1,721,237 research outputs found
Electron localisation descriptors in ONETEP: a tool for interpreting localisation and bonding in large-scale DFT calculations
No full textElectron localisation descriptors, such as the electron localisation function (ELF) and localisedorbital locator (LOL) provide a visual tool for interpreting the results of electronic structurecalculations. The descriptors produce a quantumvalence shell electron pair repulsion (VSEPR)representation, indicating the localisation of electron pairs into bonding pairs and lone pairs insingle molecules, coordination compounds andcrystalline solids. We have implemented the ELFand LOL within ONETEP, a DFT code designed to perform calculations on systems containingthousands of atoms with plane-wave accuracy. This is possible using a linear-scaling formulation ofDFT in which the Kohn–Sham orbitals are expressed in terms of a set of strictly localisednon-orthogonal generalised Wannier functions (NGWFs), themselves expanded in a psinc basisset. In this paper, we describe our implementation and explore the chemical insights offered byelectron localisation descriptors in ONETEP in a range of bonding and nonbondedsituations
Massively parallel linear-scaling Hartree–Fock exchange and hybrid exchange–correlation functionals with plane wave basis set accuracy
No full textWe extend our linear-scaling approach for the calculation of Hartree–Fock exchange energy using localized in situ optimized orbitals [Dziedzic et al., J. Chem. Phys. 139, 214103 (2013)] to leverage massive parallelism. Our approach has been implemented in the onetep (Order-N Electronic Total Energy Package) density functional theory framework, which employs a basis of non-orthogonal generalized Wannier functions (NGWFs) to achieve linear scaling with system size while retaining controllable near-complete-basis-set accuracy. For the calculation of Hartree–Fock exchange, we use a resolution-of-identity approach, where an auxiliary basis set of truncated spherical waves is used to fit products of NGWFs. The fact that the electrostatic potential of spherical waves (SWs) is known analytically, combined with the use of a distance-based cutoff for exchange interactions, leads to a calculation cost that scales linearly with the system size. Our new implementation, which we describe in detail, combines distributed memory parallelism (using the message passing interface) with shared memory parallelism (OpenMP threads) to efficiently utilize numbers of central processing unit cores comparable to, or exceeding, the number of atoms in the system. We show how the use of multiple time-memory trade-offs substantially increases performance, enabling our approach to achieve superlinear strong parallel scaling in many cases and excellent, although sublinear, parallel scaling otherwise. We demonstrate that in scenarios with low available memory, which preclude or limit the use of time-memory trade-offs, the performance degradation of our algorithm is graceful. We show that, crucially, linear scaling with system size is maintained in all cases. We demonstrate the practicability of our approach by performing a set of fully converged production calculations with a hybrid functional on large imogolite nanotubes up to over 1400 atoms. We finish with a brief study of how the employed approximations (exchange cutoff and the quality of the SW basis) affect the calculation walltime and the accuracy of the obtained results
Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package
Get PDFAccurate and computationally efficient exchange-correlation functionals are critical to the successful application of linear-scaling density functional theory (DFT). Local and semi-local functionals of the density are naturally compatible with linear-scaling approaches, having a general form which assumes the locality of electronic interactions and which can be efficiently evaluated by numerical quadrature. Presently, the most sophisticated and flexible semi-local functionals are members of the meta-generalized-gradient approximation (meta-GGA) family, and depend upon the kinetic energy density, tau, in addition to the charge density and its gradient. In order to extend the theoretical and computational advantages of tau-dependent meta-GGA functionals to large-scale DFT calculations on thousands of atoms, we have implemented support for tau-dependent meta-GGA functionals in the ONETEP program. In this paper we lay out the theoretical innovations necessary to implement tau-dependent meta-GGA functionals within ONETEP's linear-scaling formalism. We present expressions for the gradient of the tau-dependent exchange-correlation energy, necessary for direct energy minimization. We also derive the forms of the tau-dependent exchange-correlation potential and kinetic energy density in terms of the strictly localized, self-consistently optimized orbitals used by ONETEP. To validate the numerical accuracy of our self-consistent meta-GGA implementation, we performed calculations using the B97M-V and PKZB meta-GGAs on a variety of small molecules. Using only a minimal basis set of self-consistently optimized local orbitals, we obtain energies in excellent agreement with large basis set calculations performed using other codes. Finally, to establish the linear-scaling computational cost and applicability of our approach to large-scale calculations, we present the outcome of self-consistent meta-GGA calculations on amyloid fibrils of increasing size, up to tens of thousands of atoms
Density fitting for three-electron integrals in explicitly correlated electronic structure theory
No full textThe principal challenge in using explicitly correlated wavefunctions for molecules is the evaluation of nonfactorizable integrals over the coordinates of three or more electrons. Immense progress was made in tackling this problem through the introduction of a single-particle resolution of the identity. Decompositions of sufficient accuracy can be achieved, but only with large auxiliary basis sets. Density fitting is an alternative integral approximation scheme, which has proven to be very reliable for two-electron integrals. Here, we extend density fitting to the treatment of all three-electron integrals that appear at the MP2-F12/3*A level of theory. We demonstrate that the convergence of energies with respect to auxiliary basis size is much more rapid with density fitting than with the traditional resolution-of-the-identity approach
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Intercalation voltages for spinel LixMn2O4 (0≤x≤2) cathode materials: Calibration of calculations with the ONETEP linear-scaling DFT code
No full textDensity functional theory (DFT) has become an engine for driving ab-initio quantum mechanical simulations spanning a vast range of applications. However, conventional DFT has limitations of the accessible system size due to computational expense. Recent progress on linear scaling DFT methods has enabled us to investigate larger systems. In this paper, we investigate the numerical agreement between conventional DFT codes and ONETEP, a linear-scaling DFT code, for important materials properties particularly calculating the intercalation potential of spinel electrode materials. Modulating materials with high energy density is an important aspect that contributes to the significant gap in our knowledge of the factors. We provide typical simulation results based on calculated intercalation potentials for discharging the spinel LixMn2O4, which plays a key role in developing high energy density lithium-ion batteries. The structural properties obtained after geometry optimisation with CASTEP yielded materials with volume within 3 % and lattice parameters within 1 % relative error with experimental values. The average intercalation potentials calculated with the CASTEP and ONETEP codes are within 3 % agreement with each other
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Use of the rVV10 nonlocal correlation functional in the B97M-V density functional: defining B97M-rV and related functionals
Get PDFThe VV10 and rVV10 nonlocal correlation functionals are consistently implemented and assessed, with the goal of determining if the rVV10 nonlocal correlation functional can replace the VV10 nonlocal correlation functional in the recently developed B97M-V density functional, to give the B97M-rV density functional. Along the way, four density functionals are simultaneously tested: VV10, rVV10, B97M-V, and B97M-rV. An initial assessment is carried out across the S22 data set, and the short-range damping variable, b, is varied for all four density functionals in order to determine the sensitivity of the functionals to the empirical parameter. The results of this test indicate that a value of b = 6 (fortuitously the same as that in B97M-V) is suitable for B97M-rV. The functionals are then compared across an extensive database of interaction energies, and it is demonstrated that B97M-rV either matches or outperforms B97M-V for all of the tests considered. Finally, the optimization of b across the S22 data set is extended to two range-separated hybrid density functionals, wB97X-V and wB97M-V, and a value of b = 6.2 is recommended for both wB97X-rV and wB97M-rV
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