Method For Structure Calculations Research Articles

Smoothed Particle Method for Real-Space Electronic Structure Calculations

We present a meshfree particle method for real-space electronic structure calculations based on symmetric smoothed particle hydrodynamics (SSPH). As a simple example, we applied SSPH to the Schrödinger equation for a one-dimensional harmonic oscillator. The results calculated using SSPH are in good agreement with analytical solutions. We compared results for different cases of kernel function, smoothing length, number of particles, and the order of the Taylor series expansion. The results using SSPH and the higher-order finite-difference method are also compared. Our results indicate that SSPH can be applied to real-space electronic structure calculations that require high accuracy.

Electronic Structure of Nonstoichiometric LaMnO<sub>3-x</sub> Calculated in the Coherent Potential Approximation

A method for electronic structure calculations of strongly correlated materials based on the coherent potential approximation is formulated and implemented. The evolution of the electronic structure of the LaMnO perovskite system in dependence on oxygen deficiency is studied.

Retrieval of Gap Fraction and Effective Plant Area Index from Phase-Shift Terrestrial Laser Scans

The characterization of canopy structure is crucial for modeling eco-physiological processes. Two commonly used metrics for characterizing canopy structure are the gap fraction and the effective Plant Area Index (PAIe). Both have been successfully retrieved with terrestrial laser scanning. However, a systematic assessment of the influence of the laser scan properties on the retrieval of these metrics is still lacking. This study investigated the effects of resolution, measurement speed, and noise compression on the retrieval of gap fraction and PAIe from phase-shift FARO Photon 120 laser scans. We demonstrate that FARO’s noise compression yields gap fractions and PAIe that deviate significantly from those based on scans without noise compression and strongly overestimate Leaf Area Index (LAI) estimates based on litter trap measurements. Scan resolution and measurement speed were also shown to impact gap fraction and PAIe, but this depended on leaf development phase, stand structure, and LAI calculation method. Nevertheless, PAIe estimates based on various scan parameter combinations without noise compression proved to be quite stable.

The coherent potential approximation for strongly correlated systems: electronic structure and magnetic properties of NiO–ZnO solid solutions

A method of electronic structure calculations for strongly correlated disordered materials is developed employing the basic idea of the coherent potential approximation. The evolution of the electronic structure and spin magnetic moment value with the concentration x in strongly correlated Ni1−xZnxO solid solutions is investigated in the framework of this method. The values of the energy gap and magnetic moment obtained are in agreement with the available experimental data.

The Analysis about the Impact of HVDC Monopole Operation on a 220kV Station

With the wide application of high voltage direct current, it also created some problems, such as transformers dc bias. This article describes the impact on the transformer of the operation of HVDC monopole mode, introducing the model used in the soil and the ground electrode potential distribution, it also calculates the ground voltage in the case of a single or double ring grounding .Besides this paper describes the potential level of the two layers of soil structure calculation method and uses this method to analyze the influence on 220kV station of the 500kV Tian-Guang HVDC monopole operation mode. The conclusion is that the operation mode has seriously affected the station.

A fire resistance design method for thin-walled steel studs in wall panel constructions exposed to parametric fires

This paper investigates the applicability of a simple fire resistance design method for axially loaded thin-walled steel studs in wall panel assemblies when exposed to parametric fires from one side. The simple method includes calculations of cross-section temperatures and ultimate load carrying capacities at elevated temperatures. The simplified calculation method for heat transfer in the cross-section is based on dividing the cross-section into a number of segments. The thermal properties of these layers are based on weighted averages of the thermal properties of the components contained within. The structural capacity calculation method is based on the Direct Strength Method. Results from the design method are compared with the results from Finite Element simulations for heat transfer and structural analysis (236 models). The calculation results are in good agreement with the simulation results and the proposed method may be used in performance-based fire engineering design of such construction.

The orbital minimization method for electronic structure calculations with finite-range atomic basis sets

The implementation of the orbital minimization method (OMM) for solving the self-consistent Kohn–Sham (KS) problem for electronic structure calculations in a basis of non-orthogonal numerical atomic orbitals of finite-range is reported. We explore the possibilities for using the OMM as an exact cubic-scaling solver for the KS problem, and compare its performance with that of explicit diagonalization in realistic systems. We analyze the efficiency of the method depending on the choice of line search algorithm and on two free parameters, the scale of the kinetic energy preconditioning and the eigenspectrum shift. The results of several timing tests are then discussed, showing that the OMM can achieve a noticeable speedup with respect to diagonalization even for minimal basis sets for which the number of occupied eigenstates represents a significant fraction of the total basis size (>15%). We investigate the hard and soft parallel scaling of the method on multiple cores, finding a performance equal to or better than diagonalization depending on the details of the OMM implementation. Finally, we discuss the possibility of making use of the natural sparsity of the operator matrices for this type of basis, leading to a method that scales linearly with basis size.

A three-dimensional domain decomposition method for large-scale DFT electronic structure calculations

With tens of petaflops supercomputers already in operation and exaflops machines expected to appear within the next 10 years, efficient parallel computational methods are required to take advantage of such extreme-scale machines. In this paper, we present a three-dimensional domain decomposition scheme for enabling large-scale electronic structure calculations based on density functional theory (DFT) on massively parallel computers. It is composed of two methods: (i) the atom decomposition method and (ii) the grid decomposition method. In the former method, we develop a modified recursive bisection method based on the moment of inertia tensor to reorder the atoms along a principal axis so that atoms that are close in real space are also close on the axis to ensure data locality. The atoms are then divided into sub-domains depending on their projections onto the principal axis in a balanced way among the processes. In the latter method, we define four data structures for the partitioning of grid points that are carefully constructed to make data locality consistent with that of the clustered atoms for minimizing data communications between the processes. We also propose a decomposition method for solving the Poisson equation using the three-dimensional FFT in Hartree potential calculation, which is shown to be better in terms of communication efficiency than a previously proposed parallelization method based on a two-dimensional decomposition. For evaluation, we perform benchmark calculations with our open-source DFT code, OpenMX, paying particular attention to the O(N) Krylov subspace method. The results show that our scheme exhibits good strong and weak scaling properties, with the parallel efficiency at 131,072 cores being 67.7% compared to the baseline of 16,384 cores with 131,072 atoms of the diamond structure on the K computer.

Nonlinear approximations for electronic structure calculations

We present a new method for electronic structure calculations based on novel algorithms for nonlinear approximations. We maintain a functional form for the spatial orbitals as a linear combination of products of decaying exponentials and spherical harmonics centred at the nuclear cusps. Although such representations bare some resemblance to the classical Slater-type orbitals, the complex-valued exponents in the representations are dynamically optimized via recently developed algorithms, yielding highly accurate solutions with guaranteed error bounds. These new algorithms make dynamic optimization an effective way to combine the efficiency of Slater-type orbitals with the adaptivity of modern multi-resolution methods. We develop numerical calculus suitable for electronic structure calculations. For any spatial orbital in this functional form, we represent its product with the Coulomb potential, its convolution with the Poisson kernel, etc., in the same functional form with optimized parameters. Algorithms for this purpose scale linearly in the number of nuclei. We compute electronic structure by casting the relevant equations in an integral form and solving for the spatial orbitals via iteration. As an example, for several diatomic molecules we solve the Hartree–Fock equations with speeds competitive to those of multi-resolution methods and achieve high accuracy using a small number of parameters.

Unfolding method for first-principles LCAO electronic structure calculations

Unfolding the band structure of a supercell to a normal cell enables us to investigate how symmetry breakers such as surfaces and impurities perturb the band structure of the normal cell. We generalize the unfolding method, originally developed based on Wannier functions, to the linear combination of atomic orbitals (LCAO) method, and present a general formula to calculate the unfolded spectral weight. The LCAO basis set is ideal for the unfolding method because the basis functions allocated to each atomic species are invariant regardless of the existence of surface and impurity. The unfolded spectral weight is well defined by the property of the LCAO basis functions. In exchange for the property, the non-orthogonality of the LCAO basis functions has to be taken into account. We show how the non-orthogonality can be properly incorporated in the general formula. As an illustration of the method, we calculate the dispersive quantized spectral weight of a ZrB2 slab and show strong spectral broadening in the out-of-plane direction, demonstrating the usefulness of the unfolding method.

Effects of NMR Spectral Resolution on Protein Structure Calculation

Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.

Quantification of swelling and erosion in the controlled release of a poorly water-soluble drug using synchrotron X-ray computed microtomography.

The hydration layer plays a key role in the controlled drug release of gel-forming matrix tablets. For poorly water-soluble drugs, matrix erosion is considered as the rate limiting step for drug release. However, few investigations have reported on the quantification of the relative importance of swelling and erosion in the release of poorly soluble drugs, and three-dimensional (3D) structures of the hydration layer are poorly understood. Here, we employed synchrotron radiation X-ray computed microtomography with 9-μm resolution to investigate the hydration dynamics and to quantify the relative importance of swelling and erosion on felodipine release by a statistical model. The 3D structures of the hydration layer were revealed by the reconstructed 3D rendering of tablets. Twenty-three structural parameters related to the volume, the surface area (SA), and the specific surface area (SSA) for the hydration layer and the tablet core were calculated. Three dominating parameters, including SA and SSA of the hydration layer (SA hydration layer and SSA hydration layer ) and SA of the glassy core (SA glassy core ), were identified to establish the statistical model. The significance order of independent variables was SA hydration layer > SSA hydration layer > SA glassy core , which quantitatively indicated that the release of felodipine was dominated by a combination of erosion and swelling. The 3D reconstruction and structural parameter calculation methods in our study, which are not available from conventional methods, are efficient tools to quantify the relative importance of swelling and erosion in the controlled release of poorly soluble drugs from a structural point of view.

First-principles study of interface structure and energy of Fe/NbC

Precipitates play an important role in the strengthening of steel. Important factors for controlling the growth of precipitates in steel are the interface energy between the precipitate and the iron and the strain energy around the precipitate. The calculations of coherent and semi-coherent interfaces that include 21 and 1463 atoms, respectively, were achieved using the O(N) Krylov-subspace method of the first-principles electronic structure calculation. Successful reproduction of a dislocation core structure at the semi-coherent interface between the iron and NbC phases provided the interface energy. A classical molecular dynamics simulation was also performed to estimate the strain energy around the precipitate. The side lengths of the broad plane of the plate-like rectangular parallelepiped shaped precipitates at the transition from the coherent to the semi-coherent interface were estimated to be 18 Å and 16 Å for precipitate thicknesses of 5.36 Å and 8.94 Å, respectively, by comparing the interface and strain energies of the semi-coherent precipitates with those of the coherent precipitates.

First principles investigations of geometric, electronic and optical properties of 5-aminotetrazole derivatives

Density functional theory (DFT) is an important computational technique to study and predict the properties of isolated molecules. It is now a leading method for electronic structure calculations in chemistry and solid state physics. In this paper, we have investigated the geometric, electronic and optical properties of six 5-aminotetrazole derivatives employing DFT. The ground state geometries were optimized at B3LYP/6-311G?? and B3LYP/6-31G?? level of theories. The density of states, HOMOs and LUMOs and absorption spectra of all the compounds under study have been computed and discussed. The HOMOs are delocalized on aminotetrazole moiety in all the compounds. A comprehensible intra charge transfer has been observed from aminotetrazole moiety to entire compounds. In the absorption spectra, the wavelength of maximum absorption for triplets in all the systems is red shifted relative to their corresponding singlet wavelengths of absorption maximum. The B3LYP/6-311G?? level of theory is found to give better results than B3LYP/6-31G?? level of theory, to reproduce previously reported experimental data. In most of the cases B3LYP/6-31G?? level of theory overestimate more the bond lengths.

Experimental and theoretical study of the σ-phase Fe–Re alloys

X-ray diffraction (XRD) and Mössbauer spectroscopy techniques combined with theoretical calculations based on the Korringa-Kohn-Rostoker (KKR) electronic structure calculation method were used to investigate σ-phase Fe100−xRex alloys (x = 43, 45, 47, 49 and 53). Structural data such as site occupancies and lattice constants were derived from the XRD patters, while the average isomer shift and distribution curves of the quadrupole splitting were obtained from the Mössbauer spectra. Fe-site charge-densities and the quadrupole splittings were computed with the KKR method for each lattice site. The calculated quantities combined with the experimentally determined site occupancies were successfully used to decompose the measured Mössbauer spectra into five components corresponding to the five sublattices.

Research on the Calculation Methods of New Wharf Structure

With the development of shipping business, the original inland-river wharf structures no longer adapt to the rapid development of inland-river shipping. New wharf structural types become more and more important. In this paper, we put forward five new structures of wharf including new slope structure, caisson structure, frame piers wharf, overhead vertical wharf and crane structure. We analyzed the merits and faults of each type, and then proposed calculation method of structure.

Theoretical Studies on Excited States of Bacteriochlorophyll A in Solutions

Chlorophylls and bacteriochlorophylls play important roles in photosynthesis, and thus the excited-state properties of chlorophylls and bacteriochlorophylls in solutions and proteins have been studied for a long time both experimentally and theoretically. It is experimentally known that the S0-S1 absorption energy of bacteriochlorophyll a (BChl a) in solution is quite insensitive to solvent, though the BChl a has polar functional groups. We investigate the excited-state properties of BChl a in several solutions by using QM/MM-RWFE-SCF method (J. Chem. Theory Comput. 8 (2012), pp 322-334), in which the geometry of a quantum mechanically treated molecule (BChl a, in this case) can be optimized effectively on a free energy surface defined with thermal distribution of the surrounding molecular environment (solvent) obtained by molecular dynamics simulation with a molecular mechanics force field. We employ TDDFT method for the excited-state electronic structure calculation, and find that excited-state properties of BChl a strongly depend on the density functional. We can reproduce the solvent insensitivity by adjusting the parameter of the density functional, and find that the solvent insensitivity results from the counterbalance between the redshift due to hydrogen bond interaction and the blueshift due to decrease in dipole moment. It is expected that the density functional with the adjusted parameter can be applied to BChl a in proteins.

Synthesis and Structural Characterization of New Cu(I) Complexes with the Antithyroid Drug 6-n-Propyl-thiouracil. Study of the Cu(I)-Catalyzed Intermolecular Cycloaddition of Iodonium Ylides toward Benzo[b]furans with Pharmaceutical Implementations

The reaction of copper(I) iodide with 6-n-propylthiouracil (ptu) in the presence or absence of the triphenylphosphine (tpp) or tri(p-tolyl)phosphine (tptp) in a 1:1:2 molar ratio forms the mixed ligand Cu(I) complex with formula [CuI(ptu)2](toluene) (1), [CuI(tpp)2(ptu)] (2), and [CuI(tptp)2(ptu)] (3). The complexes have been characterized by FT-IR, (1)H NMR, UV-vis, spectroscopic techniques, and single crystal X-ray crystallography. Two sulfur atoms from two ptu ligands and one iodide form a trigonal geometry around the metal center in 1. Intramolecular interactions through hydrogen bonds lead to a bend ribbon polymeric supramolecular architecture with zigzag conformation. Two phosphorus atoms from two arylphosphines, one sulfur atom, and one iodide anion form a tetrahedron around the copper ion in case of 2 and 3. Intramolecular hydrogen bonding interactions lead to dimerization. Complexes 1-3 and the already known ones with formulas, [(tpSb)2Cu(μ2-I)2Cu(tpSb)2] (4) (tbSb = triphenylstibine), [(tpp)Cu(μ2-I)2Cu(tpp)2] (5), [(tpp)Cu(μ2-Cl)2Cu(tpp)2] (6), [CuCl(tpp)3·(CH3CN)] (7), and [AuCl(tpp)] (8), were used to study their catalytic activity on the intermolecular cycloaddition of iodonium ylides toward benzo[b]furans formation. The results show that both the metal and the ligand type affect the catalytic affinity of the complexes. The highest yield of benzo[b]furan was derived when complexes 2, 3, and 4 were used as catalysts. The mechanism of the Cu(I)-catalyzed and uncatalyzed intramolecular cycloaddition of iodonium ylide has been also thoroughly explored by means of ab initio electronic structure calculation methods, and the results are compared with the experimental ones.

Loading Aromatic Six-Membered Carbocyclic Rings with Coinage Metals: Aromatic Metalated Benzenes C6M6 and 1,3,5-C6H3M3 (M = Cu, Ag, Au) Exhibiting Intriguing Properties

The trimerization of coinage metal acetylides MC≡CH and MC≡CM (M = Cu, Ag, Au) to form 1,3,5-C6H3M3 and C6M6 aromatic metalated benzenes, respectively, is investigated using electronic structure calculation methods. The structural, energetic, magnetotropic, and spectroscopic properties of the aromatic coinage metalated benzenes are analyzed at the PBE0/Def2-QZVPP level of theory and compared to the respective properties of the unsubstituted archetype aromatic benzene molecule. These exotic molecules exhibit unique properties which are of interest for potential application in several technological issues.

Dynamic load balancing for petascale quantum Monte Carlo applications: The Alias method

Diffusion Monte Carlo is a highly accurate Quantum Monte Carlo method for electronic structure calculations of materials, but it requires frequent load balancing or population redistribution steps to maintain efficiency on parallel machines. This step can be a significant factor affecting performance, and will become more important as the number of processing elements increases. We propose a new dynamic load balancing algorithm, the Alias Method, and evaluate it theoretically and empirically. An important feature of the new algorithm is that the load can be perfectly balanced with each process receiving at most one message. It is also optimal in the maximum size of messages received by any process. We also optimize its implementation to reduce network contention, a process facilitated by the low messaging requirement of the algorithm: a simple renumbering of the MPI ranks based on proximity and a space filling curve significantly improves the MPI Allgather performance. Empirical results on the petaflop Cray XT Jaguar supercomputer at ORNL show up to 30% improvement in performance on 120,000 cores. The load balancing algorithm may be straightforwardly implemented in existing codes. The algorithm may also be employed by any method with many near identical computational tasks that require load balancing.