Article
Chemistry, Multidisciplinary
Samet Y. Kadioglu, Ersin Ozugurlu
Summary: This paper introduces a Jacobian-free Newton-Krylov (JFNK) method with effective preconditioning strategies to solve a diffusion-based tumor growth model, also known as the Fisher-Kolmogorov partial differential equation (PDE). The time discretization is based on the backward Euler and the Crank-Nicolson methods, with second-order centered finite differencing for the spatial derivatives. Two physics-based preconditioners associated with the first- and second-order temporal discretizations are introduced. Convergence tables and graphs are used to verify the theoretical time and spatial accuracies of the numerical scheme under different computational settings. Efficiency studies show the excellent performance of the newly proposed preconditioning strategies, significantly reducing the average number of GMRES and Newton iterations when the preconditioners are turned on.
APPLIED SCIENCES-BASEL
(2023)
Article
Computer Science, Interdisciplinary Applications
Jie Fan, Junli Gou, Jun Huang, Jianqiang Shan
Summary: Jacobian-Free Newton-Krylov (JFNK) method is a stable and high-efficiency method for solving the multi-physics coupling problem in nuclear reactor modeling and simulation. In this research, a fully-implicit numerical algorithm was proposed to solve the two-fluid two-phase flow model based on the JFNK method. The algorithm was validated through various experiments and compared with the semi-implicit numerical algorithm, showing higher efficiency and accuracy in practical simulations.
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS
(2023)
Article
Computer Science, Interdisciplinary Applications
Martin Campos Pinto, Valentin Pages
Summary: This article presents a new charge- and energy-conserving semi-implicit method (ChECSIM) for the Vlasov-Maxwell system. It improves Lapenta's energy-conserving semi-implicit method by adding appropriate charge-conserving current deposition terms and an explicit correction step, resulting in a scheme that is free of nonlinear iterations and preserves both energy and charge exactly.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Zhuoning Li, Zhenli Xu, Zhiguo Yang
Summary: In this paper, we present an efficient and accurate energy-conserving implicit particle-in-cell (PIC) algorithm for simulating complex plasma systems with multiple physical scales.
JOURNAL OF COMPUTATIONAL PHYSICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Eirik Endeve, Cory D. Hauck
Summary: The micro-macro (mM) decomposition approach is applied to the numerical solution of the Vlasov-Poisson-Lenard-Bernstein (VPLB) system, which is relevant for plasma physics applications. The mM approach decomposes the kinetic distribution function into a local equilibrium distribution and a microscopic distribution, and combines the discontinuous Galerkin (DG) method and implicit-explicit (IMEX) time integration to design numerical methods. The resulting mM method maintains the constraint of the system and demonstrates good performance compared to a corresponding DG-IMEX method solving directly for the distribution function f.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Astronomy & Astrophysics
Fabio Bacchini
Summary: This paper presents a novel Relativistic Semi-Implicit Method (RelSIM) for particle-in-cell (PIC) simulations of astrophysical plasmas. The authors demonstrate through various tests that the RelSIM method can produce more accurate results in certain cases.
ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES
(2023)
Article
Physics, Multidisciplinary
ZhaoHong Han, Gang Bao
Summary: The Critical Period Hypothesis in second language acquisition research has sparked intense debates on theoretical, methodological, and practical grounds, leading to contradictory findings and competing explanations.
FRONTIERS IN PHYSICS
(2023)
Article
Physics, Mathematical
Lijie Ji, Zhiguo Yang, Zhuoning Li, Dong Wu, Shi Jin, Zhenli Xu
Summary: In this paper, an asymptotic-preserving and energy-conserving (APEC) Particle-In-Cell (PIC) algorithm is developed for the Vlasov-Maxwell system. This algorithm ensures consistent and stable discretization of the quasi-neutral limit of the continuous model while maintaining Gauss's law and energy conservation. The method is shown to accurately and stably simulate kinetic and quasi-neutral regimes, making it promising for complex plasma system simulations.
JOURNAL OF MATHEMATICAL PHYSICS
(2023)
Article
Physics, Particles & Fields
Daniel N. Blaschke, Francois Gieres
Summary: In classical gauge field theories, the kinematical energy momentum vector and Dirac brackets need to be considered, instead of Poisson brackets. The proton spin involves the angular momentum vector of gluons, which requires proper treatment.
Article
Physics, Fluids & Plasmas
G. Sary, L. Gremillet
Summary: In this paper, a novel 2D reduced numerical model for stimulated Raman scattering (SRS) in laser fusion plasmas is presented. It couples envelope equations for electromagnetic fields with a hybrid description of the electron species. The model accurately reproduces linear Landau damping and trapped-particle instabilities, and shows good agreement with experimental data.
PHYSICS OF PLASMAS
(2022)
Article
Physics, Nuclear
Kadir Ocalan
Summary: This study investigates the impact of lepton transverse momentum threshold on boson charge asymmetry predictions, showing good agreement with experimental data and suggesting further research on PDF models and parton distribution functions.
Article
Mathematics, Applied
Harsha Hutridurga, Krishan Kumar, Amiya K. Pani
Summary: In this paper, a semi-discrete numerical scheme for the approximation of the periodic Vlasov-viscous Burgers' system is proposed and analyzed. The scheme utilizes discontinuous Galerkin approximations for the Vlasov equation and local discontinuous Galerkin approximations for the viscous Burgers' equation, both using generalized numerical fluxes. The proposed scheme is proven to be mass and momentum conservative, and optimal rates of convergence are derived for smooth compactly supported initial data using generalized Gauss-Radau projections. Computational results confirm the theoretical findings.
JOURNAL OF SCIENTIFIC COMPUTING
(2023)
Article
Computer Science, Interdisciplinary Applications
G. Chen, L. Chacon, L. Yin, B. J. Albright, D. J. Stark, R. F. Bird
JOURNAL OF COMPUTATIONAL PHYSICS
(2020)
Article
Computer Science, Interdisciplinary Applications
Don Daniel, William T. Taitano, Luis Chacon
COMPUTER PHYSICS COMMUNICATIONS
(2020)
Article
Computer Science, Interdisciplinary Applications
L. F. Ricketson, L. Chacon
JOURNAL OF COMPUTATIONAL PHYSICS
(2020)
Article
Computer Science, Interdisciplinary Applications
S. E. Anderson, W. T. Taitano, L. Chacon, A. N. Simakov
JOURNAL OF COMPUTATIONAL PHYSICS
(2020)
Article
Computer Science, Interdisciplinary Applications
D. C. Barnes, L. Chacon
Summary: Finite-grid instabilities in particle-in-cell plasma simulation algorithms arise from interpolation errors, but strictly energy-conserving algorithms offer enhanced stability. These algorithms are stable for stationary plasmas and have a benign stability threshold for drifting plasmas with finite temperatures. Momentum-conserving algorithms lack this stability threshold and become unstable beyond a certain cell size compared to the Debye length.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Computer Science, Interdisciplinary Applications
W. T. Taitano, B. D. Keenan, L. Chacon, S. E. Anderson, H. R. Hammer, A. N. Simakov
Summary: An algorithm for numerical simulation of inertial confinement fusion (ICF) capsule implosions using a phase-space adaptive Eulerian Vlasov-Fokker-Planck (VFP) approach in spherical geometry is presented. Mesh motion is transformed into computational coordinates to ensure conservation and accuracy of the solution. The strategy includes a novel nonlinear stabilization method for spatially and temporally varying dynamics in spherically imploding systems.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Physics, Fluids & Plasmas
Benjamin J. Sturdevant, S. Ku, L. Chacon, Y. Chen, D. Hatch, M. D. J. Cole, A. Y. Sharma, M. F. Adams, C. S. Chang, S. E. Parker, R. Hager
Summary: In XGC, a fully implicit particle-in-cell method has been implemented to handle the v(parallel to)-formalism of electromagnetic gyrokinetics. By choosing this formalism, nonphysical skin terms in Ampere's law are avoided, which eliminates the cancellation problem in the p(parallel to)-formalism. The algorithm demonstrates numerical stability and accurate dispersive properties through tests on shear Alfven wave propagation and ITG-KBM transition cases, and comparison with other delta f gyrokinetic codes/schemes.
PHYSICS OF PLASMAS
(2021)
Article
Computer Science, Interdisciplinary Applications
Paul Tranquilli, Lee Ricketson, Luis Chacon
Summary: This paper introduces a rigorous method for verifying electrostatic particle-in-cell codes, focusing on the examination of errors of grid quantities. The method is shown to be non-intrusive and able to detect order reduction due to incorrect implementation, providing a more efficient and effective approach compared to previous methods. Numerical results support the theoretical findings presented in the paper.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Computer Science, Interdisciplinary Applications
L. Chacon, D. Daniel, W. T. Taitano
Summary: The proposed numerical scheme is an asymptotic-preserving, uniformly convergent algorithm for simulating runaway electrons in tokamak devices. It is simple and efficient, providing accurate results regardless of plasma collisionality.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Benjamin J. Sturdevant, Luis Chacon
Summary: Finite-grid instabilities in momentum-conserving particle-in-cell (PIC) methods applied to gyrokinetic models are known to impose limitations on resolving the Debye length. This paper presents a simple reformulation of the discrete equations that eliminates this instability for practical purposes. Numerical dispersion analyses show that the reformulated scheme is numerically stable for stationary plasmas at any spatial resolution. This reformulation is particularly useful for codes with complicated meshes and can help explain the success of previously considered methods to remove particle instabilities.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Computer Science, Interdisciplinary Applications
A. Stanier, L. Chacon
Summary: The hybrid kinetic-ion fluid-electron plasma model is a widely used method for studying complex multi-scale problems in space and laboratory plasma physics. In this paper, a novel conservative scheme based on implicit particle-in-cell techniques is extended to arbitrary coordinate systems using curvilinear maps. The scheme is shown to conserve total energy and momentum for arbitrary curvilinear meshes, and its effectiveness is demonstrated through numerical simulations on different curvilinear meshes.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Qi Tang, Luis Chacon, Tzanio Kolev, John N. Shadid, Xian-Zhu Tang
Summary: This paper presents a high-order stabilized finite-element algorithm based on the MFEM finite element library for solving the reduced visco-resistive MHD equations. The use of physics-based preconditioning strategy and adaptive mesh refinement scheme is also discussed. Experimental results demonstrate the accuracy, efficiency, and scalability of the implicit scheme in the presence of large scale disparity.
JOURNAL OF COMPUTATIONAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
L. Yin, T. B. Nguyen, G. Chen, L. Chacon, D. J. Stark, L. Green, B. M. Haines
Summary: This study examines the nonlinear physics of cross-beam energy transfer (CBET) for multi-speckled laser beams using large-scale particle-in-cell simulations. The time-dependent growth and saturation of CBET involve complex, nonlinear ion and electron dynamics, including ion trapping-induced enhancement and detuning, ion acoustic wave nonlinearity, oblique forward stimulated Raman scattering, and backward stimulated Brillouin scattering. A nonlinear CBET model is constructed to accurately predict the CBET gain and energy deposition into the plasma.
PHYSICS OF PLASMAS
(2023)
Article
Nanoscience & Nanotechnology
L. Spinicci, D. Bonfiglio, L. Chacon, S. Cappello, M. Veranda
Summary: This study presents a nonlinear verification benchmark between the 3D MHD codes SPECYL and PIXIE3D. The focus is on the recently implemented thin-shell resistive-wall boundary conditions in both codes. The results demonstrate excellent agreement between the codes in studying the linear growth and nonlinear saturation of external kink modes in tokamak and reversed-field pinch magnetic configurations.
Article
Physics, Fluids & Plasmas
S. E. Anderson, L. Chacon, W. T. Taitano, A. N. Simakov, B. D. Keenan
Summary: The simulations of strong, steady-state collisional planar plasma shocks with fully kinetic ions and electrons were independently confirmed by two fully kinetic codes. While kinetic electrons do not fundamentally change the shock structure compared to fluid electrons, there is an appreciable rearrangement of the preheat layer, associated with nonlocal electron heat transport effects. Good agreement was found with nonlocal electron heat-flux closures proposed in the literature.
Article
Computer Science, Interdisciplinary Applications
Usman Riaz, E. Seegyoung Seol, Robert Hager, Mark S. Shephard
Summary: The accurate representation and effective discretization of a problem domain into a mesh are crucial for achieving high-quality simulation results and computational efficiency. This work presents recent developments in extending an automated tokamak modeling and meshing infrastructure to better support the near flux field following meshing requirements of the XGC Gyro-kinetic Code.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Zhenglu Li, Gabriel Antonius, Yang-Hao Chan, Steven G. Louie
Summary: This article presents a workflow for practical calculations of electron-phonon coupling and includes the effect of many-electron correlations using GW perturbation theory. The workflow combines different software packages to enable accurate calculations at the level of quasiparticle band structures.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Akihiro Koide, Sara Rabouli, Pierre Le Meur, Sylvain Tricot, Philippe Schieffer, Didier Sebilleau, Calogero R. Natoli
Summary: We present the MsSpec Atomic Scattering Amplitude Package (MASAP), which includes a computation program and a graphical interface for generating atomic scattering amplitude (ASA). The study investigates the applicability of plane wave (PW) and curved spherical wave (SW) scattering in describing electron propagation. The results show that the imaginary part of the optical potential enhances the elastic scattering in the forward direction but causes damping effects in other directions.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
A. Bagci, Gustavo A. Aucar
Summary: The electron repulsion integrals over Slater-type orbitals with non-integer principal quantum numbers are investigated in this study. These integrals are important in calculations of many-electron systems. New relationships free from hyper-geometric functions are derived to simplify the calculations. With the use of auxiliary functions and straightforward recurrence relationships, these integrals can be efficiently computed, providing initial conditions for the evaluation of expectation values and potentials.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Andrzej Daniluk
Summary: RHEED_DIFF_2D is an open-source software for qualitative numerical simulations of RHEED oscillation intensity changes with layer deposition, used for interpreting heteroepitaxial structures under different scattering crystal potential models.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Niklas Kuehl, Hendrik Fischer, Michael Hinze, Thomas Rung
Summary: The article presents a strategy and algorithm for simulation-accompanying, incremental Singular Value Decomposition (SVD) for time-evolving, spatially parallel discrete data sets. The proposed method improves computational efficiency by introducing a bunch matrix, resulting in higher accuracy and practical applicability.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Jose M. Rodriguez-Borbon, Xian Wang, Adrian P. Dieguez, Khaled Z. Ibrahim, Bryan M. Wong
Summary: This paper presents an open-source software package called TRAVOLTA for massively parallelized quantum optimal control calculations on GPUs. The TRAVOLTA package is an improvement on the previous NIC-CAGE algorithm and incorporates algorithmic improvements for faster convergence. Three different variants of GPU parallelization are examined to evaluate their performance in constructing optimal control fields in various quantum systems. The benchmarks show that the GPU-enhanced TRAVOLTA code produces the same results as previous CPU-based algorithms but with a speedup of more than ten times. The GPU enhancements and algorithmic improvements allow large quantum optimal control calculations to be efficiently executed on modern multi-core computational hardware.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Weijie Hua
Summary: This work introduces a program called MCNOX for computing and analyzing ultrafast nonlinear X-ray spectra. It is designed for cutting-edge applications in photochemistry/photophysics enabled by X-ray free-electron lasers and high harmonic generation light sources. The program can calculate steady-state X-ray absorption spectroscopy and three types of ultrafast nonlinear X-ray spectra, and it is capable of identifying major electronic transitions and providing physical and chemical insights from complex signals.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Leandro Benatto, Omar Mesquita, Lucimara S. Roman, Rodrigo B. Capaz, Graziani Candiotto, Marlus Koehler
Summary: Photoluminescence Quenching Simulator (PLQ-Sim) is a user-friendly software for studying the dynamics of photoexcited states at the interface between organic semiconductors. It provides important information on organic photovoltaic and photothermal devices and calculates transfer rates and quenching efficiency.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Dongming Li, James Kestyn, Eric Polizzi
Summary: This study introduces a practical and efficient approach to calculate the all-electron full potential band structure in real space using a finite element basis. Instead of the k-space method, this method solves the Kohn-Sham equation self-consistently within a larger finite system enclosing the unit-cell. Non-self-consistent calculations are then performed in the Brillouin zone to obtain the band structure results, which are found to be in excellent agreement with the pseudopotential k-space method. Furthermore, the study successfully observes the band bending of core electrons.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
R. Kleiber, M. Borchardt, R. Hatzky, A. Koenies, H. Leyh, A. Mishchenko, J. Riemann, C. Slaby, J. M. Garcia-Regana, E. Sanchez, M. Cole
Summary: This paper describes the current state of the EUTERPE code, focusing on the implemented models and their numerical implementation. The code is capable of solving the multi-species electromagnetic gyrokinetic equations in a three-dimensional domain. It utilizes noise reduction techniques and grid resolution transformation for efficient computation. Additionally, various hybrid models are implemented for comparison and the study of plasma-particle interactions. The code is parallelized for high scalability on multiple CPUs.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Pengliang Yang
Summary: This paper presents an open source software called SMIwiz, which combines seismic modelling, reverse time migration, and full waveform inversion into a unified computer implementation. SMIwiz supports both 2D and 3D simulations and provides various computational recipes for efficient calculation. Its independent processing and batchwise job scheduling ensure scalability, and its viability is demonstrated through applications on benchmark models.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Christian Tantardini, Miroslav Ilias, Matteo Giantomassi, Alexander G. Kvashnin, Valeria Pershina, Xavier Gonze
Summary: Material discovery has been an active research field, and this study focuses on developing pseudopotentials for actinides and super-heavy elements. These pseudopotentials are crucial for accurate first-principles calculations and simulations.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
S. Blanes, F. Casas, C. Gonzalez, M. Thalhammer
Summary: This paper explores the extension of modified potential operator splitting methods to specific classes of nonlinear evolution equations. Numerical experiments confirm the advantages of the proposed fourth-order modified operator splitting method over traditional splitting methods in dealing with Gross-Pitaevskii systems.
COMPUTER PHYSICS COMMUNICATIONS
(2024)
Article
Computer Science, Interdisciplinary Applications
Siegfried Kaidisch, Thomas U. Hilger, Andreas Krassnigg, Wolfgang Lucha
Summary: Motivated by a use case in theoretical hadron physics, this paper revisits an application of a pole-sum fit to dressing functions of a confined quark propagator. Specifically, it investigates approaches to determine the number and positions of singularities closest to the origin for a function known numerically on a specific grid on the positive real axis. Comparing the efficiency of standard techniques to a pure artificial-neural-network approach and a combination of both, it finds that the combined approach is more efficient. This approach can be applied to similar situations where the positions of poles need to be estimated quickly and reliably from real-axis information alone.
COMPUTER PHYSICS COMMUNICATIONS
(2024)