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NASA NTRS1995

Using SCR methods to analyze requirements documentation

Software Cost Reduction (SCR) methods are being utilized to analyze and verify selected parts of NASA's EOS-DIS Core System (ECS) requirements documentation. SCR is being used as a spot-inspection tool. Through this formal and systematic approach of the SCR requirements methods, insights as to whether the requirements are internally inconsistent or incomplete as the scenarios of intended usage evolve in the OC (Operations Concept) documentation. Thus, by modelling the scenarios and requirements as mode charts using the SCR methods, we have been able to identify problems within and between the documents.

Callahan, John↗

DOE OSTI2014

Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of O(N{sup 2}). This work introduces a fast FRI (fFRI) algorithm for the flexibility analysis of large macromolecules. The proposed fFRI further reduces the computational complexity to O(N). Additionally, we propose anisotropic FRI (aFRI) algorithms for the analysis of protein collective dynamics. The aFRI algorithms permit adaptive Hessian matrices, from a completely global 3N × 3N matrix to completely local 3 × 3 matrices. These 3 × 3 matrices, despite being calculated locally, also contain non-local correlation information. Eigenvectors obtained from the proposed aFRI algorithms are able to demonstrate collective motions. Moreover, we investigate the performance of FRI by employing four families of radial basis correlation functions. Both parameter optimized and parameter-free FRI methods are explored. Furthermore, we compare the accuracy and efficiency of FRI with some established approaches to flexibility analysis, namely, normal mode analysis and Gaussian network model (GNM). The accuracy of the FRI method is tested using four sets of proteins, three sets of relatively small-, medium-, and large-sized structures and an extended set of 365 proteins. A fifth set of proteins is used to compare the efficiency of the FRI, fFRI, aFRI, and GNM methods. Intensive validation and comparison indicate that the FRI, particularly the fFRI, is orders of magnitude more efficient and about 10% more accurate overall than some of the most popular methods in the field. The proposed fFRI is able to predict B-factors for α-carbons of the HIV virus capsid (313 236 residues) in less than 30 seconds on a single processor using only one core. Finally, we demonstrate the application of FRI and aFRI to protein domain analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1989

A method for exponential propagation of large systems of stiff nonlinear differential equations

A new time integrator for large, stiff systems of linear and nonlinear coupled differential equations is described. For linear systems, the method consists of forming a small (5-15-term) Krylov space using the Jacobian of the system and carrying out exact exponential propagation within this space. Nonlinear corrections are incorporated via a convolution integral formalism; the integral is evaluated via approximate Krylov methods as well. Gains in efficiency ranging from factors of 2 to 30 are demonstrated for several test problems as compared to a forward Euler scheme and to the integration package LSODE.

Friesner, Richard A.↗

DOE OSTI2015

Time-dependent density-functional tight-binding method with the third-order expansion of electron density

We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2012

Hybrid Theory of P-Wave Electron-Hydrogen Elastic Scattering

We report on a study of electron-hydrogen scattering, using a combination of a modified method of polarized orbitals and the optical potential formalism. The calculation is restricted to P waves in the elastic region, where the correlation functions are of Hylleraas type. It is found that the phase shifts are not significantly affected by the modification of the target function by a method similar to the method of polarized orbitals and they are close to the phase shifts calculated earlier by Bhatia. This indicates that the correlation function is general enough to include the target distortion (polarization) in the presence of the incident electron. The important fact is that in the present calculation, to obtain similar results only 35-term correlation function is needed in the wave function compared to the 220-term wave function required in the above-mentioned previous calculation. Results for the phase shifts, obtained in the present hybrid formalism, are rigorous lower bounds to the exact phase shifts.

Bhatia, Anand↗

DOE OSTI2014

A Bayesian method for using simulator data to enhance human error probabilities assigned by existing HRA methods

In the past several years, several international organizations have begun to collect data on human performance in nuclear power plant simulators. The data collected provide a valuable opportunity to improve human reliability analysis (HRA), but these improvements will not be realized without implementation of Bayesian methods. Bayesian methods are widely used to incorporate sparse data into models in many parts of probabilistic risk assessment (PRA), but Bayesian methods have not been adopted by the HRA community. In this paper, we provide a Bayesian methodology to formally use simulator data to refine the human error probabilities (HEPs) assigned by existing HRA methods. We demonstrate the methodology with a case study, wherein we use simulator data from the Halden Reactor Project to update the probability assignments from the SPAR-H method. The case study demonstrates the ability to use performance data, even sparse data, to improve existing HRA methods. Furthermore, this paper also serves as a demonstration of the value of Bayesian methods to improve the technical basis of HRA.

99 GENERAL AND MISCELLANEOUS↗

NASA NTRS1983

Three-dimensional inversion of satellite observed radiances A proposal

Fully three-dimensional temperature fields are obtained from observed satellite radiances through the use of variational methods which generalize the method of Wahba and Wendelberger (1980). This variational formalism allows a variety of different information types to contribute to the inversion process. Full use can be made of the horizontal smoothness of the temperature field in the calculation of three-dimensional retrievals. The present method facilitates the acquisition of maximum vertical resolution, accomplishes cloud effect filtering, and minimizes the effects of instrument noise, to yield horizontally coherent retrievals.

Hoffman, R. N.↗

DOE OSTI2013

Asymptotic method for determining the amplitude for three-particle breakup: Neutron-deuteron scattering

The process of neutron-deuteron scattering at energies above the deuteron-breakup threshold is described within the three-body formalism of Faddeev equations. Use is made of the method of solving Faddeev equations in configuration space on the basis of expanding wave-function components in the asymptotic region in bases of eigenfunctions of specially chosen operators. Asymptotically, wave-function components are represented in the form of an expansion in an orthonormalized basis of functions depending on the hyperangle. This basis makes it possible to orthogonalize the contributions of elastic-scattering and breakup channels. The proposed method permits determining scattering and breakup parameters from the asymptotic representation of the wave function without reconstructing it over the entire configuration space. The scattering and breakup amplitudes for states of total spin S = 1/2 and 3/2 were obtained for the s-wave Faddeev equation.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2014

Inclusion of trial functions in the Langevin equation path integral ground state method: Application to parahydrogen clusters and their isotopologues

We developed and studied the implementation of trial wavefunctions in the newly proposed Langevin equation Path Integral Ground State (LePIGS) method [S. Constable, M. Schmidt, C. Ing, T. Zeng, and P.-N. Roy, J. Phys. Chem. A 117, 7461 (2013)]. The LePIGS method is based on the Path Integral Ground State (PIGS) formalism combined with Path Integral Molecular Dynamics sampling using a Langevin equation based sampling of the canonical distribution. This LePIGS method originally incorporated a trivial trial wavefunction, ψ{sub T}, equal to unity. The present paper assesses the effectiveness of three different trial wavefunctions on three isotopes of hydrogen for cluster sizes N = 4, 8, and 13. The trial wavefunctions of interest are the unity trial wavefunction used in the original LePIGS work, a Jastrow trial wavefunction that includes correlations due to hard-core repulsions, and a normal mode trial wavefunction that includes information on the equilibrium geometry. Based on this analysis, we opt for the Jastrow wavefunction to calculate energetic and structural properties for parahydrogen, orthodeuterium, and paratritium clusters of size N = 4 − 19, 33. Energetic and structural properties are obtained and compared to earlier work based on Monte Carlo PIGS simulations to study the accuracy of the proposed approach. The new results for paratritium clusters will serve as benchmark for future studies. This paper provides a detailed, yet general method for optimizing the necessary parameters required for the study of the ground state of a large variety of systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Ab initio non-relativistic spin dynamics

Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Towards a Verifiable Domain-Specific Language for Hardware-Accelerated Stencils

Defining a domain-specific language (DSL) that supports vector-calculus abstractions eases the porting of partial differential equation (PDE) solvers to specialized architectures. Sufficiently high-level abstractions empower users to express universal laws with sufficient generality that the laws must always hold true within their domain of validity. A broad class of PDE solvers employs stencil-based algorithms, the target domain of Berkeley Lab's stencil accelerator chip co-design project. First released as open-source in January 2026, the Formal software framework lays a foundation for defining an embedded DSL based on composable operators that implement mimetic numerical methods -- stencil algorithms that guarantee satisfaction of discrete versions of important vector calculus theorems. The Formal DSL will be the frontend to a new class of stencil-PDE accelerators developed jointly by LBNL, UHCL, and UC Berkeley through the DOE Competitive Portfolios for Computer Science Project. This offers the potential of an order of magnitude acceleration for this important category of computational methods to serve the DOE mission. Future work on the Formal DSL will facilitate software verification via type-safe templates that enable problem-specific correctness proofs relying upon generic function theory and carefully crafted unit tests.

Rouson, Damian↗

DOE OSTI2018

Mechanical and Dynamic Stability of Complete and Nonstoichiometric 3C-Si{sub x}C{sub y} from Ab Initio Calculations

The energies of formation of vacancies in the carbon and silicon sublattices, the independent elastic constants, the all-round compression, shear and Young’s moduli, and the anisotropy coefficients are determined for the complete and nonstoichiometric cubic phases of 3C-Si{sub x}C{sub y} (x, y = 1.0–0.75) by ab initio methods of the band theory. In the formalism of the density functional perturbation theory (DFPT), the phonon dispersion dependences are obtained for these phases (the comparison with the experiment is given for the complete phase). It is shown that the mechanical characteristics of the phases become strongly anisotropic upon the transition from 3C-SiC{sub 0.875} to 3C-SiC{sub 0.75}. It is established from the analysis of the phonon dispersion curves that the 3C-SiC{sub 0.875} and 3C-SiC{sub 0.75} phases, in contrast to the complete 3C-SiC phase, are dynamically unstable at T = 0 K.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2014

Comparison of nonmesonic hypernuclear decay rates computed in laboratory and center-of-mass coordinates

In this work we compute the one-nucleon-induced nonmesonic hypernuclear decay rates of {sub Λ}{sup 5}He, {sub Λ}{sup 12}C and {sub Λ}{sup 13}C using a formalism based on the independent particle shell model in terms of laboratory coordinates. To ascertain the correctness and precision of the method, these results are compared with those obtained using a formalism in terms of center-of-mass coordinates, which has been previously reported in the literature. The formalism in terms of laboratory coordinates will be useful in the shell-model approach to two-nucleon-induced transitions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2013

Proton beam scattering system optimization for clinical and research applications

Purpose: To develop and test a method for optimizing and constructing a dual scattering system in passively scattered proton therapy. Methods: A beam optics optimization algorithm was developed to optimize the thickness of the first scatterer (S1) and the profile (of both the high-Z material and Lexan) of the second scatterer (S2) to deliver a proton beam matching a given set of parameters, including field diameter, fluence, flatness, and symmetry. A new manufacturing process was also tested that allows the contoured second scattering foil to be created much more economically and quickly using Cerrobend casting. Two application-specific scattering systems were developed and tested using both experimental and Monte Carlo techniques to validate the optimization process described. Results: A scattering system was optimized and constructed to deliver large uniform irradiations of radiobiology samples at low dose rates. This system was successfully built and tested using film and ionization chambers. The system delivered a uniform radiation field of 50 cm diameter (to a dose of {+-}7% of the central axis) while the depth dose profile could be tuned to match the specifications of the particular investigator using modulator wheels and range shifters. A second scattering system for intermediate field size (4 cm < diameter < 10 cm) stereotactic radiosurgery and radiation therapy (SRS and SRT) treatments was also developed and tested using GEANT4. This system improved beam efficiency by over 70% compared with existing scattering systems while maintaining field flatness and depth dose profile. In both cases the proton range uniformity across the radiation field was maintained, further indicating the accuracy of the energy loss formalism in the optimization algorithm. Conclusions: The methods described allow for rapid prototyping of scattering foils to meet the demands of both research and clinical beam delivery applications in proton therapy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Perturbative universal state-selective correction for state-specific multi-reference coupled cluster methods

The implementation details of the universal state-selective (USS) multi-reference coupled cluster (MRCC) formalism with singles and doubles (USS(2)) are discussed on the example of several benchmark systems. We demonstrate that the USS(2) formalism is capable of improving accuracies of state specific multi-reference coupled-cluster (MRCC) methods based on the Brillouin-Wigner and Mukherjee’s sufficiency conditions. Additionally, it is shown that the USS(2) approach significantly alleviates problems associated with the lack of invariance of MRCC theories upon the rotation of active orbitals. We also discuss the perturbative USS(2) formulations that significantly reduce numerical overhead of the full USS(2) method.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Performance of high-order Godunov-type methods in simulations of astrophysical low Mach number flows

High-order Godunov methods for gas dynamics have become a standard tool for simulating different classes of astrophysical flows. Their accuracy is mostly determined by the spatial interpolant used to reconstruct the pair of Riemann states at cell interfaces and by the Riemann solver that computes the interface fluxes. In most Godunov-type methods, these two steps can be treated independently, so that many different schemes can in principle be built from the same numerical framework. Because astrophysical simulations often test out the limits of what is feasible with the computational resources available, it is essential to find the scheme that produces the numerical solution with the desired accuracy at the lowest computational cost. However, establishing the best combination of numerical options in a Godunov-type method to be used for simulating a complex hydrodynamic problem is a nontrivial task. In fact, formally more accurate schemes do not always outperform simpler and more diffusive methods, especially if sharp gradients are present in the flow. For this work, we used our fully compressible Seven-League Hydro (SLH) code to test the accuracy of six reconstruction methods and three approximate Riemann solvers on two- and three-dimensional (2D and 3D) problems involving subsonic flows only. We considered Mach numbers in the range from 10 −3 to 10 −1 , which are characteristic of many stellar and geophysical flows. In particular, we considered a well-posed, 2D, Kelvin–Helmholtz instability problem and a 3D turbulent convection zone that excites internal gravity waves in an overlying stable layer. Although the different combinations of numerical methods converge to the same solution with increasing grid resolution for most of the quantities analyzed here, we find that (i) there is a spread of almost four orders of magnitude in computational cost per fixed accuracy between the methods tested in this study, with the most performant method being a combination of a low-dissipation Riemann solver and a sextic reconstruction scheme; (ii) the low-dissipation solver always outperforms conventional Riemann solvers on a fixed grid when the reconstruction scheme is kept the same; (iii) in simulations of turbulent flows, increasing the order of spatial reconstruction reduces the characteristic dissipation length scale achieved on a given grid even if the overall scheme is only second order accurate; (iv) reconstruction methods based on slope-limiting techniques tend to generate artificial, high-frequency acoustic waves during the evolution of the flow; and (v) unlimited reconstruction methods introduce oscillations in the thermal stratification near the convective boundary, where the entropy gradient is steep.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Data-Driven Learning for the Mori--Zwanzig Formalism: A Generalization of the Koopman Learning Framework

A theoretical framework which unifies the conventional Mori--Zwanzig formalism and the approximate Koopman learning of deterministic dynamical systems from noiseless observation is presented. In this framework, the Mori--Zwanzig formalism, developed in statistical mechanics to tackle the hard problem of construction of reduced-order dynamics for high-dimensional dynamical systems, can be considered as a natural generalization of the Koopman description of the dynamical system. We next show that, similar to the approximate Koopman learning methods, data-driven methods can be developed for the Mori--Zwanzig formalism with Mori's linear projection operator. We have developed two algorithms to extract the key operators, the Markov and the memory kernel, using time series of a reduced set of observables in a dynamical system. We have adopted the Lorenz `96 system as a test problem and solved for the above operators. These operators exhibit complex behaviors, which are unlikely to be captured by traditional modeling approaches in Mori--Zwanzig analysis. The nontrivial generalized fluctuation-dissipation relationship, which relates the memory kernel with the two-time correlation statistics of the orthogonal dynamics, was numerically verified as a validation of the solved operators. Here we present numerical evidence that the generalized Langevin equation, a key construct in the Mori--Zwanzig formalism, is more advantageous in predicting the evolution of the reduced set of observables than the conventional approximate Koopman operators.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1977

Theory of viscous transonic flow over airfoils at high Reynolds number

This paper considers viscous flows with unseparated turbulent boundary layers over two-dimensional airfoils at transonic speeds. Conventional theoretical methods are based on boundary layer formulations which do not account for the effect of the curved wake and static pressure variations across the boundary layer in the trailing edge region. In this investigation an extended viscous theory is developed that accounts for both effects. The theory is based on a rational analysis of the strong turbulent interaction at airfoil trailing edges. The method of matched asymptotic expansions is employed to develop formal series solutions of the full Reynolds equations in the limit of Reynolds numbers tending to infinity. Procedures are developed for combining the local trailing edge solution with numerical methods for solving the full potential flow and boundary layer equations. Theoretical results indicate that conventional boundary layer methods account for only about 50% of the viscous effect on lift, the remaining contribution arising from wake curvature and normal pressure gradient effects.

Melnik, R. E.↗