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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Embedding Methods for Quantum Chemistry: Applications from Materials to Life Sciences

Quantum mechanical embedding methods hold the promise to transform not just the way calculations are performed, but to significantly reduce computational costs and improve scaling for macro molecular systems containing hundreds if not thousands of atoms. The field of embedding has grown increasingly broad with many approaches of different intersecting flavors. Here, we lay out the methods into two streams: QM:MM and QM:QM, showcasing the advantages and disadvantages of both. We provide a review of the literature, the underpinning theories including our contributions, and we highlight current applications with select examples spanning both materials and life sciences. Lastly, we conclude with prospects and future outlook on embedding, and our view on the use of universal test case scenarios for cross comparisons of the many available (and future) embedding theories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Local-Field Effects in Linear Response Properties within a Polarizable Frozen Density Embedding Method

In this work, we present a polarizable frozen density embedding (FDE) method for calculating polarizabilities of coupled subsystems. The method (FDE-pol) combines a FDE method with an explicit polarization model such that the expensive freeze/thaw cycles can be bypassed, and approximate nonadditive kinetic potentials are avoided by enforcing external orthogonality between the subsystems. To describe the polarization of the frozen environment, we introduce a Hirshfeld partition-based density-dependent method for calculating the atomic polarizabilities of atoms in molecules, which alleviates the need to fit the atomic parameters to a specific system of interest or to a larger general set of molecules. Further, we show that the Hirshfeld partition-based method predicts molecular polarizabilities close to the basis set limit, and thus, a single basis set-dependent scaling parameter can be introduced to improve the agreement against the reference polarizability data. To test the model, we characterized the uncoupled and coupled response of small interacting molecular complexes. Here, the coupled response properties include the perturbation of the frozen system due to the external perturbation which is ignored in the uncoupled response. We show that FDE-pol can accurately reproduce both the exact uncoupled polarizability and the coupled polarizabilities of the supermolecular systems. Using damped response theory, we also demonstrate that the coupled frequency-dependent polarizability can be described by including local field effects. The results emphasize the necessity of including local-field effects for describing the response properties of coupled subsystems, as well as the importance of accurate atomic polarizability models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1989

The free-wake prediction of rotor hover performance using a vortex embedding method

A method is developed to predict the rotor hover performance. This method solves the compressible mass conservation equation much like current full potential codes and can therefore predict the transonic flows on a rotor. However, the newly developed approach also allows for the free convection of shed vorticity and permits the computation of the entire hover wake system. The method uses a vortex embedding scheme in potential flow and has been implemented in a computer code, HELIX -I. To predict power we implement a simple boundary layer and two different induced-drag integration schemes. The induced-drag is obtained from surface pressure integration and an energy flux integral. Comparisons between computations and experiment show good agreement for the prediction of power polars, surface pressure distribution, and tip vortex geometry.

Ramachandran, K.↗
DOE OSTI2024

How Well Can Quantum Embedding Method Predict the Reaction Profiles for Hydrogenation of Small Li Clusters?

Quantum computing leverages the principles of quantum mechanics in novel ways to tackle complex chemistry problems that cannot be accurately addressed using traditional quantum chemistry methods. However, the high computational cost and available number of physical qubits with high fidelity limit its application to small chemical systems. This work employed a quantum-classical framework which features a quantum active space-embedding approach to perform simulations of chemical reactions that require up to 14 qubits. This framework was applied to prototypical example metal hydrogenation reactions: the coupling between hydrogen and Li 2 , Li 3 , and Li 4 clusters. Particular attention was paid to the computation of barriers and reaction energies. The predicted reaction profiles compare well with advanced classical quantum chemistry methods, demonstrating the potential of the quantum embedding algorithm to map out reaction profiles of realistic gas-phase chemical reactions to ascertain qualitative energetic trends. Additionally, the predicted potential energy curves provide a benchmark to compare against both current and future quantum embedding approaches.

36 MATERIALS SCIENCE↗
NASA NTRS1982

Singularity embedding method in potential flow calculations

The so-called H-type mesh is used in a finite-element (or finite-volume) calculation of the potential flow past an airfoil. Due to coordinate singularity at the leading edge, a special singular trial function is used for the elements neighboring the leading edge. The results using the special singular elements are compared to those using the regular elements. It is found that the unreasonable pressure distribution obtained by the latter is removed by the embedding of the singular element. Suggestions to extend the present method to transonic cases are given.

Jou, W. H.↗
NASA NTRS1986

An embedding method for the steady Euler equations

Certain difficulties arise in connection with the numerical solution of a direct finite difference representation of the steady Euler equations. Johnson (1979, 1981, 1982) has, therefore, proposed a surrogate-equation technique, in which the first-order steady Euler equations are embedded in a certain second-order system of equations. The present paper is concerned with the theoretical justification for such an embedding approach. For the numerical solution of the two-dimensional steady Euler equations, it is shown that, under a continuity restriction, it is possible to solve a second-order embedded system together with appropriate additional boundary conditions. The result indicates that a more direct and potentially more efficient approach to the steady solutions exists than the alternative of solving the unsteady equations.

Chang, S.-H.↗
NASA NTRS1983

Embedding methods for the steady Euler equations

An approach to the numerical solution of the steady Euler equations is to embed the first-order Euler system in a second-order system and then to recapture the original solution by imposing additional boundary conditions. Initial development of this approach and computational experimentation with it were previously based on heuristic physical reasoning. This has led to the construction of a relaxation procedure for the solution of two-dimensional steady flow problems. The theoretical justification for the embedding approach is addressed. It is proven that, with the appropriate choice of embedding operator and additional boundary conditions, the solution to the embedded system is exactly the one to the original Euler equations. Hence, solving the embedded version of the Euler equations will not produce extraneous solutions.

Chang, S. H.↗
DOE OSTI2019

High-order gradients with the shifted boundary method: An embedded enriched mixed formulation for elliptic PDEs

Here, we propose an extension of the embedded boundary method known as “shifted boundary method” to elliptic diffusion equations in mixed form (e.g., Darcy flow, heat diffusion problems with rough coefficients, etc.). Our aim is to obtain an improved formulation that, for linear finite elements, is at least second-order accurate for both flux and primary variable, when either Dirichlet or Neumann boundary conditions are applied. Following previous work of Nishikawa and Mazaheri in the context of residual distribution methods, we consider the mixed form of the diffusion equation (i.e., with Darcy-type operators), and introduce an enrichment of the primary variable. This enrichment is obtained exploiting the relation between the primary variable and the flux variable, which is explicitly available at nodes in the mixed formulation. The proposed enrichment mimics a formally quadratic pressure approximation, although only nodal unknowns are stored, similar to a linear finite element approximation. We consider both continuous and discontinuous finite element approximations and present two approaches: a non-symmetric enrichment, which, as in the original references, only improves the consistency of the overall method; and a symmetric enrichment, which enables a full error analysis in the classical finite element context. Combined with the shifted boundary method, these two approaches are extended to high-order embedded computations, and enable the approximation of both primary and flux (gradient) variables with second-order accuracy, independently on the type of boundary conditions applied. We also show that the primary variable is third-order accurate, when pure Dirichlet boundary conditions are embedded.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1990

Application of the embedded atom method to Pb and Be

We have derived the embedding energy functional and two-body potential of the embedded atom method using decreasing exponentials for both the electron density and the two body potential. The embedding function was obtained from the equation of state given by Rose et al. (1984). Because of the form of the embedding function, the equilibrium lattice constant, cohesive energy, and bulk modulus are automatically satisfied. The two parameters phi(e) and gamma of the two-body potential were determined by fitting to shear modulus and the single vacancy formation energy. Contributions of up to the third nearest neighbors were included in the evaluation of the charge density rho and the two-body potential phi. The stability and anisotropy of each structure were estimated and compared with the available experimental data.

Karimi, M.↗
DOE OSTI2025

Strongly Correlated States of Transition Metal Spin Defects: The Case of an Iron Impurity in Aluminum Nitride

We investigate the electronic properties of an exemplar transition metal impurity in an insulator, with the goal of accurately describing strongly correlated defect states. Here, we consider iron in aluminum nitride, a material of interest for hybrid quantum technologies, and we carry out calculations with quantum embedding methods, density matrix embedding theory (DMET) and quantum defect embedding theory (QDET), and with spin-flip time-dependent density functional theory (TDDFT). We show that both DMET and QDET accurately describe the ground state and low-lying excited states of the defect and that TDDFT yields photoluminescence spectra in agreement with experiments. In addition, we provide a detailed discussion of the convergence of our results as a function of the active space used in the embedding methods, thus defining a protocol to obtain converged data directly comparable with experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1994

Embedded function methods for compressible high speed turbulent flow

This is the final report on the work performed on the grant 'Embedded Function Methods for Compressible High Speed Turbulent Flow' carried out at Lehigh University during the contract period from September, 1987, to October of 1991. Work has continued at Lehigh on this project on an unfunded basis to the present. The original proposed work had two separate thrusts which were associated with developing embedded function methods in order to obviate the need to expend computational resources on turbulent wall layers in Navier Stokes and boundary-layer calculations. Previous work on the incompressible problem had indicated that this could be done successfully for two-dimensional and three-dimensional incompressible flows. The central objective here was to extend the basic approach to the high speed compressible problem.

Walker, J. D. A.↗
DOE OSTI2023

Improving nanoparticle superlattice stability with deformable polymer gels

The self-assembly of colloidal nanoparticles into ordered superlattices typically uses dynamic interactions to govern particle crystallization, as these non-permanent bonds prevent the formation of kinetically trapped, disordered aggregates. However, while the use of reversible bonding is critical in the formation of highly ordered particle arrangements, dynamic interactions also inherently make the structures more prone to disassembly or disruption when subjected to different environmental stimuli. Thus, there is typically a trade-off between the ability to initially form an ordered colloidal material and the ability of that material to retain its order under different conditions. Here, we present a method for embedding colloidal nanoparticle superlattices into a polymer gel matrix. This encapsulation strategy physically prevents the nanoparticles from dissociating upon heating, drying, or the introduction of chemicals that would normally disrupt the lattice. However, the use of a gel as the embedding medium still permits further modification of the colloidal nanoparticle lattice by introducing stimuli that deform the gel network (as this deformation in turn alters the nanoparticle lattice structure in a predictable manner). Moreover, encapsulation of the lattice within a gel permits further stabilization into fully solid materials by removing the solvent from the gel or by replacing the solvent with a liquid monomer that can be photopolymerized. This embedding method therefore makes it possible to incorporate ordered colloidal arrays into a polymer matrix as either dynamic or static structures, expanding their potential for use in responsive materials.

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

An energy-based study of the embedded element method for explicit dynamics

Abstract The embedded finite element technique provides a unique approach for modeling of fiber-reinforced composites. Meshing fibers as distinct bundles represented by truss elements embedded in a matrix material mesh allows for the assignment of more specific material properties for each component rather than homogenization of all of the properties. However, the implementations of the embedded element technique available in commercial software do not replace the material of the matrix elements with the material of the embedded elements. This causes a redundancy in the volume calculation of the overlapping meshes leading to artificially increased stiffness and mass. This paper investigates the consequences in the energy calculations of an explicit dynamic model due to this redundancy. A method for the correction of the edundancy within a finite element code is suggested which removes extra energy and is shown to be effective at correcting the energy calculations for large amounts of redundant volume.

Martin, Valerie A.↗
DOE OSTI2025

Pore Resolved Simulations of Joule Heating in Fibrous Media using an Embedded Boundary Method

Joule heating has been regarded as an energy-efficient and sustainable method for heating materials and gases at large scales. The modeling of local temperature effects at pore-resolved scales for such systems, however, has been difficult to achieve due to challenges in coupling thermo-chemical processes in complex porous media and in large representative volume elements (RVEs). To this end, we developed an electro-thermal model at the pore scale to study Joule heating effects in large heterogeneous systems with different microstructures. This was achieved using the level set method to implicitly delineate distinct regions within the domain, and an embedded boundary method to facilitate heat exchange across the fluid-solid interface. Moreover, we applied this method to investigate unsteady non-linear electro-thermal effects in non-woven fibrous graphite conductors for RVEs with characteristic lengths of 2 mm, with different fiber orientations, porosity (80% – 90%) and fiber diameters (10 – 20µm). The coupled equations were solved numerically and they produced peak temperatures greater than 2000 K resulting in heating rates as high as 80,000 K/s. Moreover, the results depended strongly on the microstructure of the fiber skeleton and current density. Geometries with large fibers (∼ 20µm) had the highest average and peak temperatures with the mean temperature increasing by 3.9 % while the peak temperature increased by 9.9 %. Anisotropic domains on the other hand had the lowest mean and peak temperatures with peak and mean temperatures of 2293 K and 1437.7K respectively representing a corresponding 12.1% and 5.1% drop in the temperatures. An increase in porosity from 80% to 90%, however, led to an increase in the peak temperature by 5.1%.

Joule heating↗
DOE OSTI2023

Analysis of phase stability and chemical segregation in the Mo-V alloys using a generalized embedded atom method potential

A new interatomic potential for the Mo-V system is introduced to facilitate the study of phase stability and mechanical properties at lower temperatures. This potential is based on a generalization of the embedded atom method and includes contributions from embedding energy, explicit two- and three-body interactions and nonlocal many-body interaction terms. The parameters of the potential are optimized by using data from ab initio density functional theory (DFT) calculations. The potential is rigorously validated across a range of physical properties, such as elastic constants, equation of states, phonon dispersion curves, point defect properties and melting temperatures for different compositions. Even though our potential is trained on a small dataset, its accuracy is comparable to available machine learning potentials for Mo and V. Furthermore, our results show that an ordered B2 phase is stable at low temperatures in alloys containing 50% V, but the solid solution phase is stable above 800 K. However, such long-range ordering is not observed in V-rich or Mo-rich alloys. In addition, our results show that V segregates to dislocation cores and grain boundaries.

36 MATERIALS SCIENCE↗
NASA NTRS2012

System and method for embedding emotion in logic systems

A system, method, and computer readable-media for creating a stable synthetic neural system. The method includes training an intellectual choice-driven synthetic neural system (SNS), training an emotional rule-driven SNS by generating emotions from rules, incorporating the rule-driven SNS into the choice-driven SNS through an evolvable interface, and balancing the emotional SNS and the intellectual SNS to achieve stability in a nontrivial autonomous environment with a Stability Algorithm for Neural Entities (SANE). Generating emotions from rules can include coding the rules into the rule-driven SNS in a self-consistent way. Training the emotional rule-driven SNS can occur during a training stage in parallel with training the choice-driven SNS. The training stage can include a self assessment loop which measures performance characteristics of the rule-driven SNS against core genetic code. The method uses a stability threshold to measure stability of the incorporated rule-driven SNS and choice-driven SNS using SANE.

Curtis, Steven A.↗
NASA NTRS1990

Embedded function methods for supersonic turbulent boundary layers

The development of embedded functions to represent the mean velocity and total enthalpy distributions in the wall layer of a supersonic turbulent boundary layer is considered. The asymptotic scaling laws (in the limit of large Reynolds number) for high speed compressible flows are obtained to facilitate eventual implementation of the embedded functions in a general prediction method. A self-consistent asymptotic structure is derived, as well as a compressible law of the wall in which the velocity and total enthalpy are logarithmic within the overlap zone, but in the Howarth-Dorodnitsyn variable. Simple outer region turbulence models are proposed (some of which are modifications of existing incompressible models) to reflect the effects of compressibility. As a test of the methodology and the new turbulence models, a set of self-similar outer region profiles is obtained for constant pressure flow; these are then coupled with embedded functions in the wall layer. The composite profiles thus obtained are compared directly with experimental data and good agreement is obtained for flows with Mach numbers up to 10.

He, J.↗