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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

PETSc Users Manual (Rev. 3.13)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear solvers, nonlinear solvers, and time integrators that may be used in application codes written in Fortran, C, C++, and Python. PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than \rolling them" yourself.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Real time evolution for ultracompact Hamiltonian eigenstates on quantum hardware

In this work we present a detailed analysis of variational quantum phase estimation (VQPE), a method based on real-time evolution for ground and excited state estimation on near-term hardware. We derive the theoretical ground on which the approach stands, and demonstrate that it provides one of the most compact variational expansions to date for solving strongly correlated Hamiltonians. At the center of VQPE lies a set of equations, with a simple geometrical interpretation, which provides conditions for the time evolution grid in order to decouple eigenstates out of the set of time evolved expansion states, and connects the method to the classical filter diagonalization algorithm. Further, we introduce what we call the unitary formulation of VQPE, in which the number of matrix elements that need to be measured scales linearly with the number of expansion states, and we provide an analysis of the effects of noise which substantially improves previous considerations. The unitary formulation allows for a direct comparison to iterative phase estimation. Our results mark VQPE as both a natural and highly efficient quantum algorithm for ground and excited state calculations of general many-body systems. We demonstrate a hardware implementation of VQPE for the transverse field Ising model. Further, we illustrate its power on a paradigmatic example of strong correlation (Cr2 in the SVP basis set), and show that it is possible to reach chemical accuracy with as few as ~50 timesteps.

Klymko, Katherine↗
DOE OSTI2023

A Fast Butterfly-Compressed Hadamard–Babich Integrator for High-Frequency Helmholtz Equations in Inhomogeneous Media with Arbitrary Sources

Here we present a butterfly-compressed representation of the Hadamard-Babich (HB) ansatz for the Green's function of the high-frequency Helmholtz equation in smooth inhomogeneous media. For a computational domain discretized with Nv discretization cells, the proposed algorithm first solves and tabulates the phase and HB coefficients via eikonal and transport equations with observation points and point sources located at the Chebyshev nodes using a set of much coarser computation grids, and then butterfly compresses the resulting HB interactions from all Nv cell centers to each other. The overall CPU time and memory requirement scale as O(Nv log2 Nv) for any bounded two-dimensional (2D) domains with arbitrary excitation sources. A direct extension of this scheme to bounded 3D domains yields an O(Nv4/3) CPU complexity, which can be further reduced to quasi-linear complexities with proposed remedies. The scheme can also efficiently handle scattering problems involving inclusions in inhomogeneous media. Although the current construction of our HB integrator does not accommodate caustics, the resulting HB integrator itself can be applied to certain sources, such as concave-shaped sources, to produce caustic effects. Compared to finite-difference frequency domain methods, the proposed HB integrator is free of numerical dispersion and requires fewer discretization points per wavelength. As a result, it can solve wave propagation problems well beyond the capability of existing solvers. Remarkably, the proposed scheme can accurately model wave propagation in 2D domains with 640 wavelengths per direction and in 3D domains with 54 wavelengths per direction on a state-of-the-art supercomputer at Lawrence Berkeley National Laboratory.

Hadamard--Babich ansatz↗
DOE OSTI2025

Adaptive PID Gain Scheduling Control for Hydropower Turbine Using Neural CDE and Stochastic Distribution Shaping

This paper introduces a gain-scheduling PID controller design strategy for hydroturbine frequency control mode. This scheme first uses real data to learn the nonlinear dynamics of the hydroturbine using neural controlled differential equations and then perturbs the obtained nonlinear system at different equilibrium points, based on which a static output feedback adaptive dynamic programming algorithm is then used to optimize the PID gains for each equilibrium point. Moreover, a continuous-time version of stochastic distribution control is proposed to further fine-tune the optimized PID gains. Finally, the controller is obtained by implementing linear interpolation between the optimized PID control gains. The simulation results show that the proposed gain-scheduling PID controller can control a larger range of operation points compared with the given fixed PID controller and the baseline method. Compared with the given fixed PID controller, the proposed gain-scheduling PID controller can regulate hydroturbine frequency against disturbances induced by power-load variation with over 50% less overshoot for some operation points.

13 HYDRO ENERGY↗
DOE OSTI2023

Shadow molecular dynamics and atomic cluster expansions for flexible charge models

A shadow molecular dynamics scheme for flexible charge models is presented, where the shadow Born-Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, are modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born-Oppenheimer molecular dynamics (BOMD) [Eur. Phys. J. B 94, 164 (2021)]. XL-BOMD provides a stable dynamics, while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using the atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO2) and a molecular system of liquid water. The combined ACE + XL-QEq dynamics are stable over a wide range of temperatures both for the oxide and the molecular systems, and provide a precise sampling of the Born-Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO 2 , predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Cauchy problems for Einstein equations in three-dimensional spacetimes

Abstract We analyze existence and properties of solutions of two-dimensional general relativistic initial data sets with a negative cosmological constant, both on spacelike and characteristic surfaces. A new family of such vacuum spacelike data parameterised by poles at the conformal boundary at infinity is constructed. We review the notions of global Hamiltonian charges, emphasizing the difficulties arising in this dimension, both in a spacelike and characteristic setting. One or two, depending upon the topology, lower bounds for energy in terms of angular momentum, linear momentum, and center of mass are established.

Chruściel, Piotr T. (ORCID:0000000183627340)↗
DOE OSTI2024

Hybrid particle-spectral method for kinetic plasma simulations

A hybrid model for numerical solutions of the Vlasov–Poisson equations is presented, which blends spectral and particle approaches. The model splits the distribution function for plasma species into both spectral and particle representations in the velocity space to combine the advantages of each approach. The spectral representation leverages asymmetrically weighted Hermite basis, whereas the particle representation leverages the particle-in-cell method. Configuration phase space is decomposed with the Fourier method, which is well suited for periodic problems. We derive conservation equations for mass, momentum, and energy for the proposed combined method. It is shown that the coupling error between the two methods is absent in the semi-discrete setting (not taking into account time discretization). Finally, numerical test cases are presented simulating a weak electron beam interaction with plasma, leading to beam–plasma instability. The initially localized electron beam evolved into a highly non-equilibrium distribution function in the velocity space. A small growth rate and the resonance nature of instability make it difficult to obtain accurate solutions for purely particle methods due to noise, which falls as ∼1/Np with a number of particles. At the same time, purely spectral methods may require a large number of modes to capture the highly non-equilibrium state of the evolved beam. We show that the hybrid method is well suited for such problems: it reproduces the linear stage as well as nonlinear dynamics with sufficient accuracy using a highly non-equilibrium distribution function.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Bayesian Poroelastic Aquifer Characterization From InSAR Surface Deformation Data. 2. Quantifying the Uncertainty

Uncertainty quantification of groundwater (GW) aquifer parameters is critical for efficient management and sustainable extraction of GW resources. These uncertainties are introduced by the data, model, and prior information on the parameters. We develop a Bayesian inversion framework that uses Interferometric Synthetic Aperture Radar (InSAR) surface deformation data to infer the laterally heterogeneous permeability of a transient linear poroelastic model of a confined GW aquifer. The Bayesian solution of this inverse problem takes the form of a posterior probability density of the permeability. Exploring this posterior using classical Markov chain Monte Carlo (MCMC) methods is computationally prohibitive due to the large dimension of the discretized permeability field and the expense of solving the poroelastic forward problem. However, in many partial differential equation (PDE)-based Bayesian inversion problems, the data are only informative in a few directions in parameter space. For the poroelasticity problem, we prove this property theoretically for a one-dimensional problem and demonstrate it numerically for a three-dimensional aquifer model. Here we design a generalized preconditioned Crank-Nicolson (gpCN) MCMC method that exploits this intrinsic low dimensionality by using a low-rank-based Laplace approximation of the posterior as a proposal, which we build scalably. The feasibility of our approach is demonstrated through a real GW aquifer test in Nevada. The inherently two-dimensional nature of InSAR surface deformation data informs a sufficient number of modes of the permeability field to allow detection of major structures within the aquifer, significantly reducing the uncertainty in the pressure and the displacement quantities of interest.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A Plasma Modeling Hierarchy and Verification Approach

This report reviews a hierarchy of formal mathematical models for describing plasma phenomena. Starting with the Boltzmann equation, a sequence of approximations and modeling assumptions can be made that progressively reduce to the equations for magnetohydrodynamics. Understanding the assumptions behind each of these models and their mathematical form is essential to appropriate use of each level of the hierarchy. A sequence of moment models of the Boltzmann equation are presented, then focused into a generalized three-fluid model for neutral species, electrons, and ions. This model is then further reduced to a two-fluid model, for which Braginskii described a useful closure. Further reduction of the two-fluid model yields a Generalized Ohm's Law model, which provides a connection to magnetohydrodynamic approaches. A verification approach based on linear plasma waves is presented alongside the model hierarchy, which is intended as an initial and necessary but not sufficient step for verification of plasma models within this hierarchy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

How to Partition a Quantum Observable

We present a partition of quantum observables in an open quantum system that is inherited from the division of the underlying Hilbert space or configuration space. It is shown that this partition leads to the definition of an inhomogeneous continuity equation for generic, non-local observables. This formalism is employed to describe the local evolution of the von Neumann entropy of a system of independent quantum particles out of equilibrium. Crucially, we find that all local fluctuations in the entropy are governed by an entropy current operator, implying that the production of entanglement entropy is not measured by this partitioned entropy. For systems linearly perturbed from equilibrium, it is shown that this entropy current is equivalent to a heat current, provided that the system-reservoir coupling is partitioned symmetrically. Finally, we show that any other partition of the coupling leads directly to a divergence of the von Neumann entropy. Thus, we conclude that Hilbert-space partitioning is the only partition of the von Neumann entropy that is consistent with the laws of thermodynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Spatially quasi-periodic bifurcations from periodic traveling water waves and a method for detecting bifurcations using signed singular values

We present a method of detecting bifurcations by locating zeros of a signed version of the smallest singular value of the Jacobian. This enables the use of quadratically convergent root-bracketing techniques or Chebyshev interpolation to locate bifurcation points. Only positive singular values have to be computed, though the method relies on the existence of an analytic or smooth singular value decomposition (SVD). The sign of the determinant of the Jacobian, computed as part of the bidiagonal reduction in the SVD algorithm, eliminates slope discontinuities at the zeros of the smallest singular value. We use the method to search for spatially quasi-periodic traveling water waves that bifurcate from large-amplitude periodic waves. The water wave equations are formulated in a conformal mapping framework to facilitate the computation of the quasi-periodic Dirichlet-Neumann operator. We find examples of pure gravity waves with zero surface tension and overhanging gravity-capillary waves. In both cases, the waves have two spatial quasi-periods whose ratio is irrational. We follow the secondary branches via numerical continuation beyond the realm of linearization about solutions on the primary branch to obtain traveling water waves that extend over the real line with no two crests or troughs of exactly the same shape. The pure gravity wave problem is of relevance to ocean waves, where capillary effects can be neglected. Such waves can only exist through secondary bifurcation as they do not persist to zero amplitude. The gravity-capillary wave problem demonstrates the effectiveness of using the signed smallest singular value as a test function for multi-parameter bifurcation problems. This test function becomes mesh independent once the mesh is fine enough.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Technical note: A modified formulation of dynamic energy budget theory for faster computation of biological growth

Abstract. The mass conservation equation in the presence of boundary fluxes and chemical reactions from non-equilibrium thermodynamics is used to derive a modified dynamic energy budget (mDEB) model. Compared to the standard dynamic energy budget (sDEB) model (Kooijman, 2009), this modified formulation does not place the dilution effect in the mobilization kinetics of reserve biomass, and it maintains the partition principle for reserve mobilization dynamics for both linear and non-linear kinetics. Overall, the mDEB model shares most features with the sDEB model. However, for biological growth that requires multiple nutrients, the mDEB model is computationally much more efficient by not requiring numerical iterations for obtaining the specific growth rate. In an example of modeling the growth of Thalassiosira weissflogii in a nitrogen-limiting chemostat, the mDEB model was found to have almost the same accuracy as the sDEB model while requiring almost half of the computing time of the sDEB model. Since the sDEB model has been successfully applied in numerous studies, we believe that the mDEB model can help improve the modeling of biological growth and the associated ecosystem processes in various contexts.

Tang, Jinyun↗
DOE OSTI2024

A note on higher-order and nonlinear limiting approaches for continuously bounds-preserving discontinuous Galerkin methods

In Dzanic (2024), a limiting approach for high-order discontinuous Galerkin schemes was introduced which allowed for imposing constraints on the solution continuously (i.e., everywhere within the element). While exact for linear constraint functionals, this approach only imposed a sufficient (but not the minimum necessary) amount of limiting for nonlinear constraint functionals. This short note shows how this limiting approach can be extended to allow exactness for general nonlinear quasiconcave constraint functionals through a nonlinear limiting procedure, reducing unnecessary numerical dissipation. Finally, some examples are shown for nonlinear pressure and entropy constraints in the compressible gas dynamics equations, where both analytic and iterative approaches are used.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Sparse-Stochastic Fragmented Exchange for Large-Scale Hybrid Time-Dependent Density Functional Theory Calculations

Here we extend our recently developed sparse-stochastic fragmented exchange formalism for ground-state near-gap hybrid DFT to calculate absorption spectra within linear-response time-dependent generalized Kohn-Sham DFT (LR-GKS-TDDFT) for systems consisting of thousands of valence electrons within a grid-based/plane-wave representation. A mixed deterministic/fragmented-stochastic compression of the exchange kernel, here using long-range explicit exchange functionals, provides an efficient method for accurate optical spectra. Both real-time propagation as well as frequency-resolved Casida-equation-type approaches for spectra are presented, and the method is applied to large molecular dyes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Droplet formation simulation using mixed finite elements

Droplet formation happens in finite time due to the surface tension force. The linear stability analysis is useful to estimate the size of a droplet but fails to approximate the shape of the droplet. This is due to a highly nonlinear flow description near the point where the first pinch-off happens. A one-dimensional axisymmetric mathematical model was first developed by Eggers and Dupont [“Drop formation in a one-dimensional approximation of the Navier–Stokes equation,” J. Fluid Mech. 262, 205–221 (1994)] using asymptotic analysis. This asymptotic approach to the Navier–Stokes equations leads to a universal scaling explaining the self-similar nature of the solution. Numerical models for the one-dimensional model were developed using the finite difference [Eggers and Dupont, “Drop formation in a one-dimensional approximation of the Navier–Stokes equation,” J. Fluid Mech. 262, 205–221 (1994)] and finite element method [Ambravaneswaran et al., “Drop formation from a capillary tube: Comparison of one-dimensional and two-dimensional analyses and occurrence of satellite drops,” Phys. Fluids 14, 2606–2621 (2002)]. The focus of this study is to provide a robust computational model for one-dimensional axisymmetric droplet formation using the Portable, Extensible Toolkit for Scientific Computation. The code is verified using the Method of Manufactured Solutions and validated using previous experimental studies done by Zhang and Basaran [“An experimental study of dynamics of drop formation,” Phys. Fluids 7, 1184–1203 (1995)]. The present model is used for simulating pendant drops of water, glycerol, and paraffin wax, with an aspiration of extending the application to simulate more complex pinch-off phenomena.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Optically controlled single-valley exciton doublet states with tunable internal spin structures and spin magnetization generation

Manipulating quantum states through light–matter interactions has been actively pursued in two-dimensional materials research. Significant progress has been made toward the optical control of the valley degrees of freedom in semiconducting monolayer transition-metal dichalcogenides, based on doubly degenerate excitons from their two distinct valleys in reciprocal space. Here, we introduce a type of optically controllable doubly degenerate exciton states that come from a single valley, dubbed as single-valley exciton doublet (SVXD) states. They are unique in that their constituent holes originate from the same valence band, making possible the direct optical control of the spin structure of the excited constituent electrons. Combining ab initio GW plus Bethe–Salpeter equation ( GW -BSE) calculations and a theoretical analysis method, we demonstrate such SVXD in substrate-supported monolayer bismuthene—which has been successfully grown using molecular beam epitaxy. In each of the two distinct valleys in the Brillouin zone, strong spin–orbit coupling and C 3 v symmetry lead to a pair of degenerate 1s exciton states (the SVXD states) with opposite spin configurations. Any coherent linear combinations of the SVXD in a single valley can be excited by light with a specific polarization, enabling full manipulation of their internal spin configurations. In particular, a controllable net spin magnetization can be generated through light excitation. Our findings open routes to control quantum degrees of freedom, paving the way for applications in spintronics and quantum information science.

2D materials↗
DOE OSTI2025

Space-Time Finite Element Tensor Network Approach for the Time-Dependent Convection–Diffusion–Reaction Equation with Variable Coefficients

In this paper, we present a new space-time Galerkin-like method, where we treat the discretization of spatial and temporal domains simultaneously. This method utilizes a mixed formulation of the tensor-train (TT) and quantized tensor-train (QTT) (please see Section Tensor-Train Decomposition), designed for the finite element discretization (Q1-FEM) of the time-dependent convection–diffusion–reaction (CDR) equation. We reformulate the assembly process of the finite element discretized CDR to enhance its compatibility with tensor operations and introduce a low-rank tensor structure for the finite element operators. Recognizing the banded structure inherent in the finite element framework’s discrete operators, we further exploit the QTT format of the CDR to achieve greater speed and compression. Additionally, we present a comprehensive approach for integrating variable coefficients of CDR into the global discrete operators within the TT/QTT framework. The effectiveness of the proposed method, in terms of memory efficiency and computational complexity, is demonstrated through a series of numerical experiments, including a semi-linear example.

convection–diffusion–reaction equation↗