL09 within the framework of the quasi-harmonic approximation of the Debye theory. It is demonstrated that the standard entropies and heat capacities as well as the temperature dependences are in satisfactory agreement with the available experimental data. The average frequency, Debye temperature, and thermal conductivity coefficient increase with external pressure, whereas the Gruneisen parameter decreases. The dependences of the potentials of free and internal energies on the temperature and volume are expressed through the Birch-Murnaghan equation of state and a square-law dependence on these parameters of their vibrational components. The thermodynamic parameters of lithium-potassium sulfate appear closer to potassium sulfate, whereas for sodium-potassium, they lie between the corresponding parameters for single compounds.

  5. Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone.

    Science.gov (United States)

    Küçük, Sami Emre; Biktagirov, Timur; Sezer, Deniz

    2015-10-14

    A computational analysis of the Overhauser effect is reported for the proton, methyl carbon, and carbonyl carbon nuclei of liquid acetone doped with the nitroxide radical TEMPOL. A practical methodology for calculating the dynamic nuclear polarization (DNP) coupling factors by accounting for both dipole-dipole and Fermi-contact interactions is presented. The contribution to the dipolar spectral density function of nuclear spins that are not too far from TEMPOL is computed through classical molecular dynamics (MD) simulations, whereas the contribution of distant spins is included analytically. Fermi contacts are obtained by subjecting a few molecules from every MD snapshot to ab initio quantum mechanical calculations. Scalar interaction is found to be an essential part of the (13)C Overhauser DNP. While mostly detrimental to the carbonyl carbon of acetone it is predicted to result in large enhancements of the methyl carbon signal at magnetic fields of 9 T and beyond. In contrast, scalar coupling is shown to be negligible for the protons of acetone. The additional influence of proton polarization on the carbon DNP (three-spin effect) is also analyzed computationally. Its effect, however, is concluded to be practically insignificant for liquid acetone.

  6. Ab initio study, investigation of NMR shielding tensors, NBO and vibrational frequency of catechol thioethers

    Directory of Open Access Journals (Sweden)

    A. Bagheri Gh

    2010-08-01

    Full Text Available The electrochemical oxidation of dopamine and 3,4-dihydroxymethamphetamine (HHMA has been studied in the presence of GSH and cysteine as a nucleophile. In order to determine the optimized geometries, energies, dipole moments, atomic charges, thermochemical analysis and other properties, we performed quantum chemical ab initio and density functional calculations at B3LYP level with 6-31G* basis set. The structural and vibrational properties of 5-S-glutathionyldopamine, 5-S-cysteinyldopamine and 5-S-N-acetylcysteinyldopamine are studied. The chemical shifts of anisotropy and Δδ are calculated. The gauge-invariant atomic orbital (GIAO method was employed to calculate isotropic atomic shielding of compounds. These calculations yield molecular geometries in good agreement with available experimental data. The bond lengths, bond angles, dipole moment, electron affinity, ionization potential, electronegativy, absolute hardness, highest occupied molecular orbital (HOMO and the energy of the lowest unoccupied molecular orbital (LUMO of the studied compounds were calculated in gas phase and water. NMR analysis of dopamine-o-quinone-glutathione conjugate revealed that the addition of glutathione was at C-5 to form glutathionyl-dopamine.

  7. Ab initio random structure search for 13-atom clusters of fcc elements.

    Science.gov (United States)

    Chou, J P; Hsing, C R; Wei, C M; Cheng, C; Chang, C M

    2013-03-27

    The 13-atom metal clusters of fcc elements (Al, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) were studied by density functional theory calculations. The global minima were searched for by the ab initio random structure searching method. In addition to some new lowest-energy structures for Pd13 and Au13, we found that the effective coordination numbers of the lowest-energy clusters would increase with the ratio of the dimer-to-bulk bond length. This correlation, together with the electronic structures of the lowest-energy clusters, divides the 13-atom clusters of these fcc elements into two groups (except for Au13, which prefers a two-dimensional structure due to the relativistic effect). Compact-like clusters that are composed exclusively of triangular motifs are preferred for elements without d-electrons (Al) or with (nearly) filled d-band electrons (Ni, Pd, Cu, Ag). Non-compact clusters composed mainly of square motifs connected by some triangular motifs (Rh, Ir, Pt) are favored for elements with unfilled d-band electrons.

  8. A theoretical study of benzaldehyde derivatives as tyrosinase inhibitors using Ab initio calculated NQCC parameters

    Directory of Open Access Journals (Sweden)

    Marjan Rafiee

    2015-09-01

    Full Text Available Tyrosinase is a multifunctional copper-containing enzyme. It can catalyze two distinct reactions of melanin synthesis and benzaldehyde derivatives, which are potential tyrosinase inhibitors. To find the relationships between charge distributions of benzaldehyde and their pharmaceutical behavior, the present study aimed at investigating nuclear quadrupole coupling constants of quadrupolare nuclei in the functional benzaldehyde group and calculating some its derivatives. In addition, the differences between the electronic structures of various derivatives of this depigmenting drug were examined. All ab initio calculations were carried out using Gaussian 03. The results predicted benzaldehyde derivatives to be bicentral inhibitors; nevertheless, the oxygen or hydrogen contents of the aldehyde group were not found to be the only active sites. Furthermore with the presence of the aldehyde group, the terminal methoxy group in C4 was found to contribute to tyrosinase inhibitory activities. In addition, an oxygen atom with high charge density in the side chain was found to play an important role in its inhibitory effect.

  9. Formation of star nanowires of sulfur-doped zinc oxide: Ab initio calculations

    Science.gov (United States)

    Lin, Qiu-Bao; Wu, Shun-Qing; Zhu, Zi-Zhong

    2016-09-01

    ZnO nanowires are hexagonally shaped under normal growth conditions, but are transformed from a hexagon to hexagram ones when sulfur dopants are added into the growth solution. The formation mechanism of the hexagram-shaped ZnO nanowires is further studied by the ab initio calculations in this paper. The present calculations support the fact that the hexagonally shaped ZnO nanowires are transformed to hexagram shaped ones when the O atoms on the side surfaces of the nanowires are replaced by S atoms in certain quantities. It indicates that the ratio of sulfur content plays an important role in the hexagram formation. The results of the electronic charge densities indicate that the charge transfer makes the S-Zn bond longer than that of O-Zn. The new charge distribution on the side planes due to the S atoms replacement leads to the formation of the hexagram-shaped nanowires. The calculation on the electronic properties shows that a sulfur-doped hexagram ZnO nanowire is an indirect band gap semiconductor with a narrow gap. When dopant is increased, the gap will decrease.

  10. An ab initio study of the polytypism in InP

    Science.gov (United States)

    Dacal, Luis C. O.; Cantarero, A.

    2016-09-01

    The existence of polytypism in semiconductor nanostructures gives rise to the appearance of stacking faults which many times can be treated as quantum wells. In some cases, despite of a careful growth, the polytypism can be hardly avoided. In this work, we perform an ab initio study of zincblende stacking faults in a wurtzite InP system, using the supercell approach and taking the limit of low density of narrow stacking faults regions. Our results confirm the type II band alignment between the phases, producing a reliable qualitative description of the band gap evolution along the growth axis. These results show an spacial asymmetry in the zincblende quantum wells, that is expected due to the fact that the wurtzite stacking sequence (ABAB) is part of the zincblende one (ABCABC), but with an unexpected asymmetry between the valence and the conduction bands. We also present results for the complex dielectric function, clearly showing the influence of the stacking on the homostructure values and surprisingly proving that the correspondent bulk results can be used to reproduce the polytypism even in the limit we considered.

  11. Optimized energy landscape exploration using the ab initio based activation-relaxation technique

    Science.gov (United States)

    Machado-Charry, Eduardo; Béland, Laurent Karim; Caliste, Damien; Genovese, Luigi; Deutsch, Thierry; Mousseau, Normand; Pochet, Pascal

    2011-07-01

    Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C20 clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.

  12. Tunneling of electrons via rotor-stator molecular interfaces: Combined ab initio and model study

    Science.gov (United States)

    Petreska, Irina; Ohanesjan, Vladimir; Pejov, Ljupčo; Kocarev, Ljupčo

    2016-07-01

    Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that conformation-dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previous work where we investigated the coherent transport via strongly coupled delocalized orbital by application of Non-equilibrium Green's Function Formalism.

  13. Ab initio study of a Y-doped Σ31 grain boundary in alumina

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The atomic structures and energetics of clean and Y-doped general grain boundary (GB) Σ31/(0001) models in α-Al2O3 are studied by a series of high precision ab initio calculations. A large supercell with 700 atoms and periodic boundary conditions is adopted for undoped and Y-doped GB with different substitution sites and con-centrations. It is shown that Y atoms preferably segregate to the central column of the 7-member Al ring. This is explained as more favorable bond formation for Y in this position and lower GB energy. The calculated GB formation energy for the clean and Y-doped cases is respectively 3.99 and 3.67 J/m2. On the average, the GB region in Σ31 has a slightly lower charge density than the bulk crystalline region. In addtition, the GB induces a long ranged asymmetric electrostatic potential distri-bution on each side of the grain boundary.

  14. Communication: Towards ab initio self-energy embedding theory in quantum chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Lan, Tran Nguyen, E-mail: latran@umich.edu [Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (United States); Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States); Kananenka, Alexei A.; Zgid, Dominika [Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (United States)

    2015-12-28

    The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green’s function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.

  15. Ab initio study of charge, spin and orbital ordering in manganites

    CERN Document Server

    Tyer, R

    2001-01-01

    The subject of this thesis was the calculation of the electronic structure for the manganites LaMnO sub 3 and CaMnO sub 3. The implementation of the Self-Interaction Corrected Local Spin Density (SIC-LSD) formalism within the Tight Binding Linear Muffin-Tin Orbital method in conjunction with the Atomic Sphere Approximation was used for these calculations. The SIC-LSD total energy functional has been used to investigate the spin ordering and valency of CaMnO sub 3 and LaMnO sub 3. In order to assess the role of the structural distortion in LaMnO sub 3 , these calculations were performed for an idealised cubic structure as well as for the observed distorted orthorhombic structure. Orbital rotations of the localised (SIC corrected) states were implemented. These orbital rotations were then used to perform the first ab-initio investigation of orbital ordering in LaMnO sub 3. For the experimentally observed A-type antiferromagnetic ordering, the correct orbital structure of alternating manganese d sub 3 sub x sub ...

  16. Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach.

    Science.gov (United States)

    Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Cohen, Aron J; Yang, Weitao

    2008-03-28

    Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H(2)O)(6)(2+/3+) and Ru(H(2)O)(6)(2+/3+). The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.

  17. Stabilization of peptide helices by length and vibrational free energies: Ab initio case study of polyalanine

    Science.gov (United States)

    Rossi, Mariana; Blum, Volker; Scheffler, Matthias

    2012-02-01

    Helices are one of the most abundant secondary structure ``building blocks" of polypeptides and proteins. Here, we explore helix stabilization as a function of peptide length and temperature [harmonic approximation to the vibrational free energy (FE)], for the alanine-based peptide, Ac-Alan-LysH^+ n=4-15, in the gas phase. For n=4-8, we predict the lowest energy structures in density-functional theory, using the van der Waals (vdW) corrected[1] PBE exchange-correlation potential. α-helices become the lowest energy structures at n 7-8 on the potential energy surface, but only barely and if including vdW interactions. At finite temperatures, the helices are further stabilized over compact conformers. While the vibrational entropy is the leading stabilizing term at 300 K, also the zero-point-energies favor the helical structures. For n>=8, the α-helix should be the only accessible conformer in the FE surface at 300 K, in agreement with experiment[2] and with our own comparison[3] of calculated ab initio anharmonic IR spectra to experimental IR multiple photon dissociation data for n=5, 10, and 15. [1] Tkatchenko and Scheffler, PRL 102, 073055 (2009); [2] Kohtani and Jarrold, JACS 108, 8454 (2004); [3] Rossi et al., JPCL 1, 3465 (2010).

  18. Communication: Towards ab initio self-energy embedding theory in quantum chemistry.

    Science.gov (United States)

    Lan, Tran Nguyen; Kananenka, Alexei A; Zgid, Dominika

    2015-12-28

    The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green's function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.

  19. A theoretical study of benzaldehyde derivatives as tyrosinase inhibitors using Ab initio calculated NQCC parameters

    Science.gov (United States)

    Rafiee, Marjan; Javaheri, Masoumeh

    2015-01-01

    Tyrosinase is a multifunctional copper-containing enzyme. It can catalyze two distinct reactions of melanin synthesis and benzaldehyde derivatives, which are potential tyrosinase inhibitors. To find the relationships between charge distributions of benzaldehyde and their pharmaceutical behavior, the present study aimed at investigating nuclear quadrupole coupling constants of quadrupolare nuclei in the functional benzaldehyde group and calculating some its derivatives. In addition, the differences between the electronic structures of various derivatives of this depigmenting drug were examined. All ab initio calculations were carried out using Gaussian 03. The results predicted benzaldehyde derivatives to be bicentral inhibitors; nevertheless, the oxygen or hydrogen contents of the aldehyde group were not found to be the only active sites. Furthermore with the presence of the aldehyde group, the terminal methoxy group in C4 was found to contribute to tyrosinase inhibitory activities. In addition, an oxygen atom with high charge density in the side chain was found to play an important role in its inhibitory effect. PMID:27844007

  20. Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.

    Science.gov (United States)

    Ishikawa, Tetsuya; Hayakawa, Daichi; Miyamoto, Hitomi; Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

    2015-11-19

    The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).

  1. Switchable magnetic moment in cobalt-doped graphene bilayer on Cu(111): An ab initio study

    Science.gov (United States)

    Souza, Everson S.; Scopel, Wanderlã L.; Miwa, R. H.

    2016-06-01

    In this work, we have performed an ab initio theoretical investigation of substitutional cobalt atoms in the graphene bilayer supported on the Cu(111) surface (Co/GBL/Cu). Initially, we examined the separated systems, namely, graphene bilayer adsorbed on Cu(111) (GBL/Cu) and a free standing Co-doped GBL (Co/GBL). In the former system, the GBL becomes n -type doped, where we map the net electronic charge density distribution along the GBL-Cu(111) interface. The substitutional Co atom in Co/GBL lies between the graphene layers, and present a net magnetic moment mostly due to the unpaired Co-3 dz2 electrons. In Co/GBL/Cu, we found that the Cu(111) substrate rules (i) the energetic stability, and (ii) the magnetic properties of substitutional Co atoms in the graphene bilayer. In (i), the substitutional Co atom becomes energetically more stable lying on the GBL surface, and in (ii), the magnetic moment of Co/GBL has been quenched due to the Cu(111) → Co/GBL electronic charge transfer. We verify that such a charge transfer can be tuned upon the application of an external electric field, and thus mediated by a suitable change on the electronic occupation of the Co-dz2 orbitals, we found a way to switch-on and -off the magnetization of the Co-doped GBL adsorbed on the Cu(111) surface.

  2. 360⁰ -View of Quantum Theory and Ab Initio Simulation at Extreme Conditions: 2014 Sanibel Symposium

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Hai-Ping [Univ. of Florida, Gainesville, FL (United States)

    2016-09-02

    The Sanibel Symposium 2014 was held February 16-21 2014 at the King and Prince, St. Simons Island, GA. It was successful in bringing condensed-matter physicists and quantum chemists together productively to drive the emergence of those specialties. The Symposium had a significant role in preparing a whole generation of quantum theorists. The 54th Sanibel meeting looked to the future in two ways. We had 360⁰-View sessions to honor the exceptional contributions of Rodney Bartlett (70), Bill Butler (70), Yngve Öhrn (80), Fritz Schaefer (70), and Malcolm Stocks (70). The work of these five has greatly impacted several generations of quantum chemists and condensed matter physicists. The “360⁰” is the sum of their ages. More significantly, it symbolizes a panoramic view of critical developments and accomplishments in theoretical and computational chemistry and physics oriented toward the future. Thus, two of the eight 360⁰-View sessions focused specifically on younger scientists. The 360⁰-View program was the major component of the 2014 Sanibel meeting. Another four sessions included a sub-symposium on ab initio Simulations at Extreme Conditions, with focus on getting past the barriers of present-day Born-Oppenheimer molecular dynamics by advances in finite-temperature density functional theory, orbital-free DFT, and new all-numerical approaches.

  3. Ab-initio study of germanium di-interstitial using a hybrid functional (HSE)

    Science.gov (United States)

    Igumbor, E.; Ouma, C. N. M.; Webb, G.; Meyer, W. E.

    2016-01-01

    In this work, we present ab-initio calculation results of Ge di-interstitials (I2(Ge)) in the framework of the density functional theory (DFT) using the Heyd, Scuseria, and Ernzerhof (HSE) hybrid functional. The formation energy, transition levels and minimum energy configurations were obtained for I2(Ge) -2, -1, 0, +1 and +2 charge states. The calculated formation energies show that for all charge states of I2(Ge), the double tetrahedral (T) configuration formed the most stable defect with a binding energy of 1.24 eV in the neutral state. We found the (+2/+1) charge state transition level for the T lying below the conduction band minimum and (+2/+1) for the split[110]-tetrahedral configuration lying deep at 0.41 eV above the valence band maximum. The di-interstitials in Ge exhibited the properties of both shallow and deep donor levels at (+2/+1) within the band gap and depending on the configurations. I2(Ge) gave rise to negative-U, with effective-U values of -0.61 and -1.6 eV in different configurations. We have compared our results with calculations of di-interstitials in silicon and available experimental data.

  4. Ab-Initio Based Computation of Rate Constants for Spin Forbidden Metalloprotein-Substrate Reactions

    Science.gov (United States)

    Ozkanlar, Abdullah; Rodriguez, Jorge H.

    2007-03-01

    Some chemical and biochemical reactions are non-adiabatic processes whereby the total spin angular momentum, before and after the reaction, is not conserved. These are named spin- forbidden reactions. The application of ab-initio methods, such as spin density functional theory (SDFT), to the prediction of rate constants is a challenging task of fundamental and practical importance. We apply non-adiabatic transition state theory (NA-TST) in conjuntion with SDFT to predict the rate constant of the spin- forbidden recombination of carbon monoxide with iron tetracarbonyl. To model the surface hopping probability between singlet and triplet states, the Landau-Zener formalism is used. The lowest energy point for singlet-triplet crossing, known as minimum energy crossing point (MECP), was located and used to compute, in a semi-quantum approach, reaction rate constants at 300 K. The predicted rates are in very good agreement with experiment. In addition, we present results for the spin- forbidden ligand binding reactions of iron-containing heme proteins such as myoglobin.

  5. Ab initio theory of exchange interactions and the Curie temperature of bulk Gd

    CERN Document Server

    Turek, I; Bihlmayer, G; Bluegel, S

    2003-01-01

    An ab initio approach to the magnetic properties of bulk hexagonal Gd is developed that is based on the local spin-density approximation with the 4f electrons treated as localized core electrons. The effective one-electron problem is solved using the tight-binding linear muffin-tin orbital method in the atomic-sphere approximation with the valence basis consisting of s-, p-and d-type orbitals. The approach leads to a correct description of the ground-state properties like the stability of the ferromagnetic structure, the magnetic moment and the equilibrium lattice constant. Application of a real-space Green-function formalism yields the exchange pair interactions between distant neighbours that are inevitable for quantitative studies of magnetic excitations. The distance dependence and anisotropy of the exchange pair interactions are presented and the Curie temperature in the mean-field approximation is evaluated. The obtained value of 334 K is in much better agreement with the experimental value of 293 K tha...

  6. Ab initio Stellar Astrophysics: Reliable Modeling of Cool White Dwarf Atmospheres

    CERN Document Server

    Kowalski, Piotr M

    2010-01-01

    Over the last decade {\\it ab initio} modeling of material properties has become widespread in diverse fields of research. It has proved to be a powerful tool for predicting various properties of matter under extreme conditions. We apply modern computational chemistry and materials science methods, including density functional theory (DFT), to solve lingering problems in the modeling of the dense atmospheres of cool white dwarfs ($T_{\\rm eff}\\rm <7000 \\, K$). Our work on the revision and improvements of the absorption mechanisms in the hydrogen and helium dominated atmospheres resulted in a new set of atmosphere models. By inclusion of the Ly-$\\rm \\alpha$ red wing opacity we successfully fitted the entire spectral energy distributions of known cool DA stars. In the subsequent work we fitted the majority of the coolest stars with hydrogen-rich models. This finding challenges our understanding of the spectral evolution of cool white dwarfs. We discuss a few examples, including the cool companion to the pulsar...

  7. Ab initio study of He trapping, diffusion and clustering in Y2O3

    Science.gov (United States)

    Lai, Wensheng; Ou, Yidian; Lou, Xiaofeng; Wang, Fei

    2017-02-01

    Ab initio calculations have been performed to study the formation and migration energies of helium atoms and the stability of helium-vacancy clusters in a Y2O3 crystal. The calculated formation energies show that a helium atom is preferred to occupy an yttrium vacancy site with a large volume and low electron density. The migration energy of the helium atom by an interstitial mechanism is 0.31 eV. Calculations of the binding energies of an extra helium atom to the helium-vacancy clusters vary with the number of helium atoms in the clusters with a typical value of 0.4-0.7 eV. This turns negative when the He atoms reach saturation; that indicates that vacancy clusters can attract a limited number of helium atoms to form small stable helium-vacancy clusters. Our calculations suggest that the use of Y2O3 in oxide dispersion strengthened ferritic steels may reduce He gas bubble formation as it may act as sink for trapping helium atoms.

  8. Optimized energy landscape exploration using the ab initio based activation-relaxation technique.

    Science.gov (United States)

    Machado-Charry, Eduardo; Béland, Laurent Karim; Caliste, Damien; Genovese, Luigi; Deutsch, Thierry; Mousseau, Normand; Pochet, Pascal

    2011-07-21

    Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C(20) clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.

  9. Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    Science.gov (United States)

    Rosenow, Phil; Tonner, Ralf

    2016-05-01

    The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

  10. Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure

    Energy Technology Data Exchange (ETDEWEB)

    Hoy, Erik P.; Mazziotti, David A., E-mail: damazz@uchicago.edu [Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

    2015-08-14

    Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

  11. Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

    Science.gov (United States)

    Hoy, Erik P; Mazziotti, David A

    2015-08-14

    Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

  12. Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory

    Science.gov (United States)

    Frandsen, Benjamin A.; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J.; Staunton, Julie B.; Billinge, Simon J. L.

    2016-05-01

    We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ˜1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

  13. Electron Transport and Thermal Transport Simulation Using Ab Initio Methods

    Science.gov (United States)

    2013-08-12

    Aobaku, Sendai, 980-8579 Japan Motivation: The motivation of our study is to realize the organic molecular conductivity computation based on...density distribution results into the Hamiltonian of the system. Then, from statistical mechanics, diagonalization of the Hamiltonian achieves new...the Hamiltonian comes from the density distribution. But the second step is replaced, and the new density distribution stems from the NEGF rather

  14. {\\it Ab initio} nuclear structure - the large sparse matrix eigenvalue problem

    CERN Document Server

    Vary, James P; Ng, Esmond; Yang, Chao; Sosonkina, Masha

    2009-01-01

    The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several {\\it ab initio} methods have now emerged that provide nearly exact solutions for some nuclear properties. The {\\it ab initio} no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds $10^{10}$ and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving t...

  15. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Nalini; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, Shimla(HP)-171005 (India); Thakur, Anil [Department of Physics, Govt. P. G. College Solan (HP)-173212 (India)

    2015-05-15

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

  16. Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

    Science.gov (United States)

    Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna

    2016-01-01

    Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.

  17. [Photoelectron Spectra of CCl2-: Ab Initio Calculation and Franck-Condon Analysis].

    Science.gov (United States)

    Wu, Jun

    2015-12-01

    Geometry optimization and harmonic vibrational frequency calculations were performed on the X¹A₁ state of CCl₂ and X²B₁ state of CCl₂⁻ at the B3LYP, MP2, CCSD levels. Franck-Condon analysis and spectral simulations were carried out on the photoelectron band of CCl₂⁻ including Duschinsky effects. The simulated spectra obtained are in excellent agreement with the experiment. Note that Duschinsky effect between bending vibration and the symmetric stretch modes should be considered in the CCl₂ (X¹A₁)-CCl₂⁻ (X²B₁) photodetachment process. By combining ab initio calculations with Franck-Condon analyses, the assignment of spectrum observed is firmly established to the X¹A₁-X²B₁ photodetachment process of the CCl₂⁻ radical, and the recommended geometric parameters of which in the literature are confirmed again base on ab initio theory and IFCA process.

  18. A highly accurate {\\it ab initio} potential energy surface for methane

    CERN Document Server

    Owens, Alec; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2016-01-01

    A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art \\textit{ab initio} theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include: core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of $^{12}$CH$_4$ reproduced with a root-mean-square error of $0.70{\\,}$cm$^{-1}$. The computed \\textit{ab initio} equilibrium C{--}H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as $J$ (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the e...

  19. Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Navratil, P; Ormand, W E; Forssen, C; Caurier, E

    2004-11-30

    There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.

  20. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Matsushita, Y., E-mail: kurita@cs.tut.ac.jp; Murakawa, T., E-mail: kurita@cs.tut.ac.jp; Shimamura, K., E-mail: kurita@cs.tut.ac.jp; Oishi, M., E-mail: kurita@cs.tut.ac.jp; Ohyama, T., E-mail: kurita@cs.tut.ac.jp; Kurita, N., E-mail: kurita@cs.tut.ac.jp [Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580 (Japan)

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  1. Ab initio calculations on the magnetic properties of transition metal complexes

    Energy Technology Data Exchange (ETDEWEB)

    Bodenstein, Tilmann; Fink, Karin [Karlsruhe Institute of Technology, Institute of Nanotechnology, POB 3640, 76021 Karlsruhe (Germany)

    2015-12-31

    We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes.

  2. Bridging a gap between continuum-QCD and ab initio predictions of hadron observables

    Directory of Open Access Journals (Sweden)

    Daniele Binosi

    2015-03-01

    Full Text Available Within contemporary hadron physics there are two common methods for determining the momentum-dependence of the interaction between quarks: the top-down approach, which works toward an ab initio computation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD's gauge sector coincides with that required in order to describe ground-state hadron observables using a nonperturbative truncation of QCD's Dyson–Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.

  3. Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective

    Science.gov (United States)

    Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge

    2013-03-01

    Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at < 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ~300 K across the entire pressure range considered.

  4. Ab initio simulations and neutron scattering studies of structure and dynamics in PdH

    CERN Document Server

    Totolici, I E

    2001-01-01

    The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...

  5. An ab initio potential function for the ν13 vibrational mode of 1,3-butadiene

    Science.gov (United States)

    Senent, M. L.

    1995-06-01

    The restricted potential of the ν13 torsional mode of 1,3-butadiene has been determined from ab initio calculations. The relative energy and geometry of the second rotamer were calculated with the optimized couple cluster method with double substitutions. This ab initio level provides that the second stable structure attaches to a gauche form situated at 140.8°. The potential energy function was obtained by fitting to a symmetry-adapted Fourier series the total electronic energies of several selected conformations. These energies were calculated by the Möller-Plesset perturbation theory up to the second order (MP2) with full and partial optimization of the geometry. Torsional Raman band positions and fundamental frequencies were determined from the periodic potentials with a good agreement with experimental data. The convenience of performing fully optimized calculations to determine the restricted function is also refuted.

  6. Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2009-01-01

    spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ([C4C1Im]+X-) salts. The rotational isomerism of the [C4C1Im]+ cation is described: the presence of anti...... systems in the future. A few examples will be discussed. Contents 12.1 Introduction...........307 12.2 Brief introduction to Raman spectroscopy ..............309 12.2.1 Basics .....................309 12.2.2 Experimental, fluorescence and fouriertransform- Raman spectroscopy instrumentation ...... 311 12.......3 Brief introduction to ab-initio model calculations .... 312 12.4 Case study on Raman spectroscopy and structure of imidazolium-based ionic liquids ..... 312 12.5 Raman spectra and structure of [C4C1Im]+ liquids ..... 315 12.6 Normal mode analysis and rotational isomerism of the [C4C1Im]+ cation...

  7. Interatomic potentials for Al and Ni from experimental data and ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Mishin, Y.; Farkas, D.; Miehl, M.J.; Papaconstantopoulos, D.A.

    1999-07-01

    New embedded-atom potentials for Al and Ni have been developed by fitting to both experimental data and the results of ab initio calculations. The ab initio data were obtained in the form of energies of different alternative computer-generated crystalline structures of these metals. The potentials accurately reproduce basic equilibrium properties of Al and Ni such as the elastic constants, phonon dispersion curves, vacancy formation and migration energies, stacking fault energies, and surface energies. The equilibrium energies of various alternative structures not included in the fitting database are calculated with these potentials. The results are compared with predictions of total-energy tight-binding calculations for the same structures. The embedded-atom potentials correctly reproduce the structural stability trends, which suggests that they are transferable to different local environments encountered in atomistic simulations of lattice defects.

  8. Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.

    Science.gov (United States)

    Yang, Jianjun; Tse, John S

    2011-11-17

    The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.

  9. Ab initio calculations to support accurate modelling of the rovibronic spectroscopy calculations of vanadium monoxide (VO)

    CERN Document Server

    McKemmish, Laura K; Tennyson, Jonathan

    2016-01-01

    Accurate knowledge of the rovibronic near-infrared and visible spectra of vanadium monoxide (VO) is very important for studies of cool stellar and hot planetary atmospheres. Here, the required ab initio dipole moment and spin-orbit coupling curves for VO are produced. This data forms the basis of a new VO line list considering 13 different electronic states and containing over 277 million transitions. Open shell transition, metal diatomics are challenging species to model through ab initio quantum mechanics due to the large number of low-lying electronic states, significant spin-orbit coupling and strong static and dynamic electron correlation. Multi-reference configuration interaction methodologies using orbitals from a complete active space self-consistent-field (CASSCF) calculation are the standard technique for these systems. We use different state-specific or minimal-state CASSCF orbitals for each electronic state to maximise the calculation accuracy. The off-diagonal dipole moment controls the intensity...

  10. Emergent properties of nuclei from ab initio coupled-cluster calculations

    CERN Document Server

    Hagen, G; Hjorth-Jensen, M; Papenbrock, T

    2016-01-01

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO$_{\\rm sat}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to $^{56}$Ni. We derive an efficient scheme for including continuum effects in coupled-clust...

  11. Electrical Resistivity of Na-K Binary Liquid Alloy Using Ab-Initio Pseudopotentials

    Institute of Scientific and Technical Information of China (English)

    Anil Thakur; P. K. Ahluwalia

    2005-01-01

    @@ The study of electrical resistivity of simple binary liquid alloy Na-K is presented as a function of concentration.Hard sphere diameters of sodium (Na) and potassium (K) are obtained through the inter ionic pair potentials evaluated using Troullier and Martins ab-initio pseudopotentials, which have been used to calculate partial structure factors S(q). The Ziman formula for calculating resistivity of binary liquid alloys has been used. Form factors are calculated using ab-initio pseudopotentials. The results suggest that the first principle approach for calculating pseudopotentials with in the frame work of Ziman formalism is quite successful in explaining the electrical resistivity data of compound forming binary liquid alloys.

  12. Controlling Magnetic and Ferroelectric Order Through Geometry: Synthesis, Ab Initio Theory, Characterization of New Multi-Ferric Fluoride Materials

    Energy Technology Data Exchange (ETDEWEB)

    Halasyamani, Shiv [Univ. of Houston, TX (United States); Fennie, Craig [Cornell Univ., Ithaca, NY (United States)

    2016-11-03

    We have focused on the synthesis, characterization, and ab initio theory on multi-functional mixed-metal fluorides. With funding from the DOE, we have successfully synthesized and characterized a variety of mixed metal fluoride materials.

  13. Diffusion within α-CuI studied using ab initio molecular dynamics simulations

    Science.gov (United States)

    Mohn, Chris E.; Stølen, Svein; Hull, Stephen

    2009-08-01

    The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 Å and 60° respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the lang111rang directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the lang100rang directions) following a markedly curved trajectory and often involving short-lived (~1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 × 10-5 cm2 s-1, is in excellent agreement with that found experimentally.

  14. First fully ab initio potential energy surface of methane with a spectroscopic accuracy

    Science.gov (United States)

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2016-09-01

    Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.

  15. Projector augmented wave method: ab initio molecular dynamics with full wave functions

    Indian Academy of Sciences (India)

    Peter E Blöchl; Clemens J Först; Johannes Schimpl

    2003-01-01

    A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends and combines the traditions of existing augmented wave methods and the pseudopotential approach. Without sacrificing efficiency, the PAW method avoids transferability problems of the pseudopotential approach and it has been valuable to predict properties that depend on the full wave functions.

  16. Simulation of Ab Initio Molecular Dynamics of Shock Wave on Copper

    Institute of Scientific and Technical Information of China (English)

    张林; 蔡灵仓; 向士凯; 经福谦; 陈栋泉

    2003-01-01

    The relation between particle velocity Up, up to 4 km/s, and shock wave velocity Us in copper has been simulated with ab initio molecular dynamics. The simulated relationship without considering the correction of zero-point and finite temperature effects is Us = 4.23 + 1.53Up. After considering the correction the relation becomes Us = 4.08 + 1.53Up, which is consistent with the experimental result.

  17. Raman and ab initio studies of simple and binary 1-alkyl-3-methylimidazolium ionic liquids

    DEFF Research Database (Denmark)

    Berg, R.W.; Deetlefs, M.; Seddon, K.R.

    2005-01-01

    Raman spectra of the ionic liquids, 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)mim][PF6]), 1-hexyl-3-methylimidazolium chloride ([C(6)mim]Cl), and 1-hexyl-3-methylimidazolium hexafluorophosphate ([C(6)mim][PF6]), and binary mixtures thereof, have been assigned using ab initio MP2...... bonding between the imidazolium headgroup and the anions, and the invariance of the essentially 50:50 mixture of the predominant conformers informs on the nature of glass formation in these systems....

  18. Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2007-01-01

    spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT-Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methylimidazolium ([C4mim][X]) salts. The rotational isomerism of the [C4mim]þ cation is described: the presence of anti...... will be applied to many more systems in the future. A few examples will be discussed....

  19. Ab Initio Study on the Anti-HIV Activities of Hydroxyflavones

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yu

    2005-01-01

    Flavone and 95 hydroxyflavones have been studied with ab initio method, and their total energies, atomic charges, dipole moments, multipole moments, molecular orbital compositions, orbital energies etc. were obtained. Among them the relationship between total atomic charges and activities against HIV is basically in accordance with the experimental results. The beneficial references are provided for the extraction and synthesis of strong active anti-HIV medicines.

  20. Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds

    DEFF Research Database (Denmark)

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1994-01-01

    We have performed ab initio calculations of the energies of antiphase boundaries as well as complex and superlattice intrinsic stacking faults in nine intermetallic compounds observed in the face-centered-cubic L1(2) and DO22 structures. The calculations were performed by means of a Green's funct......'s function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations....

  1. Influence of the ab-initio nd cross sections in the critical heavy-water benchmarks

    CERN Document Server

    Morillon, B; Carbonell, J

    2013-01-01

    The n-d elastic and breakup cross sections are computed by solving the three-body Faddeev equations for realistic and semi-realistic Nucleon-Nucleon potentials. These cross sections are inserted in the Monte Carlo simulation of the nuclear processes considered in the International Handbook of Evaluated Criticality Safety Benchmark Experiments (ICSBEP). The results obtained using thes ab initio n-d cross sections are compared with those provided by the most renown international libraries.

  2. Ab initio verification of the analytical R-matrix theory for strong field ionization

    Science.gov (United States)

    Torlina, Lisa; Morales, Felipe; Muller, H. G.; Smirnova, Olga

    2014-10-01

    We summarize the key aspects of the recently developed analytical R-matrix (ARM) theory for strong field ionization (Torlina and Smirnova 2012 Phys. Rev. A 86 043408; Kaushal and Smirnova 2013 Phys. Rev. A 88 013421), and present tests of this theory using ab initio numerical simulations for hydrogen and helium atoms in long circularly polarized laser pulses. We find excellent agreement between the predictions of ARM and the numerical calculations.

  3. Lattice dynamics of wurtzite CdS: Neutron scattering and ab-initio calculations

    Science.gov (United States)

    Debernardi, A.; Pyka, N. M.; Göbel, A.; Ruf, T.; Lauck, R.; Kramp, S.; Cardona, M.

    1997-08-01

    We have measured the phonon dispersion of wurtzite CdS by inelastic neutron scattering in a single crystal made from the nonabsorbing isotope 114Cd. One of the two silent B 1-modes occurs at 3.96 THz ( k = 0 ). It is significantly lower and less dispersive than so far assumed. Previous semiempirical lattice dynamical models need to be reanalyzed. However, the observed dispersion branches compare favorably with an ab-initio calculation.

  4. Steady state Ab-initio Theory of Lasers with Injected Signals

    CERN Document Server

    Cerjan, Alexander

    2013-01-01

    We present an ab-initio treatment of steady-state lasing with injected signals that treats both multimode lasing and spatial hole burning, and describes the transition to injection locking or partial locking in the multimode case. The theory shows that spatial hole burning causes a shift in the frequency of free-running laser modes away from the injection frequency, in contrast to standard approaches.

  5. Ab initio molecular dynamics simulations of the Li4F4 cluster

    Science.gov (United States)

    Heidenreich, A.; Sauer, J.

    1995-12-01

    Molecular dynamics simulations have been performed directly on the ab initio potential energy surface of Li4F4, which was generated within the Hartree-Fock approximation using a Gaussian basis set (split valence contraction). Trajectories at different temperatures yield the temperature dependence of the infrared spectra and the photoelectron spectra. For the infrared spectra comparison is made with MD results using a shell model ion pair potential function.

  6. Condensed-matter ab initio approach for strongly correlated electrons: Application to a quantum spin liquid candidate

    Energy Technology Data Exchange (ETDEWEB)

    Yamaji, Youhei [Quantum-Phase Electronics Center, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-8656 (Japan)

    2015-12-31

    Recently, condensed-matter ab initio approaches to strongly correlated electrons confined in crystalline solids have been developed and applied to transition-metal oxides and molecular conductors. In this paper, an ab initio scheme based on constrained random phase approximations and localized Wannier orbitals is applied to a spin liquid candidate Na{sub 2}IrO{sub 3} and is shown to reproduce experimentally observed specific heat.

  7. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    CERN Document Server

    Geng, Hua Y

    2014-01-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibration...

  8. Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.

    Science.gov (United States)

    Yang, Lina; Minnich, Austin J

    2017-03-14

    Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.

  9. Ab initio nuclear structure and reactions with chiral three-body forces

    Energy Technology Data Exchange (ETDEWEB)

    Langhammer, Joachim; Roth, Robert; Calci, Angelo [Institut fuer Kernphysik - Theoriezentrum, TU Darmstadt (Germany); Navratil, Petr [TRIUMF, Vancouver (Canada)

    2014-07-01

    One major ambition of ab initio nuclear theory is the description of nuclear-structure and reaction observables on equal footing. This is accomplished by combining the no-core shell model (NCSM) with the resonating-group method (RGM) to a unified ab initio approach to bound and continuum states, which is developed further to the no-core shell model with continuum (NCSMC). We present the formal developments to include three-nucleon interactions in both the NCSM/RGM and NCSMC formalism. This provides the possibility to assess the predictive power of chiral two- and three-nucleon forces in the variety of scattering observables. We study three-nucleon force effects on phase-shifts, cross sections and analyzing powers in first ab-initio studies of nucleon-{sup 4}He scattering with chiral two- and three-nucleon forces. Finally, we focus on heavier target nuclei using the NCSMC, e.g., in neutron-{sup 8}Be scattering and study the impact of the continuum on the spectrum of {sup 9}Be.

  10. Ab-initio Simulations of Molten Ni Alloys

    Science.gov (United States)

    2010-04-01

    Mukai’s experimental measurements using the (modified) sessile drop method and (modified) py- 12 cnometric method place β in the range of 2.0 × 10...optimization of the site specific proper- ties of a component. The balance of material and component properties could then take advantage of variations...several other re- cent measurements of liquid Ni alloy densities. Using a sesslie drop method Feng and co-workers measured the density of elemental Ni and

  11. Ab initio theory of spin entanglement in atoms and molecules

    Science.gov (United States)

    Pittalis, S.; Troiani, F.; Rozzi, C. A.; Vignale, G.

    2015-02-01

    We investigate spin entanglement in many-electron systems within the framework of density functional theory. We show that the entanglement length, which is extracted from the spatial dependence of the local concurrence, is a sensitive indicator of atomic shells and reveals the character, covalent or metallic, of chemical bonds. These findings shed light on the remarkable success of modern density functionals, which tacitly employ the entanglement length as a variable. This opens the way to further research on entanglement-based functionals.

  12. Thermodynamics of water modeled using ab initio simulations

    CERN Document Server

    Weber, Valéry

    2010-01-01

    We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. The calculated free energy is in fair agreement with experiments but the excess internal energy and hence also the excess entropy are not. Our work emphasizes the importance of thermodynamic characterization in assessing the quality of electron density functionals in describing liquid water and hydration phenomena.

  13. MP2, DFT and ab initio calculations on thioxanthone.

    Science.gov (United States)

    Beni, Alireza Salimi; Chermahini, Alireza Najafi; Sharghi, Hashem; Monfared, Setareh Mirzaei

    2011-11-01

    Density functional theory (DFT), HF and MP2 calculations have been carried out to investigate thioxanthone molecule using the standard 6-31+G(d,p) basis set. The results of MP2 calculations show a butterfly structure for thioxanthone. The calculated results show that the predicted geometry can well reproduce the structural parameters. The predicted vibrational frequencies were assigned and compared with experimental IR spectra. A good harmony between theory and experiment is found. The theoretical electronic absorption spectra have been calculated using CIS method. (13)C and (1)H NMR of the title compound have been calculated by means of B3LYP density functional method with 6-31+G(d,p) basis set. The comparison of the experimental and the theoretical results indicate that density functional B3LYP method is able to provide satisfactory results for predicting NMR properties. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. AN AB INITIO STUDY OF HYDROTREATING OF THIIRENE AND ...

    African Journals Online (AJOL)

    a

    In the DFT method, the energy is a density functional. ..... Distribution of the charge during thiirene desulfurization on some atoms. This type of ..... C.Y., Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P.M.W.; Johnson, B.G.; Chen,.

  15. Ab initio electronic properties of dual phosphorus monolayers in silicon

    DEFF Research Database (Denmark)

    Drumm, Daniel W.; Per, Manolo C.; Budi, Akin;

    2014-01-01

    , investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device...

  16. Ab initio charge analysis of pure and hydrogenated perovskites

    DEFF Research Database (Denmark)

    Bork, Nicolai Christian; Bonanos, Nikolaos; Rossmeisl, Jan

    2011-01-01

    these findings. The distribution of the remaining electronic density decays exponentially with distance to the hydrogen defect. Diffusional paths are calculated wherein the hydrogenic species retain a charge between +0.57 and +0.54e showing that hydrogen permeation cannot be viewed as consisting of virtually...... independent protonic and electronic transport processes. © 2011 American Institute of Physics....

  17. Ab initio molecular dynamics study of Fe-containing smectites

    NARCIS (Netherlands)

    Liu, X.; Meijer, E.J.; Lu, X.; Wang, R.

    2010-01-01

    In order to identify the influences imposed by Fe substitution, density functional theory-based Car-Parrinello molecular dynamics simulations were employed to study both oxidized and reduced Fe-bearing smectites. The following basic properties were investigated: local structures in the clay layer, h

  18. Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics.

    Science.gov (United States)

    Skelton, A A; Wesolowski, D J; Cummings, P T

    2011-07-19

    Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.

  19. Substituent Inductive Effects on the Electrochemical Oxidation of Flavonoids Studied by Square Wave Voltammetry and Ab Initio Calculations.

    Science.gov (United States)

    Arroyo-Currás, Netzahualcóyotl; Rosas-García, Víctor M; Videa, Marcelo

    2016-10-27

    Flavonoids are natural products commonly found in the human diet that show antioxidant, anti-inflammatory and anti-hepatotoxic activities. These nutraceutical properties may relate to the electrochemical activity of flavonoids. To increase the understanding of structure-electrochemical activity relations and the inductive effects that OH substituents have on the redox potential of flavonoids, we carried out square-wave voltammetry experiments and ab initio calculations of eight flavonoids selected following a systematic variation in the number of hydroxyl substituents and their location on the flavan backbone: three flavonols, three anthocyanidins, one anthocyanin and the flavonoid backbone flavone. We compared the effect that the number of -OH groups in the ring B of flavan has on the oxidation potential of the flavonoids considered, finding linear correlations for both flavonols and anthocyanidins ( R 2 = 0.98 ). We analyzed the effects that position and number of -OH substituents have on electron density distributions via ab initio quantum chemical calculations. We present direct correlations between structural features and oxidation potentials that provide a deeper insight into the redox chemistry of these molecules.

  20. Surface structure of CdSe Nanorods revealed by combined X-rayabsorption fine structure measurements and ab-initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Aruguete, Deborah A.; Marcus, Matthew A.; Li, Liang-shi; Williamson, Andrew; Fakra, Sirine; Gygi, Francois; Galli, Giulia; Alivisatos, A. Paul

    2006-01-27

    We report orientation-specific, surface-sensitive structural characterization of colloidal CdSe nanorods with extended X-ray absorption fine structure spectroscopy and ab-initio density functional theory calculations. Our measurements of crystallographically-aligned CdSe nanorods show that they have reconstructed Cd-rich surfaces. They exhibit orientation-dependent changes in interatomic distances which are qualitatively reproduced by our calculations. These calculations reveal that the measured interatomic distance anisotropy originates from the nanorod surface.

  1. A Theoretical Study on a Reaction of Iron(III) Hydroxide with Boron Trichloride by Ab Initio Calculation

    CERN Document Server

    Ichikawa, Kazuhide; Fukushima, Akinori; Ishihara, Yoshio; Isaki, Ryuichiro; Takeguchi, Toshio; Tachibana, Akitomo; 10.1016/j.theochem.2009.08.026

    2009-01-01

    We investigate a reaction of boron trichloride (BCl3) with iron(III) hydroxide (Fe(OH)3) by ab initio quantum chemical calculation as a simple model for a reaction of iron impurities in BCl3 gas. We also examine a reaction with water. We find that compounds such as Fe(Cl)(OBCl2)2(OHBCl2) and Fe(Cl)2(OBCl2)(OHBCl2) are formed while producing HCl and reaction paths to them are revealed. We also analyze the stabilization mechanism of these paths using newly-developed interaction energy density derived from electronic stress tensor in the framework of the Regional DFT (Density Functional Theory) and Rigged QED (Quantum ElectroDynamics).

  2. On the full exploitation of symmetry in periodic (as well as molecular) self-consistent-field ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Orlando, Roberto, E-mail: roberto.orlando@unito.it; Erba, Alessandro; Dovesi, Roberto [Dipartimento di Chimica, Università di Torino and NIS, Nanostructured Interfaces and Surfaces, Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); De La Pierre, Marco [Dipartimento di Chimica, Università di Torino and NIS, Nanostructured Interfaces and Surfaces, Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); Nanochemistry Research Institute, Department of Chemistry, Curtin University, GPO Box U1987, Perth, WA 6845 (Australia); Zicovich-Wilson, Claudio M. [Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad, 1001, Col. Chamilpa, 62209 Cuernavaca (Morelos) (Mexico)

    2014-09-14

    Use of symmetry can dramatically reduce the computational cost (running time and memory allocation) of self-consistent-field ab initio calculations for molecular and crystalline systems. Crucial for running time is symmetry exploitation in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices (overlap, Fock, and density) in the Atomic Orbital (AO) basis are avoided and a direct transformation from the packed AO to the symmetry adapted crystalline orbital basis is performed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. Quantitative examples, referring to the implementation in the CRYSTAL code, are given for high symmetry families of compounds such as carbon fullerenes and nanotubes.

  3. Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature.

    Science.gov (United States)

    Taioli, Simone; Garberoglio, Giovanni; Simonucci, Stefano; a Beccara, Silvio; Aversa, Lucrezia; Nardi, Marco; Verucchi, Roberto; Iannotta, Salvatore; Dapor, Maurizio; Alfè, Dario

    2013-01-28

    In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C(60) collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C(60) impact on the Si surface is in good agreement with our experimental findings.

  4. Ab Initio Description of Disordered Sr1−xKxFe2As2 Using the Coherent Potential Approximation

    KAUST Repository

    Pulikkotil, J. J.

    2010-04-29

    The electronic structure of disordered Sr1−xKxFe2As2 is studied by ab initio density functional theory. As no superstructure and/or atomic short range ordering is reported for Sr1−xKxFe2As2, the coherent potential approximation can be used to describe the effects of chemical disorder. We find clear deviations from the rigid band model characteristics. Nonmagnetic calculations show an enhancement of the density of states at the Fermi energy in the range 0.4≤x≤0.65, which coincides with the region where experiments observe an enhanced superconducting transition temperature, and antiferromagnetic calculations indicate a significant renormalization of states at Fermi energy. Analyzing the distribution of the Fe 3d states over the range 0≤x≤1 we propose an effective three band model.

  5. Ab initio molecular dynamics simulations of the static, dynamic and electronic properties of liquid lead using real-space pseudopotentials

    Energy Technology Data Exchange (ETDEWEB)

    Alemany, Manuel M. G. [Universidad de Santiago de Compostela; Longo, Roberto [Universidad de Santiago de Compostela; Gallego, Luis [Universidad de Santiago de Compostela; Gonzales, D. J. [Universidad de Valladolid; Gonzales, L. E. [Universidad de Valladolid; Tiago, Murilo L [ORNL; Chelikowsky, James [University of Texas, Austin

    2007-01-01

    We performed a comprehensive study of the static, dynamic and electronic properties of liquid Pb at T = 650 kelvins, density 0.0309 angstroms^{-3} by means of 216-particle ab initio molecular dynamics simulations based on a real-space implementation of pseudopotentials constructed within density-functional theory. The predicted results and available experimental data are very in good agreement, which confirms the adequacy of this technique to achieve a reliable description of the behavior of liquid metals, including their dynamic properties. Although some of the computed properties of liquid Pb are similar to those of simple liquid metals, others differ markedly. Our results show that an appropriate description of liquid Pb requires the inclusion of relativistic effects in the determination of the pseudopotentials of Pb.

  6. Van der Waals Interactions in Pyridine and Pyridine-like Molecular Crystals: An ab initio Molecular Dynamics Study

    Science.gov (United States)

    Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto

    2014-03-01

    Pyridine has recently been investigated as a potentially effective material for use in artificial light harvesting.In this work, we propose the use of ab initio molecular dynamics (AIMD) to gain valuable physical insight into the artificial photosynthetic processes occurring in condensed-phase pyridine, the study of which has been limited to semi-empirical force fields to date.For this purpose, we introduce an accurate and efficient AIMD method, based on density functional theory (DFT) and a self-consistent pairwise description of van der Waals (vdW) interactions, for use in finite temperature and pressure (NPT) simulations on pyridine and several pyridine-like molecular crystals (PLMCs). Utilizing this approach, we demonstrate that vdW forces play a crucial role in the theoretical prediction of the structure and density of pyridine and PLMCs, and therefore must be accounted for in studies of these potential alternative energy materials. DOE: DE-SC0008626, NSF: DMS-1065894.

  7. Ab initio molecular dynamics study of liquid methanol

    CERN Document Server

    Handgraaf, J W; Meijer, E J; Handgraaf, Jan-Willem; Erp, Titus S. van; Meijer, Evert Jan

    2003-01-01

    We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen-oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.

  8. Ab Initio Calculations for the Polarizabilities of Small Sulfur Clusters

    Institute of Scientific and Technical Information of China (English)

    BAI Yu-Lin; CHEN Xiang-Rong; CHENG Xiao-Hong; YANG Xiang-Dong

    2005-01-01

    @@ Polarizabilities of small Sn (n = 2-8) clusters are calculated by using the higher-order finite-difference pseudopotential density functional method in real space. We find that the polarizabilities of the clusters are considered to be higher than the value estimated from the "hard sphere" model using the bulk static dielectric constant.The computed polarizabilities per atom tend to decrease with the increasing cluster size. The polarizabilities are closely related to the HOMO-LUMO gaps and the geometrical configurations.

  9. Structural properties of rutherfordium: An ab-initio study

    Science.gov (United States)

    Gyanchandani, Jyoti; Sikka, S. K.

    2012-01-01

    The structural and electronic properties of rutherfordium, the latest group IV B element, have been evaluated by first principles density functional theory in scalar relativistic formalism with and without spin-orbit coupling and compared with its 5d homologue Hf. It is found that Rf will crystallize in the hexagonal close packed structure as in Hf. However, under pressure, it will have different sequence of phase transitions than Hf: hcp→bcc instead of hcp→ω→bcc. An explanation is offered for this difference in terms of the competition between the band structure and the Ewald energy contributions.

  10. Structural properties of rutherfordium: An ab-initio study

    Energy Technology Data Exchange (ETDEWEB)

    Gyanchandani, Jyoti [Material Science Division, Bhabha Atomic Research Center, Mumbai 400085 (India); Sikka, S.K., E-mail: sksikka@barc.gov.in [Bhabha Atomic Research Center, Mumbai 400085 (India)

    2012-01-09

    The structural and electronic properties of rutherfordium, the latest group IV B element, have been evaluated by first principles density functional theory in scalar relativistic formalism with and without spin–orbit coupling and compared with its 5d homologue Hf. It is found that Rf will crystallize in the hexagonal close packed structure as in Hf. However, under pressure, it will have different sequence of phase transitions than Hf: hcp→bcc instead of hcp→ω→bcc. An explanation is offered for this difference in terms of the competition between the band structure and the Ewald energy contributions. -- Highlights: ► The solid properties of the new element Rf have been found for the first time. ► The density functional theory is used including spin–orbit interactions. ► The atomic volume of Rf is found to be expanded compared to its homologue Hf. ► It is shown that Rf will have different phase transformations than Hf under pressure. ► The absence of the omega phase in Rf and its presence in Hf is explained.

  11. Transport properties of boron nanotubes investigated by ab initio calculation

    Institute of Scientific and Technical Information of China (English)

    Guo Wei; Hu Yi-Bin; Zhang Yu-Yang; Du Shi-Xuan; Gao Hong-Jun

    2009-01-01

    We investigate atomic and electronic structures of boron nanotubes (BNTs) by using the density functional theory(DFT). The transport properties of BNTs with different diameters and chiralities are studied by the Keldysh nonequi-librium Green function (NEGF) method. It is found that the cohesive energies and conductances of BNTs decrease as their diameters decrease. It is more difficult to form (N, 0) tubes than (M, M) tubes when the diameters of the two kinds of tubes are comparable. However, the (N, 0) tubes have a higher conductance than the (M, M) tubes. When the BNTs are connected to gold electrodes, the coupling between the BNTs and the electrodes will affect the transport properties of tubes significantly.

  12. Ab initio dynamics of field emission from diamond surfaces

    Science.gov (United States)

    Miyamoto, Yoshiyuki; Miyazaki, Takehide; Takeuchi, Daisuke; Okushi, Hideyo; Yamasaki, Satoshi

    2013-09-01

    We propose a new interpretation of the efficiency of field emission, which is understood based on the concept of electron affinity. We use time-dependent density functional theory to simulate field emission from clean and chemically modified diamond (001) surfaces under applied electric fields. We find that the emission efficiency is governed by the self-consistent electrostatic potential (VSCF) at the surface rather than by the sign of the electron affinity, which is determined by VSCF in the vacuum region far from the surface. We resolve the paradox that the emission efficiency of a clean (001) surface with positive electron affinity is even higher than that of a H/OH-co-terminated (001) surface with negative electron affinity.

  13. Experimental and Ab Initio Ultrafast Carrier Dynamics in Plasmonic Nanoparticles

    Science.gov (United States)

    Brown, Ana M.; Sundararaman, Ravishankar; Narang, Prineha; Schwartzberg, Adam M.; Goddard, William A.; Atwater, Harry A.

    2017-02-01

    Ultrafast pump-probe measurements of plasmonic nanostructures probe the nonequilibrium behavior of excited carriers, which involves several competing effects obscured in typical empirical analyses. Here we present pump-probe measurements of plasmonic nanoparticles along with a complete theoretical description based on first-principles calculations of carrier dynamics and optical response, free of any fitting parameters. We account for detailed electronic-structure effects in the density of states, excited carrier distributions, electron-phonon coupling, and dielectric functions that allow us to avoid effective electron temperature approximations. Using this calculation method, we obtain excellent quantitative agreement with spectral and temporal features in transient-absorption measurements. In both our experiments and calculations, we identify the two major contributions of the initial response with distinct signatures: short-lived highly nonthermal excited carriers and longer-lived thermalizing carriers.

  14. Experimental and ab initio ultrafast carrier dynamics in plasmonic nanoparticles

    CERN Document Server

    Brown, Ana M; Narang, Prineha; Schwartzberg, Adam M; Goddard, William A; Atwater, Harry A

    2016-01-01

    Ultrafast pump-probe measurements of plasmonic nanostructures probe the non-equilibrium behavior of excited carriers, which involves several competing effects obscured in typical empirical analyses. Here we present pump-probe measurements of plasmonic nanoparticles along with a complete theoretical description based on first-principles calculations of carrier dynamics and optical response, free of any fitting parameters. We account for detailed electronic-structure effects in the density of states, excited carrier distributions, electron-phonon coupling, and dielectric functions which allow us to avoid effective electron temperature approximations. Using this calculation method, we obtain excellent quantitative agreement with spectral and temporal features in transient-absorption measurements. In both our experiments and calculations, we identify the two major contributions of the initial response with distinct signatures: short-lived highly non-thermal excited carriers and longer-lived thermalizing carriers.

  15. Polymerization of Silicon-Doped Heterofullerenes: an Ab Initio Study

    Institute of Scientific and Technical Information of China (English)

    LI Ji-Ling; XIA Yue-Yuan; ZHAO Ming-Wen; LIU Xiang-Dong; SONG Chen; LI Li-Juan; LI Feng; HUANG Bo-Da

    2008-01-01

    We perform the calculations on geometric and electronic structures of Si-doped heterofullerene C50Si10 and its derivatives,a 640Si20-CaoSi20 dimer and a C40Si20-based nanowire by using density-functional theory.The optimized configuration of the C40Si20-based nanowire exhibits a regular dumbbell-shaped chain nanostructure.The electronic structure calculations indicate that the HOMO-LUMO gaps of the heterofullerene-based materials can be greatly modified by substitutionally doping with Si atoms and show a decreasing trend with increase cluster size.Unlike the band structures of the conventional wide band gap silicon carbide nanomaterials,the C40Si20-based nanowire has a very narrow direct band gap of 0.087eV.

  16. AB INITIO PULSAR MAGNETOSPHERE: THE ROLE OF GENERAL RELATIVITY

    Energy Technology Data Exchange (ETDEWEB)

    Philippov, Alexander A.; Cerutti, Benoit; Spitkovsky, Anatoly [Department of Astrophysical Sciences, Princeton University, Ivy Lane, Princeton, NJ 08544 (United States); Tchekhovskoy, Alexander, E-mail: sashaph@princeton.edu [Departments of Physics and Astronomy, University of California, Berkeley, CA 94720 (United States)

    2015-12-20

    It has recently been demonstrated that self-consistent particle-in-cell simulations of low-obliquity pulsar magnetospheres in flat spacetime show weak particle acceleration and no pair production near the poles. We investigate the validity of this conclusion in a more realistic spacetime geometry via general-relativistic particle-in-cell simulations of the aligned pulsar magnetosphere with pair formation. We find that the addition of the frame-dragging effect makes the local current density along the magnetic field larger than the Goldreich–Julian value, which leads to unscreened parallel electric fields and the ignition of a pair cascade. When pair production is active, we observe field oscillations in the open field bundle, which could be related to pulsar radio emission. We conclude that general-relativistic effects are essential for the existence of the pulsar mechanism in low-obliquity rotators.

  17. Ab initio calculation of chromium oxide containing Ti dopant

    Energy Technology Data Exchange (ETDEWEB)

    Maldonado, Frank [Grupo de Fisicoquimica de Materiales, Universidad Tecnica Particular de Loja, Apartado 11-01-608, Loja (Ecuador); Novillo, Corina [Escuela de Ingenieria Quimica, Universidad Tecnica Particular de Loja, Apartado 11-01-608, Loja (Ecuador); Stashans, Arvids, E-mail: arvids@utpl.edu.ec [Grupo de Fisicoquimica de Materiales, Universidad Tecnica Particular de Loja, Apartado 11-01-608, Loja (Ecuador)

    2012-01-17

    Highlights: Black-Right-Pointing-Pointer Microstructure changes in chromium oxide due to the Ti doping. Black-Right-Pointing-Pointer Discovery of magnetism in Ti-doped {alpha}-Cr{sub 2}O{sub 3} crystal. Black-Right-Pointing-Pointer Explanation of the origin of n-type electrical conductivity. Black-Right-Pointing-Pointer Detailed analysis of electronic properties and density of states. Black-Right-Pointing-Pointer As to authors' knowledge, Ti-doped crystal is studied for the first time by the DFT. - Abstract: First-principles computations based on the density functional theory within the generalised gradient approximation and introduced intra-atomic interaction term for strongly correlated electrons (DFT + U method) has been used in this work. Ti impurity doping in the {alpha}-Cr{sub 2}O{sub 3} crystal has been carried out considering single defect model within the periodic crystalline structure. Atomic displacements, Bader charges on atoms have been computed showing that Ti dopant converts the chemical bonding in its neighbourhood into more ionic one. The defect-local microstructure is such as there exist general tendency of atomic rearrangements away with respect to the Ti imperfection. It is found that defect incorporation produces some local changes upon the band structure of the material and also induces a metallic state. That implies n-type electrical conductivity in the Ti-doped {alpha}-Cr{sub 2}O{sub 3} crystals and relates our work directly to a number of experimental studies in this area. Our results provide evidence over change in magnetic moments in the vicinity of defect, which means that the chromium oxide doped with Ti impurity might not act as an antiferromagnetic substance.

  18. Unified ab initio treatment of attosecond photoionization and Compton scattering

    Science.gov (United States)

    Yudin, G. L.; Bondar, D. I.; Patchkovskii, S.; Corkum, P. B.; Bandrauk, A. D.

    2009-10-01

    We present a new theoretical approach to attosecond laser-assisted photo- and Compton ionization. Attosecond x-ray absorption and scattering are described by \\hat{\\mathscr{S}}^{(1,2)} -matrices, which are coherent superpositions of 'monochromatic' \\skew{3}\\hat{S}^{(1,2)} -matrices in a laser-modified Furry representation. Besides refining the existing theory of the soft x-ray photoelectron attosecond streak camera and spectral phase interferometry (ASC and ASPI), we formulate a theory of hard x-ray photoelectron and Compton ASC and ASPI. The resulting scheme has a simple structure and leads to closed-form expressions for ionization amplitudes. We investigate Compton electron interference in the separable Coulomb-Volkov continuum with both Coulomb and laser fields treated non-perturbatively. We find that at laser-field intensities below 1013 Wcm-2 normalized Compton lines almost coincide with the lines obtained in the laser-free regime. At higher intensities, attosecond interferences survive integration over electron momenta, and feature prominently in the Compton lines themselves. We define a regime where the electron ground-state density can be measured with controllable accuracy in an attosecond time interval. The new theory provides a firm basis for extracting photo- and Compton electron phases and atomic and molecular wavefunctions from experimental data.

  19. Ab initio modelling of UN grain boundary interfaces

    Science.gov (United States)

    Kotomin, E. A.; Zhukovkii, Yu F.; Bocharov, D.; Gryaznov, D.

    2012-08-01

    The uranium mononitride (UN) is a material considered as a promising candidate for Generation-IV nuclear reactor fuels. Unfortunately, oxygen in air affects UN fuel performance and stability. Therefore, it is necessary to understand the mechanism of oxygen adsorption and further UN oxidation in the bulk and at surface. Recently, we performed a detailed study on oxygen interaction with UN surface using density functional theory (DFT) calculations. We were able to identify an atomistic mechanism of UN surface oxidation consisting of several important steps, starting with the oxygen molecule dissociation and finishing with oxygen atom incorporation into vacancies on the surface. However, in reality most of processes occur at the interfaces and on UN grain boundaries. In this study, we present the results of first DFT calculations on O behaviour inside UN grain boundaries performed using GGA exchange-correlation functional PW91 as implemented into the VASP computer code. We consider a simple interface (310)[001](36.8°) tilt grain boundary. The N vacancy formation energies and energies of O incorporation into pre-existing vacancies in the grain boundaries as well as O solution energies were compared with those obtained for the UN (001) and (110) surfaces

  20. Ab Initio Prediction of Piezoelectricity in Two-Dimensional Materials.

    Science.gov (United States)

    Blonsky, Michael N; Zhuang, Houlong L; Singh, Arunima K; Hennig, Richard G

    2015-10-27

    Two-dimensional (2D) materials present many unique materials concepts, including material properties that sometimes differ dramatically from those of their bulk counterparts. One of these properties, piezoelectricity, is important for micro- and nanoelectromechanical systems applications. Using symmetry analysis, we determine the independent piezoelectric coefficients for four groups of predicted and synthesized 2D materials. We calculate with density-functional perturbation theory the stiffness and piezoelectric tensors of these materials. We determine the in-plane piezoelectric coefficient d11 for 37 materials within the families of 2D metal dichalcogenides, metal oxides, and III-V semiconductor materials. A majority of the structures, including CrSe2, CrTe2, CaO, CdO, ZnO, and InN, have d11 coefficients greater than 5 pm/V, a typical value for bulk piezoelectric materials. Our symmetry analysis shows that buckled 2D materials exhibit an out-of-plane coefficient d31. We find that d31 for 8 III-V semiconductors ranges from 0.02 to 0.6 pm/V. From statistical analysis, we identify correlations between the piezoelectric coefficients and the electronic and structural properties of the 2D materials that elucidate the origin of the piezoelectricity. Among the 37 2D materials, CdO, ZnO, and CrTe2 stand out for their combination of large piezoelectric coefficient and low formation energy and are recommended for experimental exploration.

  1. An ab-initio study of pyrrole and imidazole arylamides

    Directory of Open Access Journals (Sweden)

    Abramyan Ara M.

    2013-01-01

    Full Text Available Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we highlight our Density Functional Theory (DFT potential energy profiles and derived force field parameters for four aryl-amide bond types for the pyrrole and imidazole building blocks extensively used in foldamer design for the DNA-binding polyamides. These results contribute to developing of computational tools for an appropriate molecular modeling of pyrrole-imidazole polyamide/DNA binding, and provide an insight into the chemical factors that influence the flexibility of the pyrrole-imidazole polyamides, and their binding to DNA.

  2. Ab Initio Calculations for the Surface Energy of Silver Nanoclusters

    Science.gov (United States)

    Medasani, Bharat; Vasiliev, Igor; Park, Young Ho

    2007-03-01

    We apply first principles computational methods to study the surface energy and the surface stress of silver nanoparticles. The structures, energies and lattice contractions of spherical Ag nanoclusters are calculated in the framework of density functional theory combined with the generalized gradient approximation. Our calculations predict the surface energies of Ag nanoclusters to be in the range of 1-2 J/m^2. These values are close to the bulk surface energy of silver, but are significantly lower than the recently reported value of 7.2 J/m^2 derived from the Kelvin equation for free Ag nanoparticles. From the lattice contraction and the nearest neighbor interatomic distance, we estimate the surface stress of the silver nanoclusters to be in the the range of 1-1.45 N/m. This result suggests that a liquid droplet model can be employed to evaluate the surface energy and the surface stress of Ag nanoparticles. K. K. Nanda et al., Phys. Rev. Lett. 91, 106102 (2003).

  3. Ab initio study of hydrogen adsorption in MOF-5.

    Science.gov (United States)

    Sillar, Kaido; Hofmann, Alexander; Sauer, Joachim

    2009-03-25

    Metal-organic frameworks (MOFs) are promising adsorbents for hydrogen storage. Density functional theory and second-order Møller-Plesset perturbation theory (MP2) are used to calculate the interaction energies between H(2) and individual structural elements of the MOF-5 framework. The strongest interaction, DeltaH(77) = -7.1 kJ/mol, is found for the alpha-site of the OZn(4)(O(2)Ph)(6) nodes. We show that dispersion interactions and zero-point vibrational energies must be taken into account. Comparison of calculations done under periodic boundary conditions for the complete structure with those done for finite models cut from the MOF-5 framework shows that the interactions with H(2) originate mainly from the local environment around the adsorption site. When used within a Multi-Langmuir model, the MP2 results reproduce measured adsorption isotherms (the predicted amount is 6 wt % at 77 K and 40 bar) if we assume that the H(2) molecules preserve their rotational degrees of freedom in the adsorbed state. This allows to discriminate between different isotherms measured for different MOF-5 samples and to reliably predict isotherms for new MOF structures.

  4. Thermodynamics and phonon dispersion of pyrope and grossular silicate garnets from ab initio simulations

    Science.gov (United States)

    Baima, Jacopo; Ferrabone, Matteo; Orlando, Roberto; Erba, Alessandro; Dovesi, Roberto

    2016-02-01

    The phonon dispersion and thermodynamic properties of pyrope ({Mg}_3{Al}_2{Si}_3{O}_{12}) and grossular ({Ca}_3{Al}_2{Si}_3{O}_{12} ) have been computed by using an ab initio quantum mechanical approach, an all-electron variational Gaussian-type basis set and the B3LYP hybrid functional, as implemented in the Crystal program. Dispersion effects in the phonon bands have been simulated by using supercells of increasing size, containing 80, 160, 320, 640, 1280 and 2160 atoms, corresponding to 1, 2, 4, 8, 16 and 27 {k} points in the first Brillouin zone. Phonon band structures, density of states and corresponding inelastic neutron scattering spectra are reported. Full convergence of the various thermodynamic properties, in particular entropy ( S) and specific heat at constant volume (CV), with the number of {k} points is achieved with 27 {k} points. The very regular behavior of the S( T) and CV(T) curves as a function of the number of {k} points, determined by high numerical stability of the code, permits extrapolation to an infinite number of {k} points. The limiting value differs from the 27-{k} case by only 0.40 % at 100 K for S (the difference decreasing to 0.11 % at 1000 K) and by 0.29 % (0.05 % at 1000 K) for CV. The agreement with the experimental data is rather satisfactory. We also address the problem of the relative entropy of pyrope and grossular, a still debated question. Our lattice dynamical calculations correctly describe the larger entropy of pyrope than grossular by taking into account merely vibrational contributions and without invoking "static disorder" of the Mg ions in dodecahedral sites. However, as the computed entropy difference is found to be larger than the experimental one by a factor of 2-3, present calculations cannot exclude possible thermally induced structural changes, which could lead to further conformational contributions to the entropy.

  5. An effective scheme for selecting basis sets for ab initio calculations

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    An effective scheme for selecting economical basis sets for ab initio calculations has been proposed for wide-range systems based on the analysis of different functions in the currently used basis sets. Accordingly, the selection of the basis sets should be made according to the different properties and real chemical surrounding of the atoms in the systems. For normal systems, the size and level of the basis sets used for the descriptions of the constituent atoms should be increased from left to right according to the position of the atom in the periodic table. Moreover, the more the atom is negatively charged, the more the basis functions and suitable polarization functions and diffuse functions should be utilized. Whereas, for the positively charged atoms, the size of basis set may be reduced. It is not necessary to use the polarization and diffuse functions for the covalently saturated atoms with normal valence states. However, for the system involving hydrogen-bonding, weak interactions, functional groups, metallic bonding with zero valence or low positive valence, and other sensitive interactions, the polarization and diffuse functions must be used. With this scheme, reliable calculation results may be obtained with suitable basis sets and smaller computational capability. By detailed analysis of a series of systems, it has been demonstrated that this scheme is very practical and effective. This scheme may be used in Hartree-Fock, M?ller-Plesset and density functional theoretical calculations. It is expected that the scheme would find important applications in the extensive calculations of large systems in chemistry, materials science, and life and biological sciences.

  6. Organic/inorganic hybrid materials: challenges for ab initio methodology.

    Science.gov (United States)

    Draxl, Claudia; Nabok, Dmitrii; Hannewald, Karsten

    2014-11-18

    CONSPECTUS: Organic/inorganic hybrid structures are most exciting since one can expect new properties that are absent in either of their building blocks. They open new perspectives toward the design and tailoring of materials with desired features and functions. Prerequisite for real progress is, however, the in-depth understanding of what happens on the atomic and electronic scale. In this respect, hybrid materials pose a challenge for electronic-structure theory. Methods that proved useful for describing one side may not be applicable for the other one, and they are likely to fail for the interfaces. In this Account, we address the question to what extent we can quantitatively describe hybrid materials and where we even miss a qualitative description. We note that we are dealing with extended systems and thus adopt a solid-state approach. Therefore, density-functional theory (DFT) and many-body perturbation theory (MBPT), the GW approach for charged and the Bethe-Salpeter equation for neutral excitations, are our methods of choice. We give a brief summary of the used methodology, focusing on those aspects where problems can be expected when materials of different character meet at an interface. These issues are then taken up when discussing hybrid materials. We argue when and why, for example, standard DFT may fall short when it comes to the electronic structure of organic/metal interfaces or where the framework of MBPT can or must take over. Selected examples of organic/inorganic interfaces, structural properties, electronic bands, optical excitation spectra, and charge-transport properties as obtained from DFT and MBPT highlight which properties can be reliably computed for such materials. The crucial role of van der Waals forces is shown for sexiphenyl films, where the subtle interplay between intermolecular and molecule-substrate interactions is decisive for growth and morphologies. With a PTCDA monolayer on metal surfaces we discuss the performance of DFT in

  7. Ab initio study of the structural, elastic, thermodynamic, electronic and vibration properties of TbMg intermetallic compound

    Science.gov (United States)

    Mogulkoc, Y.; Ciftci, Y. O.; Kabak, M.; Colakoglu, K.

    2014-07-01

    The structural, elastic, thermodynamic, electronic and vibrational properties of CsCl-type TbMg have been studied by performing ab initio calculations based on density functional theory using the Vienna Ab initio Simulation Package (VASP). The exchange correlation potential within the generalized-gradient approximation (GGA) of projector augmented wave (PAW) method is used. The calculated structural parameters, such as the lattice constant, bulk modulus, its pressure derivative, formation energy and second-order elastic constants are presented in this paper. The obtained results are compared with related experimental and theoretical studies. The electronic band calculations, total density of states (DOS), partial DOS and charge density are also presented. Formation enthalpy and Cauchy pressure are determined. In order to obtain more information the elastic properties such as Zener anisotropy factor, Poisson’s ratio, Young modulus, isotropic shear modulus, Debye temperature and melting point have been carried out. The elastic constants are calculated in zero and different pressure ranges (0-50 GPa) with bulk modulus. We have performed the thermodynamic properties of TbMg by using quasi-harmonic Debye model. The temperature and pressure variation of the volume, bulk modulus, and thermal expansion coefficient have been predicted over a pressure range of 0-25 GPa for of TbMg. Pressure dependence of the anisotropy factors, Young’s modulus, Poisson’s ratios, bulk modulus and axis compressibility of TbMg are presented along different directions and planes. Finally, the phonon dispersion curves are presented for TbMg.

  8. Poly(aryl-ether-ether-ketone) as a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation

    Science.gov (United States)

    2014-12-01

    Poly(aryl-ether-ether-ketone) as a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio...Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation Janet Ho and Marco Olguin Sensors...a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation 5a. CONTRACT NUMBER 5b. GRANT

  9. Ab initio study of the thermopower of biphenyl-based single-molecule junctions

    Science.gov (United States)

    Bürkle, M.; Zotti, L. A.; Viljas, J. K.; Vonlanthen, D.; Mishchenko, A.; Wandlowski, T.; Mayor, M.; Schön, G.; Pauly, F.

    2012-09-01

    By employing ab initio electronic-structure calculations combined with the nonequilibrium Green's function technique, we study the dependence of the thermopower Q on the conformation in biphenyl-based single-molecule junctions. For the series of experimentally available biphenyl molecules, alkyl side chains allow us to gradually adjust the torsion angle ϕ between the two phenyl rings from 0∘ to 90∘ and to control in this way the degree of π-electron conjugation. Studying different anchoring groups and binding positions, our theory predicts that the absolute values of the thermopower decrease slightly towards larger torsion angles, following an a+bcos2ϕ dependence. The anchoring group determines the sign of Q and a,b simultaneously. Sulfur and amine groups give rise to Q,a,b>0, while for cyano, Q,a,bbinding positions can lead to substantial variations of the thermopower mostly due to changes in the alignment of the frontier molecular orbital levels and the Fermi energy. We explain our ab initio results in terms of a π-orbital tight-binding model and a minimal two-level model, which describes the pair of hybridizing frontier orbital states on the two phenyl rings. The variations of the thermopower with ϕ seem to be within experimental resolution.

  10. Ab initio aqueous thermochemistry: application to the oxidation of hydroxylamine in nitric acid solution.

    Science.gov (United States)

    Ashcraft, Robert W; Raman, Sumathy; Green, William H

    2007-10-18

    Ab initio molecular orbital calculations were performed and thermochemical parameters estimated for 46 species involved in the oxidation of hydroxylamine in aqueous nitric acid solution. Solution-phase properties were estimated using the several levels of theory in Gaussian03 and using COSMOtherm. The use of computational chemistry calculations for the estimation of physical properties and constants in solution is addressed. The connection between the pseudochemical potential of Ben-Naim and the traditional standard state-based thermochemistry is shown, and the connection of these ideas to computational chemistry results is established. This theoretical framework provides a basis for the practical use of the solution-phase computational chemistry estimates for real systems, without the implicit assumptions that often hide the nuances of solution-phase thermochemistry. The effect of nonidealities and a method to account for them is also discussed. A method is presented for estimating the solvation enthalpy and entropy for dilute aqueous solutions based on the solvation free energy from the ab initio calculations. The accuracy of the estimated thermochemical parameters was determined through comparison with (i) enthalpies of formation in the gas phase and in solution, (ii) Henry's law data for aqueous solutions, and (iii) various reaction equilibria in aqueous solution. Typical mean absolute deviations (MAD) for the solvation free energy in room-temperature water appear to be ~1.5 kcal/mol for most methods investigated. The MAD for computed enthalpies of formation in solution was 1.5-3 kcal/mol, depending on the methodology employed and the type of species (ion, radical, closed-shell) being computed. This work provides a relatively simple and unambiguous approach that can be used to estimate the thermochemical parameters needed to build detailed ab initio kinetic models of systems in aqueous solution. Technical challenges that limit the accuracy of the estimates are

  11. Full Dimensional Vibrational Calculations for Methane Using AN Accurate New AB Initio Based Potential Energy Surface

    Science.gov (United States)

    Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei

    2014-06-01

    New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).

  12. The effects of magnetic annealing of transition metal alloys deduced from ab initio electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Razee, S.S.A.; Staunton, J.B. [Department of Physics, University of Warwick, Coventry (United Kingdom); Ginatempo, B.; Bruno, E. [Dipartimento di Fisica and Unita INFM, Universita di Messina, Messina (Italy); Pinski, F.J. [Department of Physics, University of Cincinnati, OH (United States)

    2001-09-24

    A theory is presented for describing the effects of annealing magnetic alloys in magnetic fields. It has an ab initio spin-polarized relativistic Korringa-Kohn-Rostoker coherent potential approximation (KKR-CPA) electronic structure basis and uses the framework of concentration waves. Alloys which would otherwise be soft magnets are found experimentally to develop directional chemical order and significant uniaxial anisotropy when annealed in magnetic fields. Our approach is able to provide a quantitative description of these effects together with the underlying electronic mechanisms. We describe applications to the soft magnetic alloys permalloy and FeCo. (author)

  13. Accurate calculation of the p Ka of trifluoroacetic acid using high-level ab initio calculations

    Science.gov (United States)

    Namazian, Mansoor; Zakery, Maryam; Noorbala, Mohammad R.; Coote, Michelle L.

    2008-01-01

    The p Ka value of trifluoroacetic acid has been successfully calculated using high-level ab initio methods such as G3 and CBS-QB3. Solvation energies have been calculated using CPCM continuum model of solvation at the HF and B3-LYP levels of theory with various basis sets. Excellent agreement with experiment (to within 0.4 p Ka units) was obtained using CPCM solvation energies at the B3-LYP/6-31+G(d) level (or larger) in conjunction with CBS-QB3 or G3 gas-phase energies of trifluoroacetic acid and its anion.

  14. Ab initio calculation of the spectrum and structure of $^{16}$O

    CERN Document Server

    Epelbaum, Evgeny; Lähde, Timo A; Lee, Dean; Meißner, Ulf-G; Rupak, Gautam

    2013-01-01

    We present ab initio lattice calculations of the low-energy even-parity states of $^{16}$O using chiral nuclear effective field theory. We find good agreement with the empirical energy spectrum, and with the electromagnetic properties and transition rates. For the ground state, we find that the nucleons are arranged in a tetrahedral configuration of alpha clusters. For the first excited spin-0 state, we find that the predominant structure is a square configuration of alpha clusters, with rotational excitations that include the first spin-2 state.

  15. Carbon dioxide capture in 2-aminoethanol aqueous solution from ab initio molecular dynamics simulations

    Science.gov (United States)

    Kubota, Yoshiyuki; Ohnuma, Toshiharu; Bučko, Tomáš

    2017-03-01

    The reaction of carbon dioxide (CO2) with aqueous 2-aminoethanol (MEA) has been investigated using both blue moon ensemble and metadynamics approaches combined with ab initio molecular dynamics (AIMD) simulations. The AIMD simulations predicted the spontaneous deprotonation of the intermediate compound, MEA zwitterion, and they were used to study two possible routes for subsequent proton transfer reactions: the formation of the protonated MEA and the formation of MEA carbamic acid. The free-energy curve depicted by blue moon ensemble technique supported the favorable deprotonation of MEA zwitterion. The overall free-energy profile showed the favorable formation of the ionic products of MEA carbamate ion and protonated MEA.

  16. Heat capacities of xenotime-type ceramics: An accurate ab initio prediction

    Science.gov (United States)

    Ji, Yaqi; Beridze, George; Bosbach, Dirk; Kowalski, Piotr M.

    2017-10-01

    Because of ability to incorporate actinides into their structure, the lanthanide phosphate ceramics (LnPO4) are considered as potential matrices for the disposal of nuclear waste. Here we present highly reliable ab initio prediction of the variation of heat capacities and the standard entropies of these compounds in zircon structure along lanthanide series (Ln = Dy, …,Lu) and validate them against the existing experimental data. These data are helpful for assessment of thermodynamic parameters of these materials in the context of using them as matrices for immobilization of radionuclides for the purpose of nuclear waste management.

  17. Prediction of adsorption of small molecules in porous materials based on ab initio force field method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Computational prediction of adsorption of small molecules in porous materials has great impact on the basic and applied research in chemical engineering and material sciences. In this work,we report an approach based on grand canonical ensemble Monte Carlo(GCMC) simulations and ab initio force fields. We calculated the adsorption curves of ammonia in ZSM-5 zeolite and hydrogen in MOF-5(a metal-organic-framework material). The predictions agree well with experimental data. Because the predictions are based on the first principle force fields,this approach can be used for the adsorption prediction of new molecules or materials without experimental data as guidance.

  18. Assessing the Thermoelectric Properties of Sintered Compounds via High-Throughput Ab-Initio Calculations

    Science.gov (United States)

    Wang, Shidong; Wang, Zhao; Setyawan, Wahyu; Mingo, Natalio; Curtarolo, Stefano

    2011-10-01

    Several thousand compounds from the Inorganic Crystal Structure Database have been considered as nanograined, sintered-powder thermoelectrics with the high-throughput ab-initio AFLOW framework. Regression analysis unveils that the power factor is positively correlated with both the electronic band gap and the carrier effective mass, and that the probability of having large thermoelectric power factors increases with the increasing number of atoms per primitive cell. Avenues for further investigation are revealed by this work. These avenues include the role of experimental and theoretical databases in the development of novel materials.

  19. Ab Initio MO Studies on the Reaction Mechanism for Carbonyl Insertion Catalyzed by Carbonyl Cobalt Complex

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Ab initio method, under the effective core potential(ECP) approximation at HF/LANL2DZ level, has been employed to study the reaction mechanism of the carbonyl insertion of olefin hydroformylation catalyzed by a carbonyl cobalt HCo(CO)3. The two reaction paths have been discussed. The calculated potential energy barriers for the carbonyl migration and the ethyl group migration are 105.0 kJ/mol and 39.17 kJ/mol, respectively. The results indicate that the reaction path via ethyl migration is more energetically favorable than that via carbonyl insertion.

  20. All-electron ab initio investigations of the electronic states of the NiC molecule

    DEFF Research Database (Denmark)

    Shim, Irene; Gingerich, Karl. A.

    1999-01-01

    momenta of F-4(g) Ni+ and S-4(u) C-. The predicted ground state, (1)Sigma(+), is well separated from the dense manifold of excited states by an energy gap of 6465 cm(-1). Multi-reference configuration-interaction (MRCI) calculations result in r(e) = 1.621 Angstrom and omega(e) = 874 cm(-1) agreeing well......The low-lying electronic states of NiC are investigated by all-electron ab initio multi-configuration self-consistent-field (CASSCF) calculations including relativistic corrections. The electronic structure of NiC is interpreted as perturbed antiferromagnetic couplings of the localized angular...