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At least 1,693 records · Page 94

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of Tuning the Structure on the Optical and Magnetic Properties by Various Transition Metal Doping in ZnO/TM (TM = Fe, FeCo, Cr, and Mn) Thin Films

We have investigated in this work the physical, optical, electronic, and the magnetic behavior (Curie temperature, magnetic moment) of Zn.1-x.MxO (M = Fe 5%, Co 1%, Cr 5%, and Mn 5%), diluted magnetic semiconductors (DMSs). The samples were deposited on glass substrate by the spray pyrolysis technique, and the results of the x-ray diffraction (XRD) of the prepared substrates was used to prove the incorporation of the dopants into the ZnO lattice host; the ferromagnetic and the antiferromagnetic state competitions and their effects on the physical, magnetic, and optical properties, were investigated. The electronic structure and magnetic properties of transition metal (TM) defects, were investigated in detail, by using the Korringa–Kohn–Rostoker (KKR) method combined with the coherent potential approximation (CPA). As a result, doping by TM impurities induce the ferromagnetism with different competitions between the ferromagnetic and antiferromagnetic states, which affects the physical properties of the TM (Fe, Fe/Co, Cr, and Mn)-doped ZnO, with a Curie temperature closer to room-temperature ferromagnetic.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Half Metallic Ferromagnetic Character in ZnXP{sub 2} (X = Ge, Si) Chalcopyrites Doped with Mn

The electronic and the magnetic properties of ZnXP{sub 2} (X = Ge, Si) were studied using the Korring-Kohn-Rostoker (KKR) method combined with the coherent potential approximation (CPA). The total and partial density of state (DOS) are computed for different Mn concentrations. The total magnetic moment, FM and DLM energies, and their variation as well as Curie temperature are also given. It is shown that the substitution of X cations (X = Ge, Si) by Mn atoms in ZnXP{sub 2} chalcopyrites leads to half metallic ferromagnetic character with double exchange mechanism. Thus, the critical temperature can be controlled by varying the concentration of manganese impurity.

36 MATERIALS SCIENCE↗

Pareto-Lognormal Modeling of Known and Unknown Metal Resources. II. Method Refinement and Further Applications

Pareto-lognormal modeling of worldwide metal deposit size–frequency distributions was proposed in an earlier paper (Agterberg in Nat Resour 26:3–20, 2017). In the current paper, the approach is applied to four metals (Cu, Zn, Au and Ag) and a number of model improvements are described and illustrated in detail for copper and gold. The new approach has become possible because of the very large inventory of worldwide metal deposit data recently published by Patiño Douce (Nat Resour 25:97–124, 2016c). Worldwide metal deposits for Cu, Zn and Ag follow basic lognormal size–frequency distributions that form straight lines on lognormal Q–Q plots. Au deposits show a departure from the straight-line model in the vicinity of their median size. Both largest and smallest deposits for the four metals taken as examples exhibit hyperbolic size–frequency relations and their Pareto coefficients are determined by fitting straight lines on log rank–log size plots. As originally pointed out by Patiño Douce (Nat Resour Res 25:365–387, 2016d), the upper Pareto tail cannot be distinguished clearly from the tail of what would be a secondary lognormal distribution. The method previously used in Agterberg (2017) for fitting the bridge function separating the largest deposit size–frequency Pareto tail from the basic lognormal is significantly improved in this paper. A new method is presented for estimating the approximate deposit size value at which the upper tail Pareto comes into effect. Although a theoretical explanation of the proposed Pareto-lognormal distribution model is not a required condition for its applicability, it is shown that existing double Pareto-lognormal models based on Brownian motion generalizations of the multiplicative central limit theorem are not applicable to worldwide metal deposits. Neither are various upper tail frequency amplification models in their present form. Although a physicochemical explanation remains possible, it is argued that preferential mining of the largest and smallest orebodies can have economic historical reasons. The size–frequency distribution of uranium can be regarded as lognormal without Pareto tails. At the end of the paper, it is shown that original copper deposit size data can be used for forward projection of discovery trends toward the end of this century.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optoelectronic properties of germanium iodide perovskites AGeI{sub 3} (A = K, Rb and Cs): first principles investigations

In this paper, we have investigated the structural, optoelectronic and elastic properties of AGeI{sub 3} (A = K, Rb and Cs) using the density functional theory with generalized gradient approximation (GGA) for potential exchange correlation. The modified Becke–Johnson (mBJ-GGA) potential approximation is also used for calculating the optoelectronic properties of the material. The results show that the band structure of the perovskites AGeI{sub 3} (have a semiconductor behavior with direct band gap at R–R direction, the gap energy values calculated with mBJ-GGA, for each compound as following: 0.58, 0.63, and 0.71 eV, respectively. The optical properties, such as real and imaginary parts of the dielectric functions, refractive index, reflectivity, conductivity and absorption coefficient are investigated. As results, these compounds are competent candidates photovoltaic application like light harvester.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Fractional Calculus in Hydrologic Modeling: A Numerical Perspective

Fractional derivatives can be viewed either as a handy extension of classical calculus or, more deeply, as mathematical operators defined by natural phenomena. This follows the view that the diffusion equation is defined as the governing equation of a Brownian motion. In this paper, we emphasize that fractional derivatives come from the governing equations of stable Levy motion, and that fractional integration is the corresponding inverse operator. Fractional integration, and its multi-dimensional extensions derived in this way, are intimately tied to fractional Brownian (and Levy) motions and noises. By following these general principles, we discuss the Eulerian and Lagrangian numerical solutions to fractional partial differential equations, and Eulerian methods for stochastic integrals. These numerical approximations illuminate the essential nature of the fractional calculus.

58 GEOSCIENCES↗

Effects of vacuum fluctuation suppression on atomic decay rates

Highlights: > Excited atoms are shot through a cavity containing an electromagnetic field. > Cavity is in the lowest mode in a non-classical state. > Such a state can suppress the decay rate of the atoms in certain situations. > We show that this effect can be correlated with periods of negative energy density. - Abstract: The use of atomic decay rates as a probe of sub-vacuum phenomena will be studied. Because electromagnetic vacuum fluctuations are essential for radiative decay of excited atomic states, decay rates can serve as a measure of the suppression of vacuum fluctuations in non-classical states, such as squeezed vacua. In such states, the renormalized expectation value of the square of the electric field or the energy density can be periodically negative, representing suppression of vacuum fluctuations. We explore the extent to which atomic decays can be used to measure the mean squared electric field or energy density. We consider a scheme in which atoms in an excited state transit a closed cavity whose lowest mode contains photons in a non-classical state. A crucial feature of our analysis is that we do not employ the rotating wave approximation. The change in the decay probability of the atom in the cavity due to the non-classical state can, under certain circumstances, serve as a measure of the mean squared electric field or energy density in the cavity. We make some estimates of the magnitude of this effect, which indicate that an experimental test might be possible, although very challenging.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Algebraic structure of general electromagnetic fields and energy flow

Highlights: > Algebraic structure of general electromagnetic fields in stationary spacetime. > Eigenvalues and eigenvectors of the electomagnetic field tensor. > Energy-momentum in terms of eigenvectors and Killing vector. > Explicit form of reference frame with vanishing Poynting vector. > Application of formalism to Bessel beams. - Abstract: The algebraic structures of a general electromagnetic field and its energy-momentum tensor in a stationary space-time are analyzed. The explicit form of the reference frame in which the energy of the field appears at rest is obtained in terms of the eigenvectors of the electromagnetic tensor and the existing Killing vector. The case of a stationary electromagnetic field is also studied and a comparison is made with the standard short-wave approximation. The results can be applied to the general case of a structured light beams, in flat or curved spaces. Bessel beams are worked out as example.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Nonclassical effects in a highly nonlinear generalized homogeneous Dicke model

An intensity dependent nonlinear coupling model of N two-level atoms (generalized Dicke model) interacting dispersively with a bimodal cavity field via two-photon transitions is investigated in a scenario where the rotating wave approximation is assumed. The model becomes homogeneous in the sense that the spin transition frequency is the same for all atoms and the coupling constants emerging from the collective interactions of the atomic system with the cavity field depend only on the particular radiation field mode. This allows us to represent the Dicke Hamiltonian entirely in terms of the total angular momentum J. It is assumed that, initially, the atomic system and the field are in a disentangled state where the field modes are in Glauber coherent states and the atomic system is a superposition of states |JM> (Dicke states). The model is numerically tested against simulations of normal squeezing variance of the field, squeezing factors based on the Heisenberg uncertainty principle, along with the statistical properties of the light leading to the possible production of nonclassical effects, such as degree of second-order coherence in the modes, degree of intermode correlation, as well as violation of the Cauchy-Schwartz inequality. Analytical expression of the total density operator matrix elements at t>0 shows the present nonlinear model to be strongly entangled, which is reflected in the time evolution of the linear entropy, where the superposition states are reduced to statistical mixtures. Thus, the present generalized Dicke model does not preserve the modulus of the Bloch vector. The computations, performed in the weak coupling and strong field limits, were conducted via second-order Dyson perturbative expansion of the time evolution operator matrix elements for the totality of the angular momentum states of the atomic system. - Highlights: > The present highly nonlinear generalized Dicke model involves two-photon transitions. > Quantum coherences significantly affect the dynamics of the atomic system. > At t>0 the time-dependent density operator matrix becomes strongly entangled. > Linear entropy shows that the superposition states turn into statistical mixtures. > The present Dicke model does not preserve the modulus of the Bloch vector.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Thermodynamically consistent algorithms for models of incompressible multiphase polymer solutions with a variable mobility

Here we present a general strategy for developing structure and property preserving numerical algorithms for thermodynamically consistent models of incompressible multiphase polymer solutions with a variable mobility. We first present a formalism to derive thermodynamically consistent, incompressible, multiphase polymer models. Then, we develop the general strategy, known as the supplementary variable method, to devise thermodynamically consistent numerical approximations to the models. We illustrate the numerical strategy using newly developed models of incompressible diblock copolymer solutions coupled with an electric and a magnetic field, respectively. Mesh refinement is conducted to verify convergence rates of the developed schemes. Some numerical examples are given to exhibit underlying dynamics absent from and driven by the external fields, respectively, highlighting differences between models with the variable and constant mobilities.

97 MATHEMATICS AND COMPUTING↗

A benchmark of Gutzwiller conjugate gradient minimization method in ground state energy calculations of dimers

Herein we present numerical results of ground-state energies of 9 molecules in the well-established G2 molecule set given by the Gutzwiller conjugate gradient minimization (GCGM) method. The method, beyond the commonly used Gutzwiller approximation, was recently developed based on Gutzwiller variational wave functions. We find that compared to benchmark data given by full configuration interaction, GCGM total energies are reasonably well reproduced with the minimum basis set. To include the dynamical correlation beyond the minimal basis calculations, we adopt the local density approximation for the dynamical correlation energy $E_c$. By comparing the results with benchmark data given by experiments and large-basis configuration interaction, the GCGM total energies with $E_c$ are in general better reproduced, but discrepancies are still observed for some dimers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fantômas unconfined: global QCD fits with Bézier parameterizations

Fantômas is a C++ toolkit for exploring the parametrization dependence of parton distribution functions (PDFs) and other correlator functions in quantum chromodynamics (QCD). Fantômas facilitates the generation of adaptable polynomial parametrizations for PDFs, called metamorphs, to find best-fit PDF solutions and quantify the epistemic uncertainty associated with the parametrizations during their fitting. The method employs Bézier curves as universal approximators for a variety of PDF shapes. Integrated into the xFitter framework for the global QCD analysis, Fantômas provides a foundation for general models of PDFs, while reducing the computational time compared to the approaches utilizing traditional polynomial parametrizations as well as providing an interpretable alternative to neural-network-based models. This paper outlines the structure and practical usage of the Fantômas toolkit, including its inputs, outputs, and implementation within xFitter. It also provides a practical example of using Fantômas for uncertainty quantification as well as the combination of PDF fits into a single ensemble.

Bézier curves↗

A hybrid (Monte Carlo/deterministic) approach for multi-dimensional radiation transport

Highlights: {yields} We introduce a variance reduction scheme for Monte Carlo (MC) transport. {yields} The primary application is atmospheric remote sensing. {yields} The technique first solves the adjoint problem using a deterministic solver. {yields} Next, the adjoint solution is used as an importance function for the MC solver. {yields} The adjoint problem is solved quickly since it ignores the volume. - Abstract: A novel hybrid Monte Carlo transport scheme is demonstrated in a scene with solar illumination, scattering and absorbing 2D atmosphere, a textured reflecting mountain, and a small detector located in the sky (mounted on a satellite or a airplane). It uses a deterministic approximation of an adjoint transport solution to reduce variance, computed quickly by ignoring atmospheric interactions. This allows significant variance and computational cost reductions when the atmospheric scattering and absorption coefficient are small. When combined with an atmospheric photon-redirection scheme, significant variance reduction (equivalently acceleration) is achieved in the presence of atmospheric interactions.

97 MATHEMATICS AND COMPUTING↗

Scalable and efficient algorithms for the propagation of uncertainty from data through inference to prediction for large-scale problems, with application to flow of the Antarctic ice sheet

The majority of research on efficient and scalable algorithms in computational science and engineering has focused on the forward problem : given parameter inputs, solve the governing equations to determine output quantities of interest. In contrast, in this paper, we consider the broader question: given a (large-scale) model containing uncertain parameters, (possibly) noisy observational data, and a prediction quantity of interest, how do we construct efficient and scalable algorithms to (1) infer the model parameters from the data (the deterministic inverse problem ), (2) quantify the uncertainty in the inferred parameters (the Bayesian inference problem), and (3) propagate the resulting uncertain parameters through the model to issue predictions with quantified uncertainties (the forward uncertainty propagation problem )? We present efficient and scalable algorithms for this end-to-end, data-to-prediction process under the Gaussian approximation and in the context of modeling the flow of the Antarctic ice sheet and its effect on loss of grounded ice to the ocean. The ice is modeled as a viscous, incompressible, creeping, shear-thinning fluid. The observational data come from satellite measurements of surface ice flow velocity, and the uncertain parameter field to be inferred is the basal sliding parameter, represented by a heterogeneous coefficient in a Robin boundary condition at the base of the ice sheet. The prediction quantity of interest is the present-day ice mass flux from the Antarctic continent to the ocean. We show that the work required for executing this data-to-prediction process—measured in number of forward (and adjoint) ice sheet model solves—is independent of the state dimension, parameter dimension, data dimension, and the number of processor cores. The key to achieving this dimension independence is to exploit the fact that, despite their large size, the observational data typically provide only sparse information on model parameters. This property can be exploited to construct a low rank approximation of the linearized parameter-to-observable map via randomized SVD methods and adjoint-based actions of Hessians of the data misfit functional.

54 ENVIRONMENTAL SCIENCES↗

Variational Bayesian strategies for high-dimensional, stochastic design problems

This paper is concerned with a lesser-studied problem in the context of model-based, uncertainty quantification (UQ), that of optimization/design/control under uncertainty. The solution of such problems is hindered not only by the usual difficulties encountered in UQ tasks (e.g. the high computational cost of each forward simulation, the large number of random variables) but also by the need to solve a nonlinear optimization problem involving large numbers of design variables and potentially constraints. We propose a framework that is suitable for a class of such problems and is based on the idea of recasting them as probabilistic inference tasks. To that end, we propose a Variational Bayesian (VB) formulation and an iterative VB–Expectation-Maximization scheme that is capable of identifying a local maximum as well as a low-dimensional set of directions in the design space, along which, the objective exhibits the largest sensitivity. We demonstrate the validity of the proposed approach in the context of two numerical examples involving thousands of random and design variables. In all cases considered the cost of the computations in terms of calls to the forward model was of the order of 100 or less. The accuracy of the approximations provided is assessed by information-theoretic metrics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Deep learning of free boundary and Stefan problems

Free boundary problems appear naturally in numerous areas of mathematics, science and engineering. These problems present a great computational challenge because they necessitate numerical methods that can yield an accurate approximation of free boundaries and complex dynamic interfaces. In this work, we propose a multi-network model based on physics-informed neural networks to tackle a general class of forward and inverse free boundary problems called Stefan problems. Specifically, we approximate the unknown solution as well as any moving boundaries by two deep neural networks. Besides, we formulate a new type of inverse Stefan problems that aim to reconstruct the solution and free boundaries directly from sparse and noisy measurements. We demonstrate the effectiveness of our approach in a series of benchmarks spanning different types of Stefan problems, and illustrate how the proposed framework can accurately recover solutions of partial differential equations with moving boundaries and dynamic interfaces. All code and data accompanying this manuscript are publicly available at https://github.com/PredictiveIntelligenceLab/DeepStefan.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Kernel learning backward SDE filter for data assimilation

In this paper, we develop a kernel learning backward SDE filter method to estimate the state of a stochastic dynamical system based on its partial noisy observations. A system of forward backward stochastic differential equations is used to propagate the state of the target dynamical model, and Bayesian inference is applied to incorporate the observational information. Further, to characterize the dynamical model in the entire state space, we introduce a kernel learning method to learn a continuous global approximation for the conditional probability density function of the target state by using discrete approximated density values as training data. Numerical experiments demonstrate that the kernel learning backward SDE is highly effective.

97 MATHEMATICS AND COMPUTING↗

High-order limiting methods using maximum principle bounds derived from the Boltzmann equation I: Euler equations

The use of limiting methods for high-order numerical approximations of hyperbolic conservation laws generally requires defining an admissible region/bounds for the solution. In this work, we present a novel approach for computing solution bounds and limiting for the Euler equations through the kinetic representation provided by the Boltzmann equation, which allows for extending limiters designed for linear advection directly to the Euler equations. Given an arbitrary set of solution values to compute bounds over (e.g., numerical stencil) and a desired linear advection limiter, the proposed approach yields an analytic expression for the admissible region of particle distribution function values, which may be numerically integrated to yield a set of bounds for the density, momentum, and total energy. Further, these solution bounds are shown to preserve positivity of density/pressure/internal energy and, when paired with a limiting technique, can robustly resolve strong discontinuities while recovering high-order accuracy in smooth regions without any ad hoc corrections (e.g., relaxing the bounds). This approach is demonstrated in the context of an explicit unstructured high-order discontinuous Galerkin/flux reconstruction scheme for a variety of difficult problems in gas dynamics, including cases with extreme shocks and shock-vortex interactions. Furthermore, this work presents a foundation for limiting techniques for more complex macroscopic governing equations that can be derived from an underlying kinetic representation for which admissible solution bounds are not well-understood.

42 ENGINEERING↗