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This project is intended to take a graph and build a smaller (upscaled) graph that is representative of the original in some way. We represent the graph Laplacian in a mixed form, solve some local eigenvalue problems to uncover near-nullspace modes, and use those modes as coarse degrees of freedom.
KSSOLV is a MATLAB toolbox for solving Kohn-Sham density functional theory based electronic structure eigenvalue problems. It uses an object oriented features of MATLAB to represent atom, molecules, wavefunctions and Hamiltonians and their operations. It is designed to make it easier for users to prototype and test new algorithms for solving the Kohn-Sham problem. KSSOLV2.0 contains significant improvement over the original KSSOLV described in a paper published in ACM Transaction on Mathematical Software (attached). In addition to performing ground state calculation for small molecules, it can also perform geometry optimization for both molecules and solids. It uses standard pseudopotentials and implements local density approximation, generalized gradient approximation and hybrid functionals. Future releases will also include time-dependent DFT and post DFT calculations such as the GW quasi-particle energy calculation and Bethe-Salpeter equation solver for optical absorption.
This product includes software developed by Members of the Geant4 Collaboration (http://cern.ch/geant4). The basic principle of ALFRED consists of a k-eigenvalue module in which all generated particles are tracked and all deposited energy is accounted for. An eigenvalue module updates the neutron source after each run based on the neutrons emitted at each fission in the previous run. As a result, the source distribution converges to the fundamental mode of the steady-state eigenvalue problem of the associated critical reactor. ALFRED leverages the High Precision neutron transport package.
We performed calculations of electronic excitation energies and associated oscillator strengths based on the time-dependent density-functional tight-binding (TD-DFTB) method [1]. The SMILES (Simplified molecular-input line-entry system) strings of the molecules from the AISD HOMO-LUMO database [2] were converted to a 3D atomistic structure and stored in a PDB file after preliminary geometry optimization using the Merck Molecular Force Field (MMFF94) in RDKit [3,4]. The primary information stored in the PDB file archive consists of Cartesian coordinates for each atom of the molecule in their 3D location in space, along with summary information about the structure, sequence, and experiment. We then performed molecular geometry optimization using the density-functional tight-binding (DFTB) method [5] in the electronic ground state, followed by single-point excited states calculations, as described below. We note that, since RDKit employs a random choice for the generation of molecular conformers, the molecular geometries obtained in this dataset could be different from the ones that were generated when the AISD HOMO-LUMO dataset was generated. The computed excitation energies and associated oscillator strengths can be converted to predict UV/Vis absorption spectra, where excitation energies correspond to absorption peak positions, and oscillator strengths are a good measure of the probability of absorption of visible or UV light in transitions between electronic ground and excited states. The conversion of SMILES strings to 3D Cartesian coordinates of fully DFTB-optimized molecules was successful for 10,502,904 out of 10,502,917 molecules. For these molecules, both geometry optimizations and excited states calculations were successful. The DFTB calculations did not complete for 13 molecules of the original AISD HOMO-LUMO dataset. We still provide information about the geometry of these molecules. The molecules are diverse for chemical compositions (which span 5 non-hydrogen elements: oxygen, carbon, nitrogen, fluorine, sulfur) and molecular size (the smallest molecule contains 5 non-hydrogen atoms, and the largest molecule contains 71 non-hydrogen atoms). The DFTB method [5] is an approximation to density functional theory (DFT), utilizing a minimal basis set in conjunction with a two-center approximation to the electronic Hamiltonian and overlap matrix elements. The DFTB total energy is the sum of an electronic and a repulsive energy contribution, and their calculation requires optimized electronic parameters and diatomic repulsive potential energy functions. All DFTB calculations were performed using the DFTB+ code [6] (version 21.2) and the wrapper for DFTB+ in the Atomic Simulation Environment (ASE) (version 3.22.1) [7], which performed an internal conversion of Cartesian coordinates from PDB to the .gen file format. For the geometry optimizations on the electronic ground state potential energy surface of the molecules, we have chosen the third-order DFTB (DFTB3) method [5c] and employed the matching 3ob set of electronic parameters and repulsive potentials [8]. The empirical γ-damping for hydrogen bond correction, and Grimme's D3 empirical dispersion correction with Becke-Johnson damping (D3(BJ)) [9] dispersion correction was included to improve the description of non-covalent interactions. For excited states single-point energy calculations, we employed the TD-DFTB method in conjunction with the DFTB2 method [5b] and the matching mio [5b,10] and halorg [11] parameter sets. We opted to request the simultaneous calculation of 50 excited states for singlet transition to investigate sufficient number of excited states, based on linear response theory using the Casida equation [Ref: T. A. Niehaus, S. Suhai, F. Della Sala, P Lugli, M. Elstner, G. Seifert, and Th. Frauenheim. Tight-binding approach to time-dependent density-functional response theory. Phys. Rev. B, 63:085108, 2001] and the ARPACK diagonalizer [R. B. Lehoucq, D. C. Sorensen, and C. Yang. Arpack users guide: Solution of large-scale eigenvalue problems by implicitly restarted arnoldi methods, 1997. 46, 51]. The dataset contains 1001 tar.gz files. Tar files are named as “ornl_aisd_ex_1.tar.gz†through “ornl_aisd_ex_1000.tar.gzâ€. Additionally, the 13 failed molecules are in “ornl_aisd_ex_unprocessed.tar.gzâ€. Except for the tar files listed below, each tar file contains 10,500 molecules. Tar files numbered 34, 121, 128, 352, 360, 429, 495, 509, 518, 627, 676, 668, and 862 contain 10,499 molecules each. The last tar file numbered 1000 contains 13,417 molecules. The total size of the uncompressed dataset is over 283 Gigabytes. The code for calculating the electronic excitation energies and statistical analysis of the dataset is provided at the following GitLab repository: https://github.com/ORNL/Analysis-of-Large-Scale-Molecular-Datasets-with-Python Calculating the UV spectrum of a molecule requires performing 3 main operations: 1. Converting the smiles string representation of a molecule into a geometric structure where each atom is assigned XYZ coordinates. The geometric structure is written to the file smiles.pdb. 2. Using smiles.pdb to compute the relaxed geometry of the molecule, which corresponds with the position of the atoms at the position of equilibrium at the ground state. This generates the files band.out, detailed.out, and geo_end.gen. 3. Using geo_end.gen to calculate the UV spectrum of the molecule which is written into the file EXC.DAT. Every molecule in the dataset has its own directory. The files contained in each molecule directory are as follows: 1. geo_end.gen 2. detailed.out 3. band.out 4. EXC.DAT 5. smiles.pdb REFERENCES [1] Niehaus, T. A.; Suhai, S.; Della Salla, F.; Lugli, P.; Elstner, M.; Seifert, G.; Frauenheim, Th. Tight-binding approach to time-dependent density-functional response theory. Phys. Rev. B, 2001, 63, 085108/1-9. [2] Blanchard, A.; Gounley, J.; Metha, K.; Yoo, P.; Irle, S. AISD HOMO-LUMO. DOI: 10.13139/ORNLNCCS/1869409 [3] RDKit: Cheminformatics and Machine Learning Software. 2013, [http://www.rdkit.org] [4] Tosco, P.; Stiefl, N. and Landrum, G. Bringing the MMFF force field to the RDKit: implementation and validation. J Cheminform. 2014, 6, 1–4. [5] a) Porezag, D.; Frauenheim, T.; Kohler, T.; Seifert, G.; Kaschner, Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon, R. Phys. Rev. B 1995, 51, 12947-12957; b) Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, Th.; Suhai, S.; Seifert, G.; Phys. Rev. B 1998, 58, 7260-7268; c) Gaus, M.; Cui, Q.; Elstner, M. DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB), J. Chem. Theory Comput. 2011, 7, 931-948; d) Cui, Q.; Elstner, M. Density functional tight binding: values of semi-empirical methods in an ab initio era, Phys. Chem. Chem. Phys. 2014, 16, 14368-14377. [6] Hourahine, B. et al. DFTB+, a software package for efficient approximate density functional theory based atomistic simulations, J. Chem. Phys. 2020, 152, 124101/1-19. [7] Larsen, A. H. et al. The atomic simulation environment—a Python library for working with atoms. J. Phys.: Cond. Matter 2017, 29, 273002. [8] Kubillus, M.; Kubar, T.; Gaus, M.; Rezac, J.; Elstner, M. Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems, J. Chem. Theory Comput. 2015, 11, 332-342. [9] Brandenburg, J. G.; Grimme, S. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB), J. Phys. Chem. Lett. 2014, 5, 1785−1789. [10] a) Niehaus, T. A.; Elstner, M.; Frauenheim, Th.; Suhai, S. Application of an approximate density-functional method to sulfur containing compounds. J. Mol. Struct.: THEOCHEM 2001, 541, 185-94; b) Elstner, M.; Hobza, P.; Frauenheim, Th.; Suhai, S.; Kaxiras, E. Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment. J. Chem. Phys. 2001, 114, 5149-55. [11] Kubar, T.; Bodrog, Z.; Gaus, M.; Köhler, C.; Aradi, B.; Frauenheim, Th.; Elstner, M. Parametrization of the SCC-DFTB Method for Halogens. J. Chem. Theory Comput. 2013, 9, 2939-49.
A reduced order modeling capability has been developed to reduce the computational burden associated with time-domain solutions of structural dynamic models with linear viscoelastic materials. The discretized equations-of-motion produce convolution integrals resulting in a linear system with nonviscous damping forces. The challenge associated with the reduction of nonviscously damped, linear systems is the selection and computation of the appropriate modal basis to perform modal projection. The system produces a nonlinear eigenvalue problem that is challenging to solve and requires use of specialized algorithms not readily available in commercial finite element packages. This SAND report summarizes the LDRD discoveries of a reduction scheme developed for monolithic finite element models and provides preliminary investigations to extensions of the method using component mode synthesis. In addition, this report provides a background overview of structural dynamic modeling of structures with linear viscoelastic materials, and provides an overview of a new code capability in Sierra Structural Dynamics to output the system level matrices computed on multiple processors.
It is desired to compute the adjoint weighted leakage time $τ_1$ for an α-eigenvalue problem. The reciprocal of the leakage time is $\frac{1}{τ_1}$ = $\frac{\langle ψ^*, Ω∙∇ψ \rangle}{\langle ψ^*, \frac{1}{v}ψ \rangle}$ where $ψ^*$ and $ψ$ are the adjoint and forward α-eigenfunctions, respectively; $v$ is neutron speed; and the angle brackets indicate an inner product over all independent variables, in this case space, energy, and angle. This memo discusses the implementation of Eq. (1) in the multigroup neutron sensitivity code SENSMG (Refs. 2 and 3), which relies for the neutron transport on the multigroup discrete ordinates code PARTISN (Ref. 4).
The project team continued with work on developing new bootstrap AMG techniques for solving symmetric and non-symmetric PDE systems. The focus of this work is to derive more reliable measures of the quality of the coarse space set than the convergence rate of the standard F-relaxation form of CR and a more robust form of interpolation than the so-called ideal form. We have successfully derived a sharp variant of CR that gives the precise convergence rate of the two-grid method using this optimal interpolation and, in addition, we derived a new Generalized Bootstrap AMG setup algorithm that uses as its main tool a multilevel eigensolver for the generalized eigenvalue problem involving the system matrix and the symmetrized smoother. In addition, the approach allows for general block smoothers with overlap. We have applied the method to scalar diffusion problems, linear elasticity, and Maxwell’s and the method shows marked improvements over existing AMG methods for these problems. In addition, the team worked with CASC members on new forms of ideal AMG interpolation.
SENSMG is a tool for computing first-order sensitivities of neutron reaction rates, reaction-rate ratios, leakage, k eff , α, and subcritical multiplication using the PARTISN multigroup discrete-ordinates code. SENSMG computes sensitivities to all of the transport cross sections and data (total, fission, a nu, chi, and all scattering moments), two edit cross sections (absorption and capture), and the density for every nuclide and energy group. It also computes sensitivities to the mass density for every material and derivatives with respect to all interface locations and outer boundaries. It computes sensitivities to user specified reactions whose cross sections are available in a user-supplied NJOY output file. The tool can be used for one-dimensional spherical and slab (r) and two-dimensional cylindrical (r-z) geometries. The tool can be used for fixed-source and eigenvalue problems. For most responses, the tool implements Generalized Perturbation Theory (GPT) as discussed by Williams and Stacey. The tool is thus limited to computing sensitivities only for GPT-allowable responses. For subcritical multiplication, the tool implements sensitivities derived by O’Brien and Clark. SENSMG has a similar role as the old SWANLAKE (Ref. 8), FORSS (Ref. 9), and SENSIT (Ref. 10) codes. It has capabilities similar to those of SUSD3D (Refs. 11 and 12), which also uses PARTISN. Section II of this report describes the theory behind adjoint-based sensitivities, gives the equations that SENSMG solves, and defines the sensitivities that are output. Section III describes the user interface, including the input file and command line options. Section IV describes the output. Section V gives some notes about the coding that may be of interest. Section VI presents some sample problems and discusses verification, which is ongoing. Section VII lists needs and ideas for future work. Appendix A lists most of the input files whose results are presented in Sec. VI. Appendix B provides some useful details on one of the cross-section libraries that SENSMG supports.
The MPACT code is designed to perform high-fidelity light-water reactor (LWR) analysis using whole-core pin-resolved neutron transport calculations on modern parallel-computing hardware. The code consists of several libraries which provide the functionality necessary to solve steady-state eigenvalue problems. Several transport capabilities are available within MPACT including both 2-D and 3-D Method of Characteristics (MOC). A three-dimensional whole core solution based on the 2D-1D solution method provides the capability for full core depletion calculations.
The phononic dispersion relations calculated by solving an eigenvalue problem while applying Bloch-Floquet boundary conditions are applied to three varieties of phononic pseudocrystals interposers useful for suppressing the transmission of structure-born vibration.
Transverse single-bunch instabilities of space-charge-dominated coasting beams with round and flat transverse geometries are studied using a unified dispersion-relation framework. The analysis combines the Burov-Lebedev formalism, which captures space-charge tune spread, Landau damping, and instability threshold behavior, with Yokoya’s projection method for representing coherent transverse mode structure and its dependence on beam aspect ratio. In the rigid-beam limit, the formulation reduces to a scalar dispersion relation of Burov-Lebedev paper. For non-rigid transverse oscillations, truncation of Yokoya’s Hermite-based expansion yields a finite-dimensional matrix eigenvalue problem in which space-charge and coupling impedance effects enter through Burov-Lebedev–type denominators. This approach provides a consistent basis for comparing rigid and non-rigid instability behavior in round and flat beams and for assessing the role of beam ellipticity in modifying coherent mode structure and stability thresholds.
Here, we analytically model single-, two-, and three-wires above ground to determine the decay lengths of common and differential modes induced by an E1 high-altitude electromagnetic pulse (HEMP) excitation. Decay length information is pivotal to determine whether any two nodes in the power grid may be treated as uncoupled. We employ a frequency-domain method based on transmission line theory named ATLOG - Analytic Transmission Line Over Ground to model infinitely long and finite single wires, as well as solve the eigenvalue problem of a single-,two-, and three-wire system. Our calculations show that a single, semi-infinite power line can be approximated by a10 km section of line and that the second electrical reflection for all line lengths longer than the decay length are below half the rated operating voltage. Moreover, our findings show that the differential mode propagates longer distances than the common mode in two- and three-wire systems, and this should be taken into account when performing damage assessment from HEMP excitation. Furthermore, this analysis is a significant step toward simplifying the modeling of practical continental grid lengths, yet maintaining accuracy, a result of enormous impact.
This study investigates the effects of magnetic constraints on a piezoelectric energy harvesting absorber while simultaneously controlling a primary structure and harnessing energy. An accurate forcing representation of the magnetic force is investigated and developed. A reduced-order model is derived using the Euler–Lagrange principle, and the impact of the magnetic force is evaluated on the absorber’s static position and coupled natural frequency of the energy harvesting absorber and the coupled primary absorber system. The results show that attractive magnet configurations cannot improve the system substantially before pull-in occurs. A rigorous eigenvalue problem analysis is performed on the absorber’s substrate thickness and tip mass to effectively design an energy harvesting absorber for multiple initial gap sizes for the repulsive configurations. Then, the effects of the forcing amplitude on the primary structure absorber are studied and characterized by determining an effective design of the system for a simultaneous reduction in the primary structure’s motion and improvement in the harvester’s efficiency.
Recent work has shown that the (block) Lanczos algorithm can be used to extract approximate energy spectra and matrix elements from (matrices of) correlation functions in quantum field theory, and identified exact coincidences between Lanczos analysis methods and others. In this work, we note another coincidence: the Lanczos algorithm is equivalent to the well-known Rayleigh-Ritz method applied to Krylov subspaces. Rayleigh-Ritz provides optimal eigenvalue approximations within subspaces; we find that spurious-state filtering allows these optimality guarantees to be retained in the presence of statistical noise. We explore the relation between Lanczos and Prony's method, their block generalizations, generalized pencil of functions (GPOF), and methods based on the generalized eigenvalue problem (GEVP), and find they all fall into a larger "Prony-Ritz equivalence class", identified as all methods which solve a finite-dimensional spectrum exactly given sufficient correlation function (matrix) data. This equivalence allows simpler and more numerically stable implementations of (block) Lanczos analyses.
Sweet-Parker current sheets in high Lundquist number plasmas are unstable to tearing, suggesting they will not form in physical systems. Understanding magnetic reconnection thus requires study of the stability of a current sheet as it forms. Formation can occur due to sheared, sub-Alfvenic incompressible flows which narrow the sheet. Standard tearing theory (Furth et al. 1963; Coppi et al. 1976; Rutherford 1973) is not immediately applicable to such forming sheets for two reasons: first, because the flow introduces terms not present in the standard calculation; second, because the changing equilibrium introduces time dependence to terms which are constant in the standard calculation, complicating the formulation of an eigenvalue problem. This paper adapts standard tearing mode analysis to confront these challenges. In an initial phase when any perturbations are primarily governed by ideal MHD, a coordinate transformation reveals that the flow compresses and stretches perturbations. A multiple scale formulation describes how linear tearing mode theory (Furth et al. 1963; Coppi et al. 1976) can be applied to an equilibrium changing under flow, showing that tearing eigenfunctions grow slowly due to the flow and undergo exponential growth at a rate given by standard scalings with time dependence added. In the nonlinear Rutherford stage, the coordinate transformation shows that standard theory can be adapted by adding to the stationary rates time dependence and an additional term due to the strengthening equilibrium magnetic field. Overall, this understanding supports the use of flow-free scalings with slight modifications to study tearing in a forming sheet.
Eigenvalue problem solved for the thermal problem of a hydrodynamically fully developed flow
Hierachy methods for random vibrations of elastic strings and beams, discussing stochastic eigenvalue problems
Longitudinal vibration of cylindrical membrane shells containing liquid, with liquid velocity potential expanded into matrix-eigenvalue problem