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At least 1,369 records · Page 76

A BOUT++ extension for full annular tokamak edge MHD and turbulence simulations

For tokamak edge plasma simulation, a plasma simulation framework BOUT++ employs a dual coordinate system to simulate moderate-n and high-n plasma instability with reasonable computational cost, where n is the toroidal mode number. This coordinate system however limits the computational domain to the toroidal wedge (full torus divided into N parts in the toroidal direction) for computational efficiency and the use of flute-ordering approximation in the field solver calculating the flow potential from the vorticity which may not be valid for low-n modes. Improving numerical treatment of low-n modes is however indispensable to address simulations of low-n current-driven edge localized mode (ELM), ELM control by resonant magnetic perturbations (RMPs), edge turbulence with RMPs and so on. In this work, BOUT++ is extended to simulate the interplay between $n=0$, low-n and high-n plasma components in a full annular tokamak edge domain through hybrid modeling of the flow potential and the vorticity. Low-n modes of flow potential are calculated in an orthogonal flux surface coordinate and high-n modes in the dual coordinate system separately in Fourier space. Finally, the proposed scheme can capture an interplay between $n=1$ global modes and high-n turbulence during pedestal collapse in a full annular torus domain with a circular cross section.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Enhancing approximate modular Bayesian inference by emulating the conditional posterior

In modular Bayesian analyses, complex models are composed of distinct modules, each representing different aspects of the data or prior information. In this context, fully Bayesian approaches can sometimes lead to undesirable feedback between modules, compromising the integrity of the inference. The “cut-distribution” prevents unwanted influence between modules by “cutting” feedback. The direct sampling (DS) algorithm is standard practice for approximating the cut-distribution, but it can be computationally intensive, especially when the number of imputations required is large. An enhanced method is proposed, the Emulating the Conditional Posterior (ECP) algorithm, which leverages emulation to increase the number of imputations. Through numerical experiment it is demonstrated that the ECP algorithm outperforms the traditional DS approach in terms of accuracy and computational efficiency, particularly when resources are constrained. Here, it is also shown how the DS algorithm can be improved using ideas from design of experiments. Some practical recommendations are given for algorithm choice in modular Bayesian analyses.

97 MATHEMATICS AND COMPUTING↗

Curated Collection of More than 20,000 Experimentally Reported One-Dimensional Metal–Organic Frameworks

Herein, a collection of more than 20,000 experimentally derived crystal structures for metal–organic frameworks (MOFs) that do not have two- or three-dimensional covalently bonded networks has been developed from the materials available at the Cambridge Crystallographic Data Centre. Of these 20,000 1D MOFs, more than 12,000 structures have been verified to be solvent-free and in exact agreement with the stoichiometry of the synthesized materials. More than 10% of the complete data set comprise materials including two or more distinct metals. The band gaps of more than 12,000 1D MOFs have been computed at the density functional theory-generalized gradient approximation level, finding more than 2000 materials that have a zero band gap. Molecular simulations of CH4 adsorption in a small number of 1D MOFs indicated that adsorbate-induced deformation plays a significant role in determining adsorption isotherms in these materials. As a result, methods that have been used previously for high-throughput predictions of molecular adsorption in 3D MOFs are not suitable for 1D MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Efficient Monte Carlo With Graph-Based Subsurface Flow and Transport Models

Simulating flow and transport in fractured porous media frequently involves solving numerical discretizations of partial differential equations with a large number of degrees of freedom using discrete fracture network (DFN) models. Uncertainty in the properties of the fracture network that controls flow and transport requires a large number of DFN simulations to statistically describe quantities of interest. However, the computational cost of solving more than a few realizations of a large DFN can be intractable. As a means of circumventing this problem, we utilize both a high-fidelity DFN model and a graphbased model of flow and transport in combination with a multifidelity Monte Carlo (MC) method to reduce the number of high-fidelity simulations that are needed to obtain an accurate estimate of the quantity of interest. We demonstrate the approach by estimating quantiles of the breakthrough time for a conservative tracer in an ensemble of fractured porous media. Our results demonstrate that a multifidelity MC estimate, whose computational cost is equal to the cost of 10 DFN simulations, can be as accurate as a standard MC estimate that utilizes 1,000 DFN simulations. Thus the combination of our graphbased model with multifidelity MC estimates effectively reduces the computational cost of the problem by a factor of approximately 100.

58 GEOSCIENCES↗

Hyporheic Exchange in Sand Dunes Under a Freely Deforming River Water Surface

Bedform-driven hyporheic exchange is conditioned by the head gradients at the sediment-water interface. Local exchange phenomena between the surface and the subsurface are often driven by the dynamic forces related to the velocity distributions around sediment waves. In open channels, the static forces are represented by the water depth, yet most computational fluid dynamics models use a rigid-lid approximation. Here, we investigated whether and when the deformation of the river’s free-surface influences bedform-driven hyporheic exchange. This was done through simulations of coupled open channel and hyporheic flows with the air-water interface modeled either as a free-surface or a rigid-lid across increasing subcritical Froude numbers from ~0.05 to ~0.95. The normalized hyporheic flux was higher when considering free-surface deformation across most of the range of Froude numbers considered. When the Froude number was larger than 0.6 and smaller than 0.85, both hydrostatic and nonhydrostatic-driven fluxes increased significantly compared to the rigid-lid approach and the total flux was about five times that predicted with the rigid-lid. These results indicate that bedform-driven hyporheic fluxes are underestimated in most studies that use a rigid-lid assumption in subcritical flows.

58 GEOSCIENCES↗

Machine learned potential for high-throughput phonon calculations of metal—organic frameworks

Metal–organic frameworks (MOFs) are highly porous and versatile materials studied extensively for applications such as carbon capture and water harvesting. However, computing phonon-mediated properties in MOFs, like thermal expansion and mechanical stability, remains challenging due to the large number of atoms per unit cell, making traditional Density Functional Theory (DFT) methods impractical for high-throughput screening. Recent advances in machine learning potentials have led to foundation atomistic models, such as MACE-MP-0, that accurately predict equilibrium structures but struggle with phonon properties of MOFs. In this work, we developed a workflow for computing phonons in MOFs within the quasi-harmonic approximation with a fine-tuned MACE model, MACE-MP-MOF0. The model was trained on a curated dataset of 127 representative and diverse MOFs. The fine-tuned MACE-MP-MOF0 improves the accuracy of phonon density of states and corrects the imaginary phonon modes of MACE-MP-0, enabling high-throughput phonon calculations with state-of-the-art precision. The model successfully predicts thermal expansion and bulk moduli in agreement with DFT and experimental data for several well-known MOFs. These results highlight the potential of MACE-MP-MOF0 in guiding MOF design for applications in energy storage and thermoelectrics.

Elena, Alin Marin↗

Reduction of the molecular hamiltonian matrix using quantum community detection

Abstract Quantum chemistry is interested in calculating ground and excited states of molecular systems by solving the electronic Schrödinger equation. The exact numerical solution of this equation, frequently represented as an eigenvalue problem, remains unfeasible for most molecules and requires approximate methods. In this paper we introduce the use of Quantum Community Detection performed using the D-Wave quantum annealer to reduce the molecular Hamiltonian matrix in Slater determinant basis without chemical knowledge. Given a molecule represented by a matrix of Slater determinants, the connectivity between Slater determinants (as off-diagonal elements) is viewed as a graph adjacency matrix for determining multiple communities based on modularity maximization. A gauge metric based on perturbation theory is used to determine the lowest energy cluster. This cluster or sub-matrix of Slater determinants is used to calculate approximate ground state and excited state energies within chemical accuracy. The details of this method are described along with demonstrating its performance across multiple molecules of interest and bond dissociation cases. These examples provide proof-of-principle results for approximate solution of the electronic structure problem using quantum computing. This approach is general and shows potential to reduce the computational complexity of post-Hartree–Fock methods as future advances in quantum hardware become available.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The backward phase flow method for the Eulerian finite time Lyapunov exponent computations

We propose a simple Eulerian approach to compute the moderate to long time flow map for approximating the Lyapunov exponent of a (periodic or aperiodic) dynamical system. The idea is to generalize a recently proposed backward phase flow method which is specially designed for long time level set propagation. Unlike the original phase flow method or the backward phase flow method, which is applicable only to autonomous systems, the current approach can also be applied to any time-dependent (periodic or aperiodic) flow. We will discuss the stability of the proposed method. Numerical examples will be given to demonstrate the effectiveness of the algorithm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Accelerating quantum instanton calculations of the kinetic isotope effects

Path integral implementation of the quantum instanton approximation currently belongs among the most accurate methods for computing quantum rate constants and kinetic isotope effects, but its use has been limited due to the rather high computational cost. Here, we demonstrate that the efficiency of quantum instanton calculations of the kinetic isotope effects can be increased by orders of magnitude by combining two approaches: The convergence to the quantum limit is accelerated by employing high-order path integral factorizations of the Boltzmann operator, while the statistical convergence is improved by implementing virial estimators for relevant quantities. After deriving several new virial estimators for the high-order factorization and evaluating the resulting increase in efficiency, using ⋅H{sub α} + H{sub β}H{sub γ} → H{sub α}H{sub β} + ⋅ H{sub γ} reaction as an example, we apply the proposed method to obtain several kinetic isotope effects on CH{sub 4} + ⋅ H ⇌ ⋅ CH{sub 3} + H{sub 2} forward and backward reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electronic excitation of molecules in solution calculated using the symmetry-adapted cluster–configuration interaction method in the polarizable continuum model

The effects from solvent environment are specific to the electronic states; therefore, a computational scheme for solvent effects consistent with the electronic states is necessary to discuss electronic excitation of molecules in solution. The PCM (polarizable continuum model) SAC (symmetry-adapted cluster) and SAC-CI (configuration interaction) methods are developed for such purposes. The PCM SAC-CI adopts the state-specific (SS) solvation scheme where solvent effects are self-consistently considered for every ground and excited states. For efficient computations of many excited states, we develop a perturbative approximation for the PCM SAC-CI method, which is called corrected linear response (cLR) scheme. Our test calculations show that the cLR PCM SAC-CI is a very good approximation of the SS PCM SAC-CI method for polar and nonpolar solvents.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Molecular anions of polydeprotonated naphthalenes: An investigation on the metastability and deprotonation energies using nuclear-charge stabilization method

The dianions and trianions of doubly- and triply-deprotonated naphthalenes are investigated using density functional theory (DFT) computations employing hybrid, long-range, and dispersion corrected exchange-correlation functionals. The investigated polyanionic species are found to be metastable with negative electron affinity and are further treated using a nuclear-charge stabilization method. The tunneling lifetimes of these anionic species were estimated to be a few femtoseconds. Notably, the deprotonated energies (DPEs) of naphthalene leading to the formation of triply deprotonated trianions are observed to be affected by the metastability of the dianions and trianions. For the deprotonation of doubly deprotonated dianions, the DPE calculated using the improved methodology based on the stabilization method is found to be nearly 100 kcal/mol more than that computed using the conventional procedure. Though the various DFT approximations employed are in a good agreement for predicting the lifetimes of the metastable species but in the prediction of electron-affinities and deprotonation energies, the dispersion-corrected DFT-D3 significantly disagrees with the long-range corrected DFT methods employing cam-B3LYP and ωB97XD exchange-correlation functionals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Linking density functional and mode coupling models for supercooled liquids

We compare predictions from two familiar models of the metastable supercooled liquid, respectively, constructed with thermodynamic and dynamic approaches. In the so called density functional theory the free energy F[ρ] of the liquid is a functional of the inhomogeneous density ρ(r). The metastable state is identified as a local minimum of F[ρ]. The sharp density profile characterizing ρ(r) is identified as a single particle oscillator, whose frequency is obtained from the parameters of the optimum density function. On the other hand, a dynamic approach to supercooled liquids is taken in the mode coupling theory (MCT) which predict a sharp ergodicity-non-ergodicity transition at a critical density. The single particle dynamics in the non-ergodic state, treated approximately, represents a propagating mode whose characteristic frequency is computed from the corresponding memory function of the MCT. The mass localization parameters in the above two models (treated in their simplest forms) are obtained, respectively, in terms of the corresponding natural frequencies depicted and are shown to have comparable magnitudes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimal renormalization of multiscale systems

While model order reduction is a promising approach in dealing with multi-scale time-dependent systems that are too large or too expensive to simulate for long times, the resulting reduced order models can suffer from instabilities. We have recently developed a time-dependent renormalization approach to stabilize such reduced models. In the current work, we extend this framework by introducing a parameter that controls the time-decay of the memory of such models and optimally selecting this parameter based on limited fully resolved simulations. First, we demonstrate our framework on the inviscid Burgers equation whose solution develops a finite-time singularity. Our renormalized reduced order models are stable and accurate for long times while using for their calibration only data from a full order simulation before the occurrence of the singularity. Furthermore, we apply this framework to the 3D Euler equations of incompressible fluid flow, where the problem of finite-time singularity formation is still open and where brute force simulation is only feasible for short times. Our approach allows us to obtain for the first time a perturbatively renormalizable model which is stable for long times and includes all the complex effects present in the 3D Euler dynamics. We find that, in each application, the renormalization coefficients display algebraic decay with increasing resolution, and that the parameter which controls the time-decay of the memory is problem-dependent.

Price, Jacob↗

PBE-GGA predicts the B8↔B2 phase boundary of FeO at Earth’s core conditions

FeO is a crucial component of the Earth’s core, and its thermodynamic properties are essential to developing more accurate core models. It is also a notorious correlated insulator in the NaCl-type (B1) phase at ambient conditions. It undergoes two polymorphic transitions at 300 K before it becomes metallic in the NiAs-type (B8) structure at ~100 GPa. Although its phase diagram is not fully mapped, it is well established that the B8 phase transforms to the CsCl-type (B2) phase at core pressures and temperatures. Here, we report a successful ab initio calculation of the B8↔B2 phase boundary in FeO at Earth’s core pressures. We show that fully anharmonic free energies computed with the Perdew–Burke–Ernzerhof-generalized gradient approximation coupled with thermal electronic excitations reproduce the experimental phase boundary within uncertainties at P > 255 GPa, including the largely negative Clapeyron slope of –52 MPa/K. This study validates the applicability of a standard density functional theory functional to FeO under Earth’s core conditions and demonstrates the theoretical framework that enables complex predictive studies of this region.

58 GEOSCIENCES↗

Compressional Alfvén eigenmodes in rotating spherical tokamak plasmas

Spherical tokamaks often have a considerable toroidal plasma rotation of several tens of kHz. Compressional Alfvén eigenmodes in such devices therefore experience a frequency shift, which if the plasma were rotating as a rigid body, would be a simple Doppler shift. However, since the rotation frequency depends on minor radius, the eigenmodes are affected in a more complicated way. The eigenmode solver CAE3B (Smith et al 2009 Plasma Phys. Control. Fusion 51 075001) has been extended to account for toroidal plasma rotation. The results show that the eigenfrequency shift due to rotation can be approximated by a rigid body rotation with a frequency computed from a spatial average of the real rotation profile weighted with the eigenmode amplitude. To investigate the effect of extending the computational domain to the vessel wall, a simplified eigenmode equation, yet retaining plasma rotation, is solved by a modified version of the CAE code used in Fredrickson et al (2013 Phys. Plasmas 20 042112). Lastly, both solving the full eigenmode equation, as in the CAE3B code, and placing the boundary at the vessel wall, as in the CAE code, significantly influences the calculated eigenfrequencies.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Nonlinear dimension reduction for surrogate modeling using gradient information

We introduce a method for the nonlinear dimension reduction of a high-dimensional function $u:{\mathbb{R}}^d\rightarrow{\mathbb{R}}$, $d\gg 1$. Our objective is to identify a nonlinear feature map $g:{\mathbb{R}}^d\rightarrow{\mathbb{R}}^m$, with a prescribed intermediate dimension $m\ll d$, so that $u$ can be well approximated by $f\circ g$ for some profile function $f:{\mathbb{R}}^m\rightarrow{\mathbb{R}}$. We propose to build the feature map by aligning the Jacobian $\nabla g$ with the gradient $\nabla u$, and we theoretically analyze the properties of the resulting $g$. Once $g$ is built, we construct $f$ by solving a gradient-enhanced least squares problem. Our practical algorithm uses a sample $\{{\textbf{x}}^{(i)},u({\textbf{x}}^{(i)}),\nabla u({\textbf{x}}^{(i)})\}_{i=1}^N$ and builds both $g$ and $f$ on adaptive downward-closed polynomial spaces, using cross validation to avoid overfitting. We numerically evaluate the performance of our algorithm across different benchmarks, and explore the impact of the intermediate dimension $m$. We show that building a nonlinear feature map $g$ can permit more accurate approximation of $u$ than a linear $g$, for the same input data set.

97 MATHEMATICS AND COMPUTING↗

flash -light on the ring : hydrodynamic simulations of expanding supernova shells near supermassive black holes

ABSTRACT The way supermassive black holes (SMBHs) in Galactic Centres (GCs) accumulate their mass is not completely determined. At large scales, it is governed by galactic encounters, mass inflows connected to spirals arms and bars, or due to expanding shells from supernova (SN) explosions in the central parts of galaxies. The investigation of the latter process requires an extensive set of gas dynamical simulations to explore the multidimensional parameter space needed to frame the phenomenon. The aims of this paper are to extend our investigation of the importance of SNe for inducing accretion on to an SMBH and carry out a comparison between the fully hydrodynamic code flash and the much less computationally intensive code ring, which uses the thin shell approximation. We simulate 3D expanding shells in a gravitational potential similar to that of the GC with a variety of homogeneous and turbulent environments. In homogeneous media, we find convincing agreement between flash and ring in the shapes of shells and their equivalent radii throughout their whole evolution until they become subsonic. In highly inhomogeneous, turbulent media, there is also a good agreement of shapes and sizes of shells, and of the times of their first contact with the central 1-pc sphere, where we assume that they join the accretion flow. The comparison supports the proposition that an SN occurring at a galactocentric distance of 5 pc typically drives 1–3 M⊙ into the central 1 pc around the GC.

79 ASTRONOMY AND ASTROPHYSICS↗

Quantum many-body calculations using body-centered cubic lattices

It is often computationally advantageous to model space as a discrete set of points forming a lattice grid. This technique is particularly useful for computationally difficult problems such as quantum many-body systems. For reasons of simplicity and familiarity, nearly all quantum many-body calculations have been performed on simple cubic lattices. Since the removal of lattice artifacts is often an important concern, it would be useful to perform calculations using more than one lattice geometry. In this paper we show how to perform quantum many-body calculations using auxiliary-field Monte Carlo simulations on a three-dimensional body-centered cubic (BCC) lattice. As a benchmark test we compute the ground state energy of 33 spin-up and 33 spin-down neutrons in the unitary limit, which is an idealized limit where the interaction range is zero and scattering length is infinite. As a fraction of the free Fermi gas energy E FG , we find that the ground state energy is E 0 /E FG =0.369(2),0.371(2), using two different definitions of the finite-system energy ratio. This is in excellent agreement with recent results obtained on a cubic lattice [He et al., Phys. Rev. A 101, 063615 (2020)]. We find that the computational effort and performance on a BCC lattice is approximately the same as that for a cubic lattice with the same number of lattice points. We discuss how the lattice simulations with different geometries can be used to constrain the size of lattice artifacts in simulations of continuum quantum many-body systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗