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At least 145 records · Page 8

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Correlation functions for the fractional generalized Langevin equation in the presence of internal and external noise

We study generalized fractional Langevin equations in the presence of a harmonic potential. General expressions for the mean velocity and particle displacement, the mean squared displacement, position and velocity correlation functions, as well as normalized displacement correlation function are derived. We report exact results for the cases of internal and external friction, that is, when the driving noise is either internal and thus the fluctuation-dissipation relation is fulfilled or when the noise is external. The asymptotic behavior of the generalized stochastic oscillator is investigated, and the case of high viscous damping (overdamped limit) is considered. Additional behaviors of the normalized displacement correlation functions different from those for the regular damped harmonic oscillator are observed. In addition, the cases of a constant external force and the force free case are obtained. The validity of the generalized Einstein relation for this process is discussed. The considered fractional generalized Langevin equation may be used to model anomalous diffusive processes including single file-type diffusion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method

Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Communication: Effect of accidental mode degeneracy on Raman intensity in 2D materials: Hybrid functional study of bilayer phosphorene

Bulk black phosphorus has two optical phonon modes labeled as A{sub g}{sup 2} and B{sub 2u}, respectively, that are nearly degenerate in frequency. However, density functional theory calculations using local or semi-local functionals cannot reproduce this degeneracy. Here, we propose a hybrid functional approach aided by van der Waals (vdW) force fields, which can accurately describe the lattice dynamic and electronic properties of both bulk and few-layer black phosphorus (phosphorene). Using this approach we show that in bilayer phosphorene, the two Raman modes derived from the B{sub 2u} and A{sub g}{sup 2} modes could exhibit strong resonance as a result of the accidental degeneracy so that both modes could be observed in Raman experiment. Without the mode degeneracy, however, the Raman intensity of the B{sub 2u}-derived mode would be too weak to be observed. We further show that the accidental degeneracy is correlated to the applied strain, which enables Raman spectroscopy to be a powerful tool for characterizing built-in strains in 2D materials, e.g., due to the interaction with substrates, which has emerged as an important issue in vdW epitaxy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Surface Functionalization of Black Phosphorus with Nitrenes: Identification of P=N Bonds Using Isotopic Labeling

Abstract: Surface functionalization of two-dimensional crystals is a key path to tuning their intrinsic physical and chemical properties. However, synthetic protocols and experimental strategies to directly probe chemical bonding in modified surfaces are scarce. Introduced here is a mild, surface-specific protocol for the surface functionalization of few-layer black phosphorus nanosheets using a family of photolytically generated nitrenes (RN) from the corresponding azides. By embedding spectroscopic tags in the organic backbone, a multitude of characterization techniques are employed to investigate in detail the chemical structure of the modified nanosheets, including vibrational (infrared, Raman), Xray (emission, photoelectron), CPMAS NMR, and UV-vis spectroscopy. To directly probe the functional groups introduced on the surface, R fragments were selected such that in conjunction with vibrational spectroscopy, 15N-labeling experiments, and DFT methods, diagnostic P=N vibrational modes indicative of iminophosphorane units on the nanosheet surface could be conclusively identified.

Walz, Kendall↗

Off-shell Partition Functions in 3d Gravity

We explore three-dimensional gravity with negative cosmological constant via canonical quantization. We focus on chiral gravity which is related to a single copy of PSL(2,R) Chern-Simons theory and is simpler to treat in canonical quantization. Its phase space for an initial value surface Σ is given by the appropriate moduli space of Riemann surfaces. We use geometric quantization to compute partition functions of chiral gravity on three-manifolds of the form Σ×S 1 , where Σ can have asymptotic boundaries. Most of these topologies do not admit a classical solution and are thus not amenable to a direct semiclassical path integral computation. We use an index theorem that expresses the partition function as an integral of characteristic classes over phase space. In the presence of n asymptotic boundaries, we use techniques from equivariant cohomology to localize the integral to a finite-dimensional integral over $\overline{M}$ g,n , which we evaluate in low genus cases. Higher genus partition functions quickly become complicated since they depend in an oscillatory way on Newton's constant. There is a precise sense in which one can isolate the non-oscillatory part which we call the fake partition function. We establish that there is a topological recursion that computes the fake partition functions for arbitrary Riemann surfaces Σ. As a result, there is a scaling limit in which the model reduces to JT gravity and our methods give a novel way to compute JT partition functions via equivariant localization.

Classical and Quantum Gravity↗

Dynamic Composition Determination in Heterogeneous Ensembles using Angular Autocorrelation Functions as Signatures

Signatures of heterogeneous ensembles composed of multiple types of random oriented particles are represented by the angular autocorrelation functions of the systems. These signatures are retrieved by averaging oversampled angular correlation functions calculated from high throughput X-ray diffraction patterns. Using a component signature matrix, the composition of the heterogeneous system will be directly calculated from the signature of the ensemble. This is the first attempt to determine dynamic composition of a heterogeneous ensemble by fluctuation X-ray scattering using the angular autocorrelation functions as signatures.

composition determination, angular correlation fun↗

Benchmarking the performance of density functional theory and point charge force fields in their description of sI methane hydrate against diffusion Monte Carlo

High quality reference data from diffusion Monte Carlo calculations are presented for bulk sI methane hydrate, a complex crystal exhibiting both hydrogen-bond and dispersion dominated interactions. The performance of some commonly used exchange-correlation functionals and all-atom point charge force fields is evaluated. Our results show that none of the exchange-correlation functionals tested are sufficient to describe both the energetics and the structure of methane hydrate accurately, while the point charge force fields perform badly in their description of the cohesive energy but fair well for the dissociation energetics. By comparing to ice I{sub h}, we show that a good prediction of the volume and cohesive energies for the hydrate relies primarily on an accurate description of the hydrogen bonded water framework, but that to correctly predict stability of the hydrate with respect to dissociation to ice I{sub h} and methane gas, accuracy in the water-methane interaction is also required. Our results highlight the difficulty that density functional theory faces in describing both the hydrogen bonded water framework and the dispersion bound methane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Communication: The description of strong correlation within self-consistent Green's function second-order perturbation theory

We report an implementation of self-consistent Green's function many-body theory within a second-order approximation (GF2) for application with molecular systems. This is done by iterative solution of the Dyson equation expressed in matrix form in an atomic orbital basis, where the Green's function and self-energy are built on the imaginary frequency and imaginary time domain, respectively, and fast Fourier transform is used to efficiently transform these quantities as needed. We apply this method to several archetypical examples of strong correlation, such as a H{sub 32} finite lattice that displays a highly multireference electronic ground state even at equilibrium lattice spacing. In all cases, GF2 gives a physically meaningful description of the metal to insulator transition in these systems, without resorting to spin-symmetry breaking. Our results show that self-consistent Green's function many-body theory offers a viable route to describing strong correlations while remaining within a computationally tractable single-particle formalism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantifying local exciton, charge resonance, and multiexciton character in correlated wave functions of multichromophoric systems

A new method for quantifying the contributions of local excitation, charge resonance, and multiexciton configurations in correlated wave functions of multichromophoric systems is presented. The approach relies on fragment-localized orbitals and employs spin correlators. Its utility is illustrated by calculations on model clusters of hydrogen, ethylene, and tetracene molecules using adiabatic restricted-active-space configuration interaction wave functions. In addition to the wave function analysis, this approach provides a basis for a simple state-specific energy correction accounting for insufficient description of electron correlation. The decomposition scheme also allows one to compute energies of the diabatic states of the local excitonic, charge-resonance, and multi-excitonic character. The new method provides insight into electronic structure of multichromophoric systems and delivers valuable reference data for validating excitonic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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

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.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterizing quasiconvex functions in terms of the Kronrod's tree of a function

As an application of Kronrod's construction of the tree of a function to convex analysis, a characterization of quasiconvex functions is obtained. Namely, a function is quasiconvex if and only if the associated function defined on the tree of the original function is quasiconvex. A new proof of one of the existence lemmas in Kronrod's construction of the tree of a function (the original proof of which turned out to be incorrect) is given. Bibliography: 4 titles. (paper)

97 MATHEMATICS AND COMPUTING↗

SU-G-206-06: Analytic Dose Function for CT Scans in Infinite Cylinders as a Function of Scan Length and Cylinder Radius

Purpose: The radiation dose absorbed at a particular radius ρ within the central plane of a long cylinder following a CT scan is a function of the length of the scan L and the cylinder radius R along with kVp and cylinder composition. An analytic function was created that that not only expresses these dependencies but is integrable in closed form over the area of the central plane. This feature facilitates explicit calculation of the planar average dose. The “approach to equilibrium” h(L) discussed in the TG111 report is seamlessly included in this function. Methods: For a cylindrically symmetric radiation field, Monte Carlo calculations were performed to compute the dose distribution to long polyethylene cylinders for scans of varying L for cylinders ranging in radius from 5 to 20 cm. The function was developed from the resultant Monte Carlo data. In addition, the function was successfully fit to data taken from measurements on the 30 cm diameter ICRU/TG200 phantom using a real-time dosimeter. Results: Symmetry and continuity dictate a local extremum at the center which is a minimum for the larger sizes. There are competing effects as the beam penetrates the cylinder from the outside: attenuation, resulting in a decrease; scatter, abruptly increasing at the circumference. This competition may result in an absolute maximum between the center and outer edge leading to a “gull wing” shape for the radial dependence. For the smallest cylinders, scatter may dominate to the extent that there is an absolute maximum at the center. Conclusion: An integrable, analytic function has been developed that provides the radial dependency of dose for the central plane of a scan of length L for cylinders of varying diameter. Equivalently, we have developed h(L,R,ρ).

60 APPLIED LIFE SCIENCES↗