Minimally Intrusive Data-Driven Approximation of Schur Complement-based Coupling Operators for Heterogeneous Numerical Methods
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de Castro, Amy Grace [Sandia National Laboratories↗
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Discontinuous Galerkin gradient discretisations for the approximation of second-order differential operators in divergence form
We include in the gradient discretisation method (GDM) framework two numerical schemes based on discontinuous Galerkin approximations: the symmetric interior penalty Galerkin (SIPG) method, and the scheme obtained by averaging the jumps in the SIPG method. We prove that these schemes meet the main mathematical gradient discretisation properties on any kind of polytopal mesh, by adapting discrete functional analysis properties to our precise geometrical hypotheses. Therefore, these schemes inherit the general convergence properties of the GDM, which hold for instance in the cases of the p-Laplace problem and of the anisotropic and heterogeneous diffusion problem. This is illustrated by simple 1D and 2D numerical examples.
97 MATHEMATICS AND COMPUTING↗
Tunneling splittings in formic acid dimer: An adiabatic approximation to the Herring formula
Small symmetric molecules and low-dimensional model Hamiltonians are excellent systems for benchmarking theories to compute tunneling splittings. In this work, we investigate a three dimensional model Hamiltonian coupled to a harmonic bath that describes concerted proton transfer in the formic acid dimer. The three modes include the symmetric proton stretch, the symmetric dimer rock, and the dimer stretch. These modes provide a paradigm for the symmetric and anti-symmetric coupled tunneling pathways, these being recognized in the literature as two of the more important classes of coupling. The effects of selective vibrational excitation and coupling to a bath on the tunneling splittings are presented. The splittings for highly excited states are computed using a novel method that makes an adiabatic approximation to the Herring estimate. Results, which are in excellent agreement with the exact splittings, are compared with those obtained using the Makri-Miller approach. This latter method has been shown to provide quality results for tunneling splittings including highly excited vibrational states.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Chasing the limits of the one electron approximation
Rapid progress in the development of computational methods for quantum chemistry is not properly balanced by the development of basis sets. Even in the case of few-electron systems it is hard to find basis set which are able to reproduce the ECG benchmarks with the mhartree accuracy. In this paper we show early work on improvements of the basis sets for small atomic and molecular systems. As a starting point the ground state of lithium atom and the lowest states of lithium dimer will be investigated. The exploratory optimization of the exponents of primitive gaussians will be based on even tempered scheme combined with CISD method.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Using hybrid implicit Monte Carlo diffusion to simulate gray radiation hydrodynamics
This work describes how to couple a hybrid Implicit Monte Carlo Diffusion (HIMCD) method with a Lagrangian hydrodynamics code to evaluate the coupled radiation hydrodynamics equations. This HIMCD method dynamically applies Implicit Monte Carlo Diffusion (IMD) [1] to regions of a problem that are opaque and diffusive while applying standard Implicit Monte Carlo (IMC) [2] to regions where the diffusion approximation is invalid. We show that this method significantly improves the computational efficiency as compared to a standard IMC/Hydrodynamics solver, when optically thick diffusive material is present, while maintaining accuracy. Two test cases are used to demonstrate the accuracy and performance of HIMCD as compared to IMC and IMD. The first is the Lowrie semi-analytic diffusive shock [3]. The second is a simple test case where the source radiation streams through optically thin material and heats a thick diffusive region of material causing it to rapidly expand. We found that HIMCD proves to be accurate, robust, and computationally efficient for these test problems.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
A Novel Algorithm for Solving the Multidimensional Neutron Transport Equation on Massively Parallel Architectures
We employ the Integral Transport Matrix Method (ITMM) as the kernel of new parallel solution methods for the discrete ordinates approximation of the within-group neutron transport equation. The ITMM abandons the repetitive mesh sweeps of the traditional source iterations (SI) scheme in favor of constructing stored operators that account for the direct coupling factors among all the cells' fluxes and between the cells' and boundary surfaces' fluxes. The main goals of this work are to develop the algorithms that construct these operators and employ them in the solution process, determine the most suitable way to parallelize the entire procedure, and evaluate the behavior and parallel performance of the developed methods with increasing number of processes, P. The fastest observed parallel solution method, Parallel Gauss-Seidel (PGS), was used in a weak scaling comparison with the PARTISN transport code, which uses the source iteration (SI) scheme parallelized with the Koch-baker-Alcouffe (KBA) method. Compared to the state-of-the-art SI-KBA with diffusion synthetic acceleration (DSA), this new method- even without acceleration/preconditioning-is completitive for optically thick problems as P is increased to the tens of thousands range. For the most optically thick cells tested, PGS reduced execution time by an approximate factor of three for problems with more than 130 million computational cells on P = 32,768. Moreover, the SI-DSA execution times's trend rises generally more steeply with increasing P than the PGS trend. Furthermore, the PGS method outperforms SI for the periodic heterogeneous layers (PHL) configuration problems. The PGS method outperforms SI and SI-DSA on as few as P = 16 for PHL problems and reduces execution time by a factor of ten or more for all problems considered with more than 2 million computational cells on P = 4.096.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Comparison of second-order spectral line widths formulae
Frequently used second-order spectral line width formulae from the projector operator and kinetic theory methods have not been formally compared previously. Here it is shown that a systematic second-order expansion of the projection operator expression including initial correlations agrees with the second-order kinetic theory result. The agreement assumes a common approximation in the projector operator method that introduces a screened radiator–perturber interaction to account for neglected electron–electron correlations. On the other hand, it is shown that the usual width expression from the projection operator approach neglecting initial correlations differs from kinetic theory. The differences, however, are at least third order in the radiator–perturber interaction. The comparisons suggest using the more compact width expression from kinetic theory, which includes initial correlations and a systematic screening of the radiator–perturber interactions, as the starting point for second-order width calculations.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Molecular polarizability of water from local dielectric response theory
Here, we propose a fully ab initio theory to compute the electron density response under the perturbation in the local field. This method is based on our recently developed local dielectric response theory [Phys. Rev. B 92, 241107(R), 2015], which provides a rigorous theoretical framework to treat local electronic excitations in both nite and extended systems beyond the commonly employed dipole approximation. We have applied this method to study the electronic part of the molecular polarizability of water in ice Ih and liquid water. Our results reveal that the crystal field of the hydrogen-bond network has strong anisotropic effects, which significantly enhance the out-of-plane component and suppress the in-plane component perpendicular to the bisector direction. The contribution from the charge transfer is equally important, which increases the isotropic molecular polarizability by 5-6%. Our study provides new insights into the dielectric properties of water, which form the basis to understand electronic excitations in water and to develop accurate polarizable force fields of water.
36 MATERIALS SCIENCE↗
Stochastic reconstructions of spectral functions: Application to lattice QCD
Here, we present a detailed study of the applications of two stochastic approaches, stochastic optimization method (SOM) and stochastic analytical inference (SAI), to extract spectral functions from Euclidean correlation functions. SOM has the advantage that it does not require prior information. On the other hand, SAI is a more generalized method based on Bayesian inference. Under mean field approximation SAI reduces to the often-used maximum entropy method (MEM), and for a specific choice of the prior SAI becomes equivalent to SOM. To test the applicability of these two stochastic methods to lattice QCD, Firstly, we apply these methods to various reasonably chosen model correlation functions, and present detailed comparisons of the reconstructed spectral functions obtained from SOM, SAI and MEM. Next, we present similar studies for charmonia correlation functions obtained from lattice QCD computations using clover-improved Wilson fermions on large, fine, isotropic lattices at 0:75 and 1:5 T c , T c being the deconfinement transition temperature of a pure gluon plasma. We find that SAI and SOM give consistent results to MEM at these two temperatures.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Boltzmann-conserving classical dynamics in quantum time-correlation functions: “Matsubara dynamics”
We show that a single change in the derivation of the linearized semiclassical-initial value representation (LSC-IVR or “classical Wigner approximation”) results in a classical dynamics which conserves the quantum Boltzmann distribution. We rederive the (standard) LSC-IVR approach by writing the (exact) quantum time-correlation function in terms of the normal modes of a free ring-polymer (i.e., a discrete imaginary-time Feynman path), taking the limit that the number of polymer beads N → ∞, such that the lowest normal-mode frequencies take their “Matsubara” values. The change we propose is to truncate the quantum Liouvillian, not explicitly in powers of ħ{sup 2} at ħ{sup 0} (which gives back the standard LSC-IVR approximation), but in the normal-mode derivatives corresponding to the lowest Matsubara frequencies. The resulting “Matsubara” dynamics is inherently classical (since all terms O(ħ{sup 2}) disappear from the Matsubara Liouvillian in the limit N → ∞) and conserves the quantum Boltzmann distribution because the Matsubara Hamiltonian is symmetric with respect to imaginary-time translation. Numerical tests show that the Matsubara approximation to the quantum time-correlation function converges with respect to the number of modes and gives better agreement than LSC-IVR with the exact quantum result. Matsubara dynamics is too computationally expensive to be applied to complex systems, but its further approximation may lead to practical methods.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Efficient analysis of small-angle scattering curves for large biomolecular assemblies using Monte Carlo methods
Structure elucidation from small-angle scattering curves of large biomolecular assemblies is notoriously challenging. This is because the simulation of high-resolution features in the structure of large macromolecular assemblies, such as de novo protein assemblies, is computationally demanding when it needs to cover a broad range of length scales. Conventional methods, such as the numerical approximation to the Debye equation or the use of spherical harmonics, do not scale well as the size of the assembly increases, which limits their application to small structures (e.g. individual proteins). This work explores the effectiveness of a Monte Carlo method to simulate and fit scattering curves for large biomolecular assemblies spanning over ranges covering atomic and molecular detail (e.g. spacing and orientation of proteins in an assembly) as well as large-scale (hundreds of nanometres) features. Owing to its speed and scalability, it can be combined with a fitting algorithm to extract structural features from experimental small-angle scattering curves in biomolecular assemblies that are otherwise intractable for interpretation. This work first demonstrates the effectiveness of the tool using experimental small-angle X-ray scattering (SAXS) data from tile-like proteins that assemble into 1D tube-like macromolecular structures. Here, the diameter distribution of tubes is extracted from SAXS fits, and this is quantitatively compared with distributions from electron microscopy. SAXS data are also obtained from 2D sheet-like protein assemblies, and the proposed method is used to quantify structural features such as the separation distance between protein building blocks and the flexing of the sheet. An open-source implementation of the methodology is provided for use in a broad range of biological systems involving multi-scale scattering analysis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Homogenization method based on the inverse problem
We present a method for deriving homogeneous multi-group cross sections to replace a heterogeneous region's multi-group cross sections; providing that the fluxes and the currents on the external boundary, and the region averaged fluxes are preserved. The method is developed using diffusion approximation to the neutron transport equation in a symmetrical slab geometry. Assuming that the boundary fluxes are given, two response matrices (RMs) can be defined. The first derives the boundary current from the boundary flux, the second derives the flux integral over the region from the boundary flux. Assuming that these RMs are known, we present a formula which reconstructs the multi-group cross-section matrix and the diffusion coefficients from the RMs of a homogeneous slab. Applying this formula to the RMs of a slab with multiple homogeneous regions yields a homogenization method; which produce such homogenized multi-group cross sections and homogenized diffusion coefficients, that the fluxes and the currents on the external boundary, and the region averaged fluxes are preserved. The method is based on the determination of the eigenvalues and the eigenvectors of the RMs. We reproduce the four-group cross section matrix and the diffusion constants from the RMs in numerical examples. We give conditions for replacing a heterogeneous region by a homogeneous one so that the boundary current and the region-averaged flux are preserved for a given boundary flux. (authors)
97 MATHEMATICS AND COMPUTING↗
Precise and direct method for the measurement of the torsion spring constant of the atomic force microscopy cantilevers
A direct method for the evaluation of the torsional spring constants of the atomic force microscope cantilevers is presented in this paper. The method uses a nanoindenter to apply forces at the long axis of the cantilever and in the certain distance from it. The torque vs torsion relation is then evaluated by the comparison of the results of the indentations experiments at different positions on the cantilever. Next, this relation is used for the precise determination of the torsional spring constant of the cantilever. The statistical analysis shows that the standard deviation of the calibration measurements is equal to approximately 1%. Furthermore, a simple method for calibration of the photodetector’s lateral response is proposed. The overall procedure of the lateral calibration constant determination has the accuracy approximately equal to 10%.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Dual-map framework for noise characterization of quantum computers
In order to understand the capabilities and limitations of quantum computers, it is necessary to develop methods that efficiently characterize and benchmark error channels present on these devices. In this paper, we present a method that faithfully reconstructs a marginal (local) approximation of the effective noise (MATEN) channel, that acts as a single layer at the end of the circuit. We first introduce a dual-map framework that allows us to analytically derive expectation values of observables with respect to noisy circuits. These findings are supported by numerical simulations of the quantum approximate optimization algorithm (QAOA) that also justify the MATEN, even in the presence of nonlocal errors that occur during a circuit. Finally, we demonstrate the performance of the method on Rigetti's Aspen-11 quantum computer for QAOA circuits up to six qubits, successfully predicting the observed measurements on a majority of the qubits.
Sud, James↗
Rate constants of chemical reactions from semiclassical transition state theory in full and one dimension
Semiclassical Transition State Theory (SCTST), a method for calculating rate constants of chemical reactions, offers gains in computational efficiency relative to more accurate quantum scattering methods. In full-dimensional (FD) SCTST, reaction probabilities are calculated from third and fourth potential derivatives along all vibrational degrees of freedom. However, the computational cost of FD SCTST scales unfavorably with system size, which prohibits its application to larger systems. In this study, the accuracy and efficiency of 1-D SCTST, in which only third and fourth derivatives along the reaction mode are used, are investigated in comparison to those of FD SCTST. Potential derivatives are obtained from numerical ab initio Hessian matrix calculations at the MP2/cc-pVTZ level of theory, and Richardson extrapolation is applied to improve the accuracy of these derivatives. Reaction barriers are calculated at the CCSD(T)/cc-pVTZ level. Results from FD SCTST agree with results from previous theoretical and experimental studies when Richardson extrapolation is applied. Results from our implementation of 1-D SCTST, which uses only 4 single-point MP2/cc-pVTZ energy calculations in addition to those for conventional TST, agree with FD results to within a factor of 5 at 250 K. This degree of agreement and the efficiency of the 1-D method suggest its potential as a means of approximating rate constants for systems too large for existing quantum scattering methods.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Least-Squares-Based Weak Galerkin Finite Element Method for Second Order Elliptic Equations
Here, in this article, we introduce a least-squares-based weak Galerkin finite element method for the second order elliptic equation. This new method is shown to provide very accurate numerical approximations for both the primal and the flux variables. In contrast to other existing least-squares finite element methods, this new method allows us to use discontinuous approximating functions on finite element partitions consisting of arbitrary polygon/polyhedron shapes. We also develop a Schur complement algorithm for the resulting discretization problem by eliminating all the unknowns that represent the solution information in the interior of each element. Optimal order error estimates for both the primal and the flux variables are established. An extensive set of numerical experiments are conducted to demonstrate the robustness, reliability, flexibility, and accuracy of the least-squares-based weak Galerkin finite element method. Finally, the numerical examples cover a wide range of applied problems, including singularly perturbed reaction-diffusion equations and the flow of fluid in porous media with strong anisotropy and heterogeneity.
nite element methods↗
A radial basis function Galerkin method for inhomogeneous nonlocal diffusion
We introduce a discretization for a nonlocal diffusion problem using a localized basis of radial basis functions. The stiffness matrix entries are assembled by a special quadrature routine unique to the localized basis. Combining the quadrature method with the localized basis produces a well-conditioned, sparse, symmetric positive definite stiffness matrix. We demonstrate that both the continuum and discrete problems are well-posed and present numerical results for the convergence behavior of the radial basis function method. As a result, we explore approximating the solution to anisotropic differential equations by solving anisotropic nonlocal integral equations using the radial basis function method.
97 MATHEMATICS AND COMPUTING↗
On the ground state calculation of a many-body system using a self-consistent basis and quasi-Monte Carlo: An application to water hexamer
Given a quantum many-body system, the Self-Consistent Phonons (SCP) method provides an optimal harmonic approximation by minimizing the free energy. In particular, the SCP estimate for the vibrational ground state (zero temperature) appears to be surprisingly accurate. We explore the possibility of going beyond the SCP approximation by considering the system Hamiltonian evaluated in the harmonic eigenbasis of the SCP Hamiltonian. It appears that the SCP ground state is already uncoupled to all singly- and doubly-excited basis functions. So, in order to improve the SCP result at least triply-excited states must be included, which then reduces the error in the ground state estimate substantially. For a multidimensional system two numerical challenges arise, namely, evaluation of the potential energy matrix elements in the harmonic basis, and handling and diagonalizing the resulting Hamiltonian matrix, whose size grows rapidly with the dimensionality of the system. Using the example of water hexamer we demonstrate that such calculation is feasible, i.e., constructing and diagonalizing the Hamiltonian matrix in a triply-excited SCP basis, without any additional assumptions or approximations. Our results indicate particularly that the ground state energy differences between different isomers (e.g., cage and prism) of water hexamer are already quite accurate within the SCP approximation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗