Molecular Packing of Amphiphilic Nanosheets Resolved by X-ray Scattering
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Results for “Formal Methods”
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COMPASO : A new halo finder for competitive assignment to spherical overdensities
We describe a new method (compaso) for identifying groups of particles in cosmological N-body simulations. compaso builds upon existing spherical overdensity (SO) algorithms by taking into consideration the tidal radius around a smaller halo before competitively assigning halo membership to the particles. In this way, the compaso finder allows for more effective deblending of haloes in close proximity as well as the formation of new haloes on the outskirts of larger ones. This halo-finding algorithm is used in the abacussummit suite of N-body simulations, designed to meet the cosmological simulation requirements of the Dark Energy Spectroscopic Instrument (DESI) survey. compaso is developed as a highly efficient on-the-fly group finder, which is crucial for enabling good load-balancing between the GPU and CPU and the creation of high-resolution merger trees. In this paper, we describe the halo-finding procedure and its particular implementation in abacus, accompanying it with a qualitative analysis of the finder. We test the robustness of the compaso catalogues before and after applying the cleaning method described in an accompanying paper and demonstrate its effectiveness by comparing it with other validation techniques. We then visualize the haloes and their density profiles, finding that they are well fit by the NFW formalism. Finally, we compare other properties such as radius–mass relationships and two-point correlation functions with that of another widely used halo finder, rockstar.
79 ASTRONOMY AND ASTROPHYSICS↗
Automated identification of dominant physical processes
The identification of processes that locally and approximately dominate dynamical system behavior has enabled significant advances in understanding and modeling nonlinear differential dynamical systems. Conventional methods of dominant process identification involve piecemeal and ad hoc (non-rigorous, informal) scaling analyses to identify dominant balances of governing equation terms and to delineate the spatiotemporal boundaries (boundaries in space and/or time) of each dominant balance. For the first time, we present an objective global measure of the fit of dominant balances to observations, which is desirable for automation, and was previously undefined. Furthermore, we propose a formal definition of the dominant balance identification problem in the form of an optimization problem. Here, we show that the optimization can be performed by various machine learning algorithms, enabling the automatic identification of dominant balances. Our method is algorithm agnostic and it eliminates reliance upon expert knowledge to identify dominant balances which are not known beforehand.
42 ENGINEERING↗
Methods for Evaluating DC Arc Incident Energy in PV Systems: Preprint
Renewable energy systems continue to be one of the fastest growing segments of the energy industry. This paper focuses on the understanding of how photovoltaic (PV) technology behaves under dc arc conditions. Emphasis is placed on the electrical safety aspect of DC arc flash incident energy evaluation. Because of the fast proliferation of PV systems and the lack of formal equivalent calculation guidelines such as IEEE 1584 for AC systems, it has been necessary to rely on different equations and models presented by various researchers over the last few years. This paper discusses the behavior of PV systems under arc conditions and presents the results of available methods to estimate the dc arc flash incident energy. This paper provides a comparative analysis of a proposed arc-flash incident energy calculation method against different laboratory tests including those performed by NREL. Detailed explanations are provided regarding the effect of PV module I-V and P-V curves under arcing conditions. Examples of the application of the proposed calculation method to the test measurements are included.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Linear-scaling explicitly correlated treatment of solids: Periodic local MP2-F12 method
Theory and implementation of the periodic local MP2-F12 method in the 3*A fixed-amplitude ansatz is presented. The method is formulated in the direct space, employing local representation for the occupied, virtual, and auxiliary orbitals in the form of Wannier functions (WFs), projected atomic orbitals (PAOs), and atom-centered Gaussian-type orbitals, respectively. Local approximations are introduced, restricting the list of the explicitly correlated pairs, as well as occupied, virtual, and auxiliary spaces in the strong orthogonality projector to the pair-specific domains on the basis of spatial proximity of respective orbitals. The 4-index two-electron integrals appearing in the formalism are approximated via the direct-space density fitting technique. In this procedure, the fitting orbital spaces are also restricted to local fit-domains surrounding the fitted densities. The formulation of the method and its implementation exploits the translational symmetry and the site-group symmetries of the WFs. Test calculations are performed on LiH crystal. The results show that the periodic LMP2-F12 method substantially accelerates basis set convergence of the total correlation energy, and even more so the correlation energy differences. The resulting energies are quite insensitive to the resolution-of-the-identity domain sizes and the quality of the auxiliary basis sets. The convergence with the orbital domain size is somewhat slower, but still acceptable. Moreover, inclusion of slightly more diffuse functions, than those usually used in the periodic calculations, improves the convergence of the LMP2-F12 correlation energy with respect to both the size of the PAO-domains and the quality of the orbital basis set. At the same time, the essentially diffuse atomic orbitals from standard molecular basis sets, commonly utilized in molecular MP2-F12 calculations, but problematic in the periodic context, are not necessary for LMP2-F12 treatment of crystals.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Tidal dissipation in a homogeneous spherical body. I. Methods
A formula for the tidal dissipation rate in a spherical body is derived from first principles to correct some mathematical inaccuracies found in the literature. The development is combined with the Darwin-Kaula formalism for tides. Our intermediate results are compared with those by Zschau and Platzman. When restricted to the special case of an incompressible spherical planet spinning synchronously without libration, our final formula can be compared with the commonly used expression from Peale and Cassen. However, the two turn out to differ, as in our expression the contributions from all Fourier modes are positive-definite, which is not the case with the formula from Peale and Cassen. Examples of the application of our expression for the tidal damping rate are provided in the work by Makarov and Efroimsky (Paper II) published back to back with the current paper.
79 ASTRONOMY AND ASTROPHYSICS↗
Dynamical chemistry: non-equilibrium effective actions for reactive fluids
Abstract We present two approaches for describing chemical reactions taking place in fluid phase. The first method mirrors the usual derivation of the hydrodynamic equations of motion by relating conserved—or to account for chemical reactions, non-conserved—currents to local-equilibrium parameters. The second method involves a higher-brow approach in which we attack the same problem from the perspective of non-equilibrium effective field theory (EFT). Non-equilibrium effective actions are defined using the in–in formalism on the Schwinger–Keldysh contour and are therefore capable of describing thermal fluctuations and dissipation as well as quantum effects. The non-equilibrium EFT approach is especially powerful as all terms in the action are fully specified by the symmetries of the system; in particular the second law of thermodynamics does not need to be included by hand, but is instead derived from the action itself. We find that the equations of motion generated by both methods agree, but the EFT approach yields certain advantages. To demonstrate some of these advantages we construct a quadratic action that is valid to very small distance scales—much smaller than the scales at which ordinary hydrodynamic theories break down. Such an action captures the full thermodynamic and quantum behavior of reactions and diffusion at quadratic order. Finally, taking the low-frequency and low-wavenumber limit, we reproduce the linearized version of the well-known reaction–diffusion equations as a final coherence check.
Mechanics↗
Breaking Computational Barriers: Real-time Analysis and Optimization with Large-scale Nonlinear Models via Model Reduction
Model reduction for dynamical systems is a promising approach for reducing the computational cost of large-scale physics-based simulations to enable high-fidelity models to be used in many- query (e.g., Bayesian inference) and near-real-time (e.g., fast-turnaround simulation) contexts. While model reduction works well for specialized problems such as linear time-invariant systems, it is much more difficult to obtain accurate, stable, and efficient reduced-order models (ROMs) for systems with general nonlinearities. This report describes several advances that enable nonlinear reduced-order models (ROMs) to be deployed in a variety of time-critical settings. First, we present an error bound for the Gauss-Newton with Approximated Tensors (GNAT) nonlinear model reduction technique. This bound allows the state-space error for the GNAT method to be quantified when applied with the backward Euler time-integration scheme. Second, we present a methodology for preserving classical Lagrangian structure in nonlinear model reduction. This technique guarantees that important properties--such as energy conservation and symplectic time-evolution maps--are preserved when performing model reduction for models described by a Lagrangian formalism (e.g., molecular dynamics, structural dynamics). Third, we present a novel technique for decreasing the temporal complexity --defined as the number of Newton-like iterations performed over the course of the simulation--by exploiting time-domain data. Fourth, we describe a novel method for refining projection-based reduced-order models a posteriori using a goal-oriented framework similar to mesh-adaptive h -refinement in finite elements. The technique allows the ROM to generate arbitrarily accurate solutions, thereby providing the ROM with a 'failsafe' mechanism in the event of insufficient training data. Finally, we present the reduced-order model error surrogate (ROMES) method for statistically quantifying reduced- order-model errors. This enables ROMs to be rigorously incorporated in uncertainty-quantification settings, as the error model can be treated as a source of epistemic uncertainty. This work was completed as part of a Truman Fellowship appointment. We note that much additional work was performed as part of the Fellowship. One salient project is the development of the Trilinos-based model-reduction software module Razor , which is currently bundled with the Albany PDE code and currently allows nonlinear reduced-order models to be constructed for any application supported in Albany. Other important projects include the following: 1. ROMES-equipped ROMs for Bayesian inference: K. Carlberg, M. Drohmann, F. Lu (Lawrence Berkeley National Laboratory), M. Morzfeld (Lawrence Berkeley National Laboratory). 2. ROM-enabled Krylov-subspace recycling: K. Carlberg, V. Forstall (University of Maryland), P. Tsuji, R. Tuminaro. 3. A pseudo balanced POD method using only dual snapshots: K. Carlberg, M. Sarovar. 4. An analysis of discrete v. continuous optimality in nonlinear model reduction: K. Carlberg, M. Barone, H. Antil (George Mason University). Journal articles for these projects are in progress at the time of this writing.
97 MATHEMATICS AND COMPUTING↗
Theoretical Investigation of Structural, Electronic, Magnetic, and Mechanical Properties of Quaternary Heusler Alloys CoVTiX (X = As, Si)
The structural, electronic, magnetic, and mechanical properties of CoVTiAs and CoVTiSi quaternary Heusler alloys are studied using the full-potential linearized augmented plane-wave (FP-LAPW) method in the framework of the density functional theory (DFT). The generalized gradient approximation (GGA) is chosen for the exchange-correlation energy, whereas the modified Becke-Johnson (mBJ) formalism is applied for the electronic properties. Both CoVTiAs and CoVTiSi are stable in the type 2 (FM) structure. The mechanical properties of CoVTiX (X = As, Si) are predicted from the calculated elastic constants. Results identify that these compounds are mechanically stable. Our results with the mBJ approximation predict that CoVTiAs and CoVTiSi alloys are half-metallic ferromagnets with band gaps of 0.450 and 0.424 eV, respectively.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Nonadiabatic Excited-State Molecular Dynamics for Open-Shell Systems
Nonadiabatic Molecular Dynamics (NAMD) of excited states has been widely used in the simulation of photoinduced phenomena. However, the inability to treat bond breaking and forming processes with single-reference electronic structure methods limits their application in photochemistry for extended molecular systems. In this work, the extension of excited-state NAMD for open-shell systems is developed and implemented in the NEXMD software. We present the spin-unrestricted CIS and TDSCF formalism for the ground and excited states, analytical derivatives, and nonadiabatic derivative couplings for the respective potential energy surfaces. Next, this methodology is employed to study the photochemical reaction of three model molecules. The results demonstrate the advantage of the open-shell approach in modeling photochemical reactions, especially involving bond breaking processes. We find that the open-shell method lowers the reaction barrier at the bond-breaking limits resulting in larger calculated photochemical quantum yields compared to the respective closed-shell results. We also address problems related to spin contamination in the open-shell method, especially when molecular geometries are far from equilibrium.
36 MATERIALS SCIENCE↗
Detector density and small field dosimetry: Integral versus point dose measurement schemes
Purpose: TheAlfonso et al. [Med. Phys.35, 5179–5186 (2008)] formalism for small field dosimetry proposes a set of correction factors (k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r}}}}}}}}}) which account for differences between the detector response in nonstandard (clinical) and machine-specific-reference fields. In this study, the Monte Carlo method was used to investigate the viability of such small field correction factors for four different detectors irradiated under a variety of conditions. Because k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r}}}}}}}}} values for single detector position measurements are influenced by several factors, a new theoretical formalism for integrated-detector-position [dose area product (DAP)] measurements is also presented and was tested using Monte Carlo simulations. Methods: A BEAMnrc linac model was built and validated for a Varian Clinac iX accelerator. Using the egs++ geometry package, detailed virtual models were built for four different detectors: a PTW 60012 unshielded diode, a PTW 60003 Diamond detector, a PTW 31006 PinPoint (ionization chamber), and a PTW 31018 MicroLion (liquid-filled ionization chamber). The egs-chamber code was used to investigate the variation ofk{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r}}}}}}}}} with detector type, detector construction, field size, off-axis position, and the azimuthal angle between the detector and beam axis. Simulations were also used to consider the DAP obtained by each detector: virtual detectors and water voxels were scanned through high resolution grids of positions extending far beyond the boundaries of the fields under consideration. Results: For each detector, the correction factor (k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r}}}}}}}}}) was shown to depend strongly on detector off-axis position and detector azimuthal angle in addition to field size. In line with previous studies, substantial interdetector variation was also observed. However, it was demonstrated that by considering DAPs rather than single-detector-position dose measurements the high level of interdetector variation could be eliminated. Under small field conditions, mass density was found to be the principal determinant of water equivalence. Additionally, the mass densities of components outside the sensitive volumes were found to influence the detector response. Conclusions: k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r}}}}}}}}} values for existing detector designs depend on a host of variables and their calculation typically relies on the use of time-intensive Monte Carlo methods. Future moves toward density-compensated detector designs or DAP based protocols may simplify the methodology of small field dosimetry.
07 ISOTOPE AND RADIATION SOURCES↗
An Eulerian–Lagrangian Weighted Essentially Nonoscillatory scheme for nonlinear conservation laws
Here, we develop a formally high order Eulerian–Lagrangian Weighted Essentially Nonoscillatory (EL-WENO) finite volume scheme for nonlinear scalar conservation laws that combines ideas of Lagrangian traceline methods with WENO reconstructions. The particles within a grid element are transported in the manner of a standard Eulerian–Lagrangian (or semi-Lagrangian) scheme using a fixed velocity v. A flux correction computation accounts for particles that cross the v-traceline during the time step. If v = 0, the scheme reduces to an almost standard WENO5 scheme. The CFL condition is relaxed when v is chosen to approximate either the characteristic or particle velocity. Excellent numerical results are obtained using relatively long time steps. The v-traceback points can fall arbitrarily within the computational grid, and linear WENO weights may not exist for the point. A general WENO technique is described to reconstruct to any order the integral of a smooth function using averages defined over a general, nonuniform computational grid. Moreover, to high accuracy, local averages can also be reconstructed. By re-averaging the function to a uniform reconstruction grid that includes a point of interest, one can apply a standard WENO reconstruction to obtain a high order point value of the function.
97 MATHEMATICS AND COMPUTING↗
Exploring temporal community evolution: algorithmic approaches and parallel optimization for dynamic community detection
Abstract Dynamic (temporal) graphs are a convenient mathematical abstraction for many practical complex systems including social contacts, business transactions, and computer communications. Community discovery is an extensively used graph analysis kernel with rich literature for static graphs. However, community discovery in a dynamic setting is challenging for two specific reasons. Firstly, the notion of temporal community lacks a widely accepted formalization, and only limited work exists on understanding how communities emerge over time. Secondly, the added temporal dimension along with the sheer size of modern graph data necessitates new scalable algorithms. In this paper, we investigate how communities evolve over time based on several graph metrics under a temporal formalization. We compare six different algorithmic approaches for dynamic community detection for their quality and runtime. We identify that a vertex-centric (local) optimization method works as efficiently as the classical modularity-based methods. To its advantage, such local computation allows for the efficient design of parallel algorithms without incurring a significant parallel overhead. Based on this insight, we design a shared-memory parallel algorithm DyComPar , which demonstrates between 4 and 18 fold speed-up on a multi-core machine with 20 threads, for several real-world and synthetic graphs from different domains.
97 MATHEMATICS AND COMPUTING↗
Geometry of quantum Hall states: Gravitational anomaly and transport coefficients
We show that universal transport coefficients of the fractional quantum Hall effect (FQHE) can be understood as a response to variations of spatial geometry. Some transport properties are essentially governed by the gravitational anomaly. We develop a general method to compute correlation functions of FQH states in a curved space, where local transformation properties of these states are examined through local geometric variations. We introduce the notion of a generating functional and relate it to geometric invariant functionals recently studied in geometry. We develop two complementary methods to study the geometry of the FQHE. One method is based on iterating a Ward identity, while the other is based on a field theoretical formulation of the FQHE through a path integral formalism.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Four-Coordinate Fe N 2 and Imido Complexes Supported by a Hemilabile NNC Heteroscorpionate Ligand
Inspired by mechanistic proposals for N 2 reduction at the nitrogenase FeMo cofactor, we report herein a new, strongly σ-donating heteroscorpionate ligand featuring two weak-field pyrazoles and an alkyl donor. This ligand supports four-coordinate Fe(I)-N 2 , Fe(II)-Cl, and Fe(III)-imido complexes, which we have characterized using a variety of spectroscopic and computational methods. Structural and quantum mechanical analysis reveal the nature of the Fe–C bonds to be essentially invariant between the complexes, with conversion between the (formally) low-valent Fe-N 2 and high-valent Fe-imido complexes mediated by pyrazole hemilability. This presents a useful strategy for substrate reduction at such low-coordinate centers and suggests a mechanism by which FeMoco might accommodate the binding of both π-acidic and π-basic nitrogenous substrates.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ab initio calculation of the electronic absorption spectrum of liquid water
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Exploring connections between statistical mechanics and Green’s functions for realistic systems: Temperature dependent electronic entropy and internal energy from a self-consistent second-order Green’s function
Including finite-temperature effects from the electronic degrees of freedom in electronic structure calculations of semiconductors and metals is desired; however, in practice it remains exceedingly difficult when using zero-temperature methods, since these methods require an explicit evaluation of multiple excited states in order to account for any finite-temperature effects. Using a Matsubara Green’s function formalism remains a viable alternative, since in this formalism it is easier to include thermal effects and to connect the dynamic quantities such as the self-energy with static thermodynamic quantities such as the Helmholtz energy, entropy, and internal energy. However, despite the promising properties of this formalism, little is known about the multiple solutions of the non-linear equations present in the self-consistent Matsubara formalism and only a few cases involving a full Coulomb Hamiltonian were investigated in the past. In this study, to shed some light onto the iterative nature of the Green’s function solutions, we self-consistently evaluate the thermodynamic quantities for a one-dimensional (1D) hydrogen solid at various interatomic separations and temperatures using the self-energy approximated to second-order (GF2). At many points in the phase diagram of this system, multiple phases such as a metal and an insulator exist, and we are able to determine the most stable phase from the analysis of Helmholtz energies. Additionally, we show the evolution of the spectrum of 1D boron nitride to demonstrate that GF2 is capable of qualitatively describing the temperature effects influencing the size of the band gap.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Explicitly correlated coupled cluster method for accurate treatment of open-shell molecules with hundreds of atoms
We present a near-linear scaling formulation of the explicitly correlated coupled-cluster singles and doubles with the perturbative triples method [CCSD(T)F12¯] for high-spin states of open-shell species. The approach is based on the conventional open-shell CCSD formalism [M. Saitow et al., J. Chem. Phys. 146, 164105 (2017)] utilizing the domain local pair-natural orbitals (DLPNO) framework. The use of spin-independent set of pair-natural orbitals ensures exact agreement with the closed-shell formalism reported previously, with only marginally impact on the cost (e.g., the open-shell formalism is only 1.5 times slower than the closed-shell counterpart for the C160H322 n-alkane, with the measured size complexity of ≈1.2). Evaluation of coupled-cluster energies near the complete-basis-set (CBS) limit for open-shell systems with more than 550 atoms and 5000 basis functions is feasible on a single multi-core computer in less than 3 days. The aug-cc-pVTZ DLPNO-CCSD(T)F12¯ contribution to the heat of formation for the 50 largest molecules among the 348 core combustion species benchmark set [J. Klippenstein et al., J. Phys. Chem. A 121, 6580–6602 (2017)] had root-mean-square deviation (RMSD) from the extrapolated CBS CCSD(T) reference values of 0.3 kcal/mol. For a more challenging set of 50 reactions involving small closed- and open-shell molecules [G. Knizia et al., J. Chem. Phys. 130, 054104 (2009)], the aug-cc-pVQ(+d)Z DLPNO-CCSD(T)F12¯ yielded a RMSD of ∼0.4 kcal/mol with respect to the CBS CCSD(T) estimate.
Kumar, Ashutosh (ORCID:0000000175896030)↗