Non-periodic Boundary Conditions Research Articles

The Simplified Approach to the Bose Gas Without Translation Invariance

The simplified approach to the Bose gas was introduced by Lieb in 1963 to study the ground state of systems of interacting Bosons. In a series of recent papers, it has been shown that the simplified approach exceeds earlier expectations, and gives asymptotically accurate predictions at both low and high density. In the intermediate density regime, the qualitative predictions of the simplified approach have also been found to agree very well with quantum Monte Carlo computations. Until now, the simplified approach had only been formulated for translation invariant systems, thus excluding external potentials, and non-periodic boundary conditions. In this paper, we extend the formulation of the simplified approach to a wide class of systems without translation invariance. This also allows us to study observables in translation invariant systems whose computation requires the symmetry to be broken. Such an observable is the momentum distribution, which counts the number of particles in excited states of the Laplacian. In this paper, we show how to compute the momentum distribution in the simplified approach, and show that, for the simple equation, our prediction matches up with Bogolyubov’s prediction at low densities, for momenta extending up to the inverse healing length.

Efficient all-electron hybrid density functionals for atomistic simulations beyond 10 000 atoms.

Hybrid density functional approximations (DFAs) offer compelling accuracy for abinitio electronic-structure simulations of molecules, nanosystems, and bulk materials, addressing some deficiencies of computationally cheaper, frequently used semilocal DFAs. However, the computational bottleneck of hybrid DFAs is the evaluation of the non-local exact exchange contribution, which is the limiting factor for the application of the method for large-scale simulations. In this work, we present a drastically optimized resolution-of-identity-based real-space implementation of the exact exchange evaluation for both non-periodic and periodic boundary conditions in the all-electron code FHI-aims, targeting high-performance central processing unit (CPU) compute clusters. The introduction of several new refined message passing interface (MPI) parallelization layers and shared memory arrays according to the MPI-3 standard were the key components of the optimization. We demonstrate significant improvements of memory and performance efficiency, scalability, and workload distribution, extending the reach of hybrid DFAs to simulation sizes beyond ten thousand atoms. In addition, we also compare the runtime performance of the PBE, HSE06, and PBE0 functionals. As a necessary byproduct of this work, other code parts in FHI-aims have been optimized as well, e.g., the computation of the Hartree potential and the evaluation of the force and stress components. We benchmark the performance and scaling of the hybrid DFA-based simulations for a broad range of chemical systems, including hybrid organic-inorganic perovskites, organic crystals, and ice crystals with up to 30 576 atoms (101 920 electrons described by 244 608 basis functions).

Render unto Numerics: Orthogonal Polynomial Neural Operator for PDEs with Nonperiodic Boundary Conditions

Render unto Numerics: Orthogonal Polynomial Neural Operator for PDEs with Nonperiodic Boundary Conditions

Numerical Simulation of Flows Using the Fourier Pseudospectral Method and the Immersed Boundary Method

The present work proposes the application of a computational methodology based on the coupling of the Fourier Pseudospectral Method (FPSM) and the Immersed Boundary Method (IBM) for conducting flow simulations over slender airfoils. This methodology, termed IMERSPEC, leverages the benefits of both high accuracy and low computational cost inherent in pseudospectral methods, thanks to the utilization of the Fast Fourier Transform algorithm. IBM is employed to impose non-periodic boundary conditions in the Navier–Stokes equations, addressing the requirement of periodicity at boundaries for FPSM convergence and to accurately represent the immersed slender airfoil in the flow. The aerodynamic behavior of the analyzed profiles was assessed by calculating lift and drag coefficients, which were then compared with existing literature results. Consistently favorable outcomes were observed, particularly in flows at lower Reynolds numbers, demonstrating the effectiveness of the IMERSPEC methodology for simulating complex flows computationally. Additionally, weight functions, fundamental to IBM, are employed flexibly for aerodynamic force calculations. Specifically, within the same simulation, a Cubic function is utilized for drag calculation while a Hat function is employed for lift calculation, yielding results more closely aligned with the literature’s findings. This approach offers an alternative to previously proposed methods for IBM implementation.

Error estimates of a space–time Legendre spectral method for solving the Korteweg–de Vries equation

In this paper, a space–time spectral method for solving the Korteweg–de Vries equation is considered. The discrete schemes of the method are based on the Legendre–Petrov–Galerkin method in spatial direction and the Legendre-tau method in temporal direction with nonperiodic boundary conditions. Stability analysis results and error estimates are obtained in L2-norm by introducing a cut-off function without Lipschitz condition. The method is also applicable to solve some (2m+1)th-order differential equations. Comparison of our numerical results with those of other spectral methods exhibits the accuracy of our methods for the Korteweg–de Vries equation.

Homogenization of 3D laminated micro-structures including bending effects

In this paper, a homogenization method which captures intrinsic size effect associated with fiber diameter is revisited and adapted for three-dimensional laminated micro-structures. Based on a unit-cell composed of matrix and reinforcement layers, enhanced deformation gradients varying through the thickness, are introduced with the aid of an additional kinematic variable reflecting the difference between the homogenized and constituent level deformation gradients. In the current work, as opposed to the original formulation, higher order terms are preserved for both phases and therefore bending stiffness of the matrix phase can be taken into account as well. The formulation is implemented within the commercial finite element solver Abaqus through user element (UEL) subroutine considering a finite strain hyperelastic response for the reinforcement layers and a von Mises type hyper-elastoplastic one for the matrix phase. Explicitly discretized unit-cells with varying reinforcement phase fraction, layer inclination angle and layer thicknesses are used as references to assess the predictive capabilities of the homogenized model and the significance of bending stiffness of the phases. Similarly, explicitly discretized model of a beam type structure with a crossed lamellar micro-structure is used to evaluate the performance of the homogenized model under more general, non-periodic boundary conditions. The findings of both cases support the effectiveness of the homogenized model.

The linear Lugiato–Lefever equation with forcing and nonzero periodic or nonperiodic boundary conditions

The linear Lugiato–Lefever equation with forcing and nonzero periodic or nonperiodic boundary conditions

A new treatment of boundary conditions in PDE solution with Galerkin methods via Partial Integral Equation framework

We present a new mathematical framework for solution of Partial Differential Equations (PDEs), which is based on an exact transformation of the underlying PDE that removes the boundary constraints from the solution state and moves them into the dynamics of the equivalent transformed equation. The framework is based on a Partial Integral Equation (PIE) representation of a PDE or a system of PDEs, where Partial Integral Equation does not require boundary conditions on its solution state. The PDE-PIE framework allows for a development of a generalized and consistent treatment of boundary conditions in constructing spectrally convergent solution approximations to a broad class of linear PDEs with non-constant coefficients governed by non-periodic boundary conditions, including, e.g., Dirichlet, Neumann and Robin boundaries, among others. The significance of this result is that a solution to almost any linear PDE in a form of a function series approximation can now be systematically constructed, irrespective of the boundary conditions. Furthermore, in many cases, the resulting ODE system for the expansion coefficients can now be integrated analytically in time, which allows us to obtain solution approximations to a broad class of unsteady PDEs with unprecedented accuracy. We present several PDE solution examples in one spatial variable implemented with the developed PIE-Galerkin methodology using both analytical and numerical integration in time. We also present comparison of the PIE methods with some classical direct PDE solution methods, further demonstrating advantages and potential limitations of the PIE approach. The developed framework can be naturally extended to multiple spatial dimensions and, potentially, to nonlinear problems.

Vlasov-Fokker-Planck-Maxwell simulations for plasmas in inertial confinement fusion

This work presents a code to simulate collisions and laser-plasma interactions of multiple-species plasmas by solving 1D3V Vlasov-Fokker-Planck-Maxwell equations. The distribution functions of all species are expanded into spherical harmonic series of arbitrary order. Each electron or ion species possesses its distinct and suitable velocity mesh and the number of harmonics. Collisions between different ion species are considered and treated with the Fokker-Planck collision term. The code employs the total variation diminishing (TVD) scheme to avoid numerical instabilities in the region of steep density, rarefied plasma-vacuum interface, and non-periodic boundary conditions, which makes it possible to simulate cases that are close to actual physical scenes. The number of particles is globally conserved for each species, the energy for each species is conserved for collisions between the same species, and total energy is conserved for collisions between different species.

Comparison between periodic and non-periodic boundary conditions in the multi-particle finite element modelling of ductile powders

In recent years, the multi-particle finite element method (MPFEM) has demonstrated its suitability for the micromechanical modelling of granular systems made up of highly deformable particles. This method combines the advantages of the finite element method to compute particles’ deformations and of the discrete element method to simulate particles’ interactions. Being computationally expensive, its main drawback is the limitation of the number of particles which can be included in a simulation. However, using a multi-scale approach, it is possible to deduce mesoscopic material properties from the simulation of a relatively small number of particles within an elementary volume, through appropriate averaging techniques. Such simulations are significantly influenced by the boundary conditions (BCs) applied. Periodic BCs are commonly admitted to be the most accurate. However, they are technically rather difficult to implement in the MPFEM because of the multiple contacts which need to be handled in the model. As a result, simplified BCs involving for example, rigid walls, remain used. This study analyses the effect of different types of BCs on the simulated mechanical response of a numerical granular sample, under quasi-static loading. Two different techniques for implementing full or simplified periodic BCs, introduced by Schmidt et al. [1] and Loidolt et al. [2], respectively, were compared with simpler, non-periodic BCs. In the comparison, the same initial microstructure was used; it consisted of an assembly of 50 spherical particles with a periodic topology. The results suggest that considering the additional computational cost induced by the implementation of multi-point constraints, the advantage brought by periodic BCs is relatively limited. The study also highlights the differences between BC types and provides interpretations relative to the particularities of the numerical method used.

Towards Digital Twins of Plasmonic Sensors: Constructing the Complex Numerical Model of a Plasmonic Sensor Based on Hexagonally Arranged Gold Nanoparticles.

In this work, we aim to design the digital twin of a plasmonic sensor based on hexagonally arranged ellipsoidal gold nanoparticles fixed to a glass substrate. Based on electron microscopy images of three experimentally realized nanoparticle arrangement types, we constructed numerical models in environments based on finite element method (FEM) and boundary element method (BEM), namely COMSOL Multiphysics for FEM and the MNPBEM Matlab Toolbox for BEM. Models with nonperiodic and periodic boundary conditions with different unit cells were constructed to study the plasmonic behavior of both the single ellipsoidal particles and the hexagonal nanoparticle arrangements. The effect of the geometrical parameters, namely the interparticle distance, the nanoparticle diameter and thickness, on the resulting LSPR peak positions and bulk refractive index sensitivities were studied in detail, also taking into account the effect of the SiO2 substrate (pillars) under the ellipsoidal particles. We have demonstrated that by optimizing the models, the LSPR peak positions (and sensitivities) can match the experimentally measured values within 1 nm (nm/RIU) precision. The comparison of simulation conditions and the detailed discussion of the effect of the geometrical parameters and used gold dielectric functions on the obtained sensitivities can be very beneficial for the optimization of plasmonic sensor constructions through numerical simulations.

Existence Results of Langevin Equations with Caputo–Hadamard Fractional Operator

In this manuscript, we deal with a nonlinear Langevin fractional differential equation that involves the Caputo–Hadamard and Caputo fractional operators, with nonperiodic and nonlocal integral boundary conditions. The results presented in this study establish the existence, uniqueness, and Hyers–Ulam (HU) stability of the solution to the proposed equation. We achieved our main result by using the Banach contraction mapping principle and Krasonoselskii’s fixed point theorem. Furthermore, we introduce an application to demonstrate the validity of the results of our findings.

Chemical Bonding in Large Systems Using Projected Population Analysis from Real-Space Density Functional Theory Calculations.

We present an efficient and scalable computational approach for conducting projected population analysis from real-space finite-element (FE)-based Kohn-Sham density functional theory calculations (DFT-FE). This work provides an important direction toward extracting chemical bonding information from large-scale DFT calculations on materials systems involving thousands of atoms while accommodating periodic, semiperiodic, or fully nonperiodic boundary conditions. Toward this, we derive the relevant mathematical expressions and develop efficient numerical implementation procedures that are scalable on multinode CPU architectures to compute the projected overlap and Hamilton populations. The population analysis is accomplished by projecting either the self-consistently converged FE discretized Kohn-Sham orbitals or the FE discretized Hamiltonian onto a subspace spanned by a localized atom-centered basis set. The proposed methods are implemented in a unified framework within the DFT-FE code where the ground-state DFT calculations and the population analysis are performed on the same FE grid. We further benchmark the accuracy and performance of this approach on representative material systems involving periodic and nonperiodic DFT calculations with LOBSTER, a widely used projected population analysis code. Finally, we discuss a case study demonstrating the advantages of our scalable approach to extract the quantitative chemical bonding information of hydrogen chemisorbed in large silicon nanoparticles alloyed with carbon, a candidate material for hydrogen storage.

On the analyticity of the pressure for a non-ideal gas with high density boundary conditions

We consider a continuous system of classical particles confined in a cubic box Λ interacting through a stable and finite range pair potential with an attractive tail. We study the Mayer series of the grand canonical pressure of the system pΛω(β,λ) at inverse temperature β and fugacity λ in the presence of boundary conditions ω belonging to a very large class of locally finite particle configurations. This class of allowed boundary conditions is the basis for any probability measure on the space of locally finite particle configurations satisfying the Ruelle estimates. We show that the pΛω(β,λ) can be written as the sum of two terms. The first term, which is analytic and bounded as the fugacity λ varies in a Λ-independent and ω-independent disk, coincides with the free-boundary-condition pressure in the thermodynamic limit. The second term, analytic in a ω-dependent convergence radius, goes to zero in the thermodynamic limit. As far as we know, this is the first rigorous analysis of the behavior of the Mayer series of a non-ideal gas subjected to non-free and non-periodic boundary conditions in the low-density/high-temperature regime when particles interact through a non-purely repulsive pair potential.

Quantum mechanics/fluctuating charge calculations for absorption spectra of aqueous green fluorescent protein chromophore

AbstractWe applied the quantum mechanics/fluctuating charges (QM/FQ) method to simulate the absorption spectra of three protonated forms of p‐hydroxybenzylidene imidazolone (p‐HBDI) in water. Configurations of solute‐solvent were generated from molecular dynamics (MD) simulation within the context of a hybrid scheme in which solute and solvents were treated at QM and molecular mechanics, respectively. Nonperiodic spherical boundary condition was used. To examine the influence on simulated spectra coming from the geometrical relaxation of solute, the MD simulations were carried out for two cases: frozen and flexible molecular geometry of solute. As a result of our calculations, the simulations using the flexible solute's structure delivered vertical excitation energies closer to experimental data than those of a frozen solute, especially for the neutral case. For spectral broadening, changing from fixed geometry of solute to a flexible one led to a significant increase for both neutral and anionic forms of p‐HBDI, but no effect happened for the cationic one.

Existence and uniqueness of non-periodic solutions to boundary value problems for discrete fractional difference equations with uncertainty

In this study, we introduce discrete interval fractional difference equations subject to non-periodic boundary conditions. We obtain two types of solutions for these problems under the generalized Hukuhara difference. Then, we present the explicit expressions of each type of solutions for the convenience of applicability. Further, we investigate the necessary and sufficient conditions which guarantee the existence and uniqueness of a non-periodic solution of each specific type by applying the Banach contraction mapping principle. Finally, we provide an example in order to illustrate the main result.

A Space-Time Legendre-Petrov-Galerkin Method for Third-Order Differential Equations

In this article, a space-time spectral method is considered to approximate third-order differential equations with non-periodic boundary conditions. The Legendre-Petrov-Galerkin discretization is employed in both space and time. In the theoretical analysis, rigorous proof of error estimates in the weighted space-time norms is obtained for the fully discrete scheme. We also formulate the matrix form of the fully discrete scheme by taking appropriate test and trial functions in both space and time. Finally, extensive numerical experiments are conducted for linear and nonlinear problems, and spectral accuracy is derived for both space and time. Moreover, the numerical results are compared with those computed by other numerical methods to confirm the efficiency of the proposed method.

Evaluation of computational homogenization methods for the prediction of mechanical properties of additively manufactured metal parts

It is well known that the strongly location-dependent microstructures observed in metal parts made using additive manufacturing (AM) processes differ from those found in components produced via traditional manufacturing processes. This is primarily because the microstructures in AM parts strongly depend on spatially-varying cooling rates that are caused by several factors including part geometry and proximity to the build plate. Consequently, it is necessary to take a fresh look into methods used for calculating resulting mechanical properties, as the increased spatial resolution that must be applied to the description of properties of AM parts calls for vast improvements in computational efficiency. Computational homogenization methods are employed for the calculation of these mechanical properties based on the polycrystalline microstructures typically encountered in metallic materials. Such calculations that enable the description of properties as a function of position increase the accuracy of a vital link in the structure–process–property–performance continuum that falls within the Integrated Computational Materials Engineering (ICME) paradigm. In this work we describe and critically review six of these methods and their application to AM microstructures. We find that the Fast Fourier Transform (FFT) method and the Finite Element Method (FEM) are the optimal choices based on several factors including accuracy, efficiency, and applicability to polycrystalline microstructures. Provided the microstructure is amenable to the use of uniform grids and the assumption of periodic boundary conditions, the FFT method has greater computational efficiency. Where unstructured meshes, adaptive remeshing and/or non-periodic boundary conditions are desired, the FEM is the method of choice. Our recommendations are equally applicable to functionally graded AM parts where site-specific microstructures are engineered using multiple materials or different process parameters. They can also be utilized for other material systems and circumstances where increased accuracy is achieved by describing mechanical properties as a function of location.

On equilibrating non-periodic molecular dynamics samples for coupled particle-continuum simulations of amorphous polymers

In the context of fracture simulations of polymers, the molecular mechanisms in the vicinity of the crack tip are of particular interest. Nevertheless, to keep the computational cost to a minimum, a coarser resolution must be used in the remaining regions of the numerical sample. For the specific case of amorphous polymers, the Capriccio method bridges the gap between the length and time scales involved at the different levels of resolution by concurrently coupling molecular dynamics (MD) with the finite element method (FEM). Within the scope of the Capriccio approach, the coupling to the molecular MD region introduces non-periodic, so-called stochastic boundary conditions (SBC). In similarity to typical simulations under periodic boundary conditions (PBC), the SBC MD simulations must reach an equilibrium state before mechanical loads are exerted on the coupled systems. In this contribution, we hence extensively study the equilibration properties of non-periodic MD samples using the Capriccio method. We demonstrate that the relaxation behavior of an MD-FE coupled MD domain utilizing non-periodic boundary conditions is rather insensitive to the specific coupling parameters of the method chosen to implement the boundary conditions. The behavior of an exemplary system equilibrated with the parameter set considered as optimal is further studied under uniaxial tension and we observe some peculiarities in view of creep and relaxation phenomena. This raises important questions to be addressed in the further development of the Capriccio method.

Recent advancement of entropy split methods for compressible gas dynamics and MHD

The entropy splitting of the compressible Euler flux derivatives based on Harten’s entropy function Harten (1983), Gerritsen and Olsson (1996), Yee et al. (2000) in conjunction with classical spatial central and DRP (dispersion relation-preserving) finite discretizations with summation-by-parts (SBP) operators Strand (1994) for both periodic and non-periodic boundary conditions is proven to be entropy conservative and stable for a thermally-perfect gas by Sjögreen and Yee (2019), Sjögreen et al. (2020), Sjögreen and Yee (2021). The various high order methods resulting from applying classical spatial central, DRP and Padé (compact) methods to the split form of the Euler flux derivative are referred to as entropy split methods as a function of the splitting parameter β. These entropy split methods are entropy conserving and stable but they are usually not conservative numerical methods without additional reformulation; e.g., those proposed in Sjögreen and Yee (2021).This is an expanded version of Sjögreen and Yee (2022) and is intended to present a more in depth study for both the compressible gas dynamics and ideal MHD equations. Here the same Harten entropy function is used for the ideal magnetohydrodynamic (MHD) governing equation set. This approach was not examined in great depth by Sjögreen & Yee and Yee & Sjögreen in two conference proceedings papers Sjögreen and Yee (2022), Yee and Sjögreen (2022), which also included the high order Padé (compact) spatial discretizations Hirsh(1975). For the extension of the entropy split method to the ideal MHD, the Godunov symmetrizable non-conservative form of the formulation is used. Due to the non-conservative portion (commonly referred to as a nonlinear source term vector) of the symmetrizable system Godunov (1972), there are variants in formulating the entropy split methods. Two different numerical treatments for these particular source terms of the symmetrizable MHD governing equation set are presented.Systematic 3D formulation in curvilinear grids with the corresponding numerical fluxes among method comparisons for the Euler and ideal MHD equations is included. The curvilinear formulation includes high order classical central, DRP and compact spatial discretizations. For readers interested in the implementation of these methods into their computer code, it is hope that these formulations and the corresponding numerical fluxes in 3D curvilinear grids will be helpful.The comparative studies concentrate on the Tadmor-type of discrete entropy conserving Tadmor (2003), momentum conserving Ducros et al. (2000), kinetic energy preserving Kennedy and Gruber (2008), Pirozzoli (2010), Coppola et al. (2019), Yee et al., Sjögreen & Yee entropy split methods Yee et al.(2000), Sjögreen and Yee (2018), Sjögreen and Yee (2019), Sjögreen et al. (2020), Sjögreen and Yee (2021), as well as the combination of these physical-preserving methods Ranocha (2020), Yee and Sjögreen (2020). All of these methods are not only preserved certain physical properties of the chosen governing equations but are also known to either improve numerical stability, and/or minimize aliasing errors in long time integration of turbulent flow computations without the aid of added numerical dissipation for selected compressible flow types. Extensive error norm comparison with grid refinement were performed to show how well this methods conserve the entropy, momentum and mass, and preserve the kinetic energy for long time integration of the various flows. In general the Tadmor-type entropy conserving methods are at least twice the CPU per time step than the rest of the skew-symmetric splitting methods.