Computer Physics Communications最新文献

{"title":"POLARIS: The POLArized RadIation Simulator for Mie scattering in optically thick dusty plasmas","authors":"Julia Kobus ,&nbsp;Stefan Reißl ,&nbsp;Moritz Lietzow-Sinjen ,&nbsp;Alexander Bensberg ,&nbsp;Andreas Petersen ,&nbsp;Franko Greiner ,&nbsp;Sebastian Wolf","doi":"10.1016/j.cpc.2025.109645","DOIUrl":"10.1016/j.cpc.2025.109645","url":null,"abstract":"<div><div>POLARIS is a 3D Monte-Carlo radiative transfer code written in C++ for simulating the Mie scattering of laser light in optically thick nanodusty plasmas. Originally developed for astrophysical applications, POLARIS has been adapted to address the specific needs of the plasma physics community. To achieve this, a given number of photon packages characterized by their traveling direction <span><math><mover><mrow><mi>d</mi></mrow><mrow><mo>→</mo></mrow></mover></math></span>, wavelength <em>λ</em>, intensity, and polarization state in terms of the Stokes vector <span><math><mover><mrow><mi>S</mi></mrow><mrow><mo>→</mo></mrow></mover></math></span> is generated to mimic the emission of a laser source with a Gaussian intensity distribution. These photon packages are then tracked along their probabilistic paths through the particle cloud, with scattering processes determined stochastically based on probability density distributions derived from the optical properties of the dust particles. POLARIS allows simulations for arbitrary wavelengths and grain sizes, as long as the far-field approximation holds. This paper introduces this adapted version of POLARIS to the plasma physics community, highlighting its capabilities for modeling light scattering in dusty plasmas and serving as a comprehensive reference for its application. In doing so, POLARIS provides a powerful tool for the in-situ analysis of optically thick dusty plasmas.</div></div><div><h3>Program summary</h3><div><em>Program Title:</em> POLARIS</div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/8d3jm3x29t.1</span><svg><path></path></svg></span></div><div><em>Developer's repository link:</em> <span><span>https://github.com/polaris-MCRT/POLARIS</span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> GPLv3</div><div><em>Programming language:</em> C++, Python 3</div><div><em>Nature of problem:</em> Simulating Mie scattering in dense dusty plasmas to enable in-situ analysis of these systems.</div><div><em>Solution method:</em> Tracing the random paths of photon packages through a three dimensional grid filled with dust particles making stochastic decisions on scattering processes based on probability density distributions given by the optical properties of the dust particles.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109645"},"PeriodicalIF":7.2,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A robust fourth-order finite-difference discretization for the strongly anisotropic transport equation in magnetized plasmas","authors":"L. Chacón,&nbsp;J. Hamilton,&nbsp;N. Krasheninnikova","doi":"10.1016/j.cpc.2025.109646","DOIUrl":"10.1016/j.cpc.2025.109646","url":null,"abstract":"<div><div>We propose a second-order temporally implicit, fourth-order-accurate spatial discretization scheme for the strongly anisotropic heat transport equation characteristic of hot, fusion-grade plasmas. Following Du Toit et al. (2018) <span><span>[17]</span></span>, the scheme transforms mixed-derivative diffusion fluxes (which are responsible for the lack of a discrete maximum principle) into nonlinear advective fluxes, amenable to nonlinear-solver-friendly monotonicity-preserving limiters. The scheme enables accurate multi-dimensional heat transport simulations with up to seven orders of magnitude of heat-transport-coefficient anisotropies with low cross-field numerical error pollution and excellent algorithmic performance, with the number of linear iterations scaling very weakly with grid resolution and grid anisotropy, and scaling with the square-root of the implicit timestep. We propose a multigrid preconditioning strategy based on a lower-order approximation that renders the scheme efficient and scalable under grid refinement. Several numerical tests are presented that display the expected spatial convergence rates and strong algorithmic performance, including fully nonlinear magnetohydrodynamics simulations of kink instabilities in a Bennett pinch in 2D helical geometry and of ITER in 3D toroidal geometry.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109646"},"PeriodicalIF":7.2,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143886149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Minimal autocorrelation in hybrid Monte Carlo simulations using exact Fourier acceleration","authors":"Johann Ostmeyer ,&nbsp;Pavel Buividovich","doi":"10.1016/j.cpc.2025.109624","DOIUrl":"10.1016/j.cpc.2025.109624","url":null,"abstract":"<div><div>The hybrid Monte Carlo (HMC) algorithm is a ubiquitous method in computational physics with applications ranging from condensed matter to lattice QCD and beyond. However, HMC simulations often suffer from long autocorrelation times, severely reducing their efficiency. In this work two of the main sources of autocorrelations are identified and eliminated. The first source is the sampling of the canonical momenta from a sub-optimal normal distribution, the second is a badly chosen trajectory length. Analytic solutions to both problems are presented and implemented in the exact Fourier acceleration (EFA) method. It completely removes autocorrelations for near-harmonic potentials and consistently yields (close-to-) optimal results for numerical simulations of the Su-Schrieffer-Heeger and the Ising models as well as in lattice gauge theory, in some cases reducing the autocorrelation by multiple orders of magnitude. EFA is advantageous for and easily applicable to any HMC simulation of an action that includes a quadratic part.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109624"},"PeriodicalIF":7.2,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143868630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PENGEOM – A general-purpose geometry package for Monte Carlo simulation of radiation transport in complex material structures (New Version Announcement)","authors":"Julio Almansa ,&nbsp;Francesc Salvat-Pujol ,&nbsp;Gloria Díaz-Londoño ,&nbsp;Artur Carnicer ,&nbsp;Antonio M. Lallena ,&nbsp;Francesc Salvat","doi":"10.1016/j.cpc.2025.109634","DOIUrl":"10.1016/j.cpc.2025.109634","url":null,"abstract":"<div><div>A new version of the code system <span>pengeom</span>, which provides a complete set of tools to handle different geometries in Monte Carlo simulations of radiation transport, is presented. The distribution package consists of a set of Fortran subroutines and a Java graphical user interface that allows building and debugging the geometry-definition file, and producing images of the geometry in two- and three dimensions. A detailed description of these tools is given in the original paper [<em>Comput. Phys. Commun.</em> <strong>199</strong> (2016) 102–113] and in the code manual included in the distribution package. The present new version differs from the previous one in that 1) it implements a more systematic handling of round-off errors, 2) the set of examples has been updated, and 3) it allows including a single voxelized box as a geometry module. With the last optional feature, a Monte Carlo code can readily be used for describing irradiation processes with complex material structures, such as medical treatments.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109634"},"PeriodicalIF":7.2,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143868631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Grover's search meets Ising models: A quantum algorithm for finding low-energy states","authors":"A.A. Zhukov ,&nbsp;A.V. Lebedev ,&nbsp;W.V. Pogosov","doi":"10.1016/j.cpc.2025.109627","DOIUrl":"10.1016/j.cpc.2025.109627","url":null,"abstract":"<div><div>We propose a methodology for implementing Grover's algorithm in the digital quantum simulation of disordered Ising models. The core concept revolves around using the evolution operator for the Ising model as the quantum oracle within Grover's search. This operator induces phase shifts for the eigenstates of the Ising Hamiltonian, with the most pronounced shifts occurring for the lowest and highest energy states. Determining these states for a disordered Ising Hamiltonian using classical methods presents an exponentially complex challenge with respect to the number of spins (or qubits) involved. Within our proposed approach, we determine the optimal evolution time by ensuring a phase flip for the target states. This method yields a quadratic speedup compared to classical computation methods and enables the identification of the lowest and highest energy states (or neighboring states) with a high probability ≲1.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109627"},"PeriodicalIF":7.2,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143868629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"QuantumDNA: A python package for analyzing quantum charge dynamics in DNA and exploring its biological relevance","authors":"Dennis Herb ,&nbsp;Marco Trenti ,&nbsp;Marilena Mantela ,&nbsp;Constantinos Simserides ,&nbsp;Joachim Ankerhold ,&nbsp;Mirko Rossini","doi":"10.1016/j.cpc.2025.109626","DOIUrl":"10.1016/j.cpc.2025.109626","url":null,"abstract":"<div><div>The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based nanotechnology. However, despite significant progress in each of these areas, knowledge often remains inaccessible to researchers in other scientific communities, limiting the broader impact of advances across disciplines. To bridge this gap, we present QuantumDNA, an open-source Python package for simulating DNA charge transfer and excited state dynamics using quantum physical methods. QuantumDNA combines an efficient Linear Combination of Atomic Orbitals (LCAO) approach combined with tight-binding models and incorporates open quantum systems techniques to account for environmental effects. This approach allows for a rapid yet sufficiently accurate analysis of large DNA ensembles, enabling statistical studies of genetic and epigenetic phenomena. To ensure accessibility, the package features a graphical user interface, making it suitable for researchers across disciplines.</div></div><div><h3>Program summary</h3><div><em>Program Title:</em> QuantumDNA</div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/5mw48c7gbb.1</span><svg><path></path></svg></span></div><div><em>Developer's repository link:</em> <span><span>https://github.com/dehe1011/QuantumDNA</span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> BSD 3-clause</div><div><em>Programming language:</em> Python</div><div><em>Nature of the Problem:</em> Over the past 60 years, a variety of advanced simulation methods have been employed to explore charge dynamics of DNA. However, most of these approaches are computationally too expensive for the large-scale statistical screening required in genetics and epigenetics. Therefore, theoretical and computational results are often restricted to specialized fields, limiting their accessibility and reproducibility to researchers across disciplines. <em>Solution Method:</em> QuantumDNA combines computational methods from quantum physics and theoretical chemistry to facilitate high-throughput analysis of DNA charge dynamics with sufficient accuracy. Unlike computationally expensive <em>ab initio</em> methods, it utilizes the efficiency of LCAO and TB models to simulate charge dynamics while considering environmental effects, making simulations more accessible and encouraging interdisciplinary research. <em>Additional comments:</em> QuantumDNA is an open-source package featuring a graphical user interface, tutorial Jupyter notebooks, and a dedicated documentation website. The package also supports CPU parallel computing.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109626"},"PeriodicalIF":7.2,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143886151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bloch-state optimal basis sets: An efficient approach for electronic structure interpolation","authors":"Sasawat Jamnuch ,&nbsp;John Vinson","doi":"10.1016/j.cpc.2025.109635","DOIUrl":"10.1016/j.cpc.2025.109635","url":null,"abstract":"<div><div>We present an efficient implementation of the <em>k</em>-space interpolation for electronic structure based on the optimal basis method originally proposed by Shirley [Phys. Rev. B <strong>54</strong>, 16,464 (1996)] The method allows interpolation onto any <em>k</em>-point from a minimal set of input density functional theory (DFT) wavefunctions. Numerically interpolated eigenvalues have an accuracy within 0.01 eV with very small computational cost. The interpolated wavefunctions were used in the Bethe-Salpeter equation to simulate x-ray absorption spectra of different systems, ranging from small bulk crystals to large intermetallic supercells. The method is extensively tested in terms of verification and accuracy for best practices. The approach is shown to be robust and will greatly help accelerate high-throughput DFT studies.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109635"},"PeriodicalIF":7.2,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143863532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-domain lattice Boltzmann method for mesh refinement with curved boundary interfaces","authors":"MohammadAli Daeian ,&nbsp;Punya Cheema ,&nbsp;W. Spencer Smith ,&nbsp;Zahra Keshavarz-Motamed","doi":"10.1016/j.cpc.2025.109637","DOIUrl":"10.1016/j.cpc.2025.109637","url":null,"abstract":"<div><div>Multi-domain grid refinement is a well-known method for mesh refinement in Lattice Boltzmann Methods (LBM). However, the method in three-dimensional cases is currently limited to problems in which the interface between domains can only be surfaces with straight boundaries, and no 3D multi-domain LBM method is specifically tailored for cases with domain interface on a complex curved boundary. Complex geometries like this are frequently observed in blood flow in cardiovascular systems. In this paper, an LBM multi-domain method was developed for grid refinement with curved boundary interfaces. The proposed method is based on using an interpolative second-order wall boundary condition in conjunction with a new image-based ghost node method for near-wall treatment at the interface. The method was verified to show second-order accuracy in space at the domain interface in a circular Poiseuille flow. The methodology was further employed in three different cases: steady idealized stenosis flow, pulsatile flow in the carotid bifurcation, and pulsatile flow in an intracranial aneurysm. The results were compared to single-resolution simulations for each case. For the resolutions used in these cases, the relative L² norm of the difference between the multi-domain and fine single-resolution simulation had the following values: 0.005 for velocity magnitude at the stenosis center, 0.002 for mass flowrate splitting in the bifurcation, and 0.008 for wall shear stress in peak systole in the aneurysm dome. For these examples, the method demonstrated up to 65 % speedup for the bifurcation simulation and 39 % speedup for the aneurysm simulation compared to single-resolution simulations.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109637"},"PeriodicalIF":7.2,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143894785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FlashSim: A novel particle-in-cell numerical model for vacuum surface flashover simulation based on finite element method","authors":"Hao-Yan Liu ,&nbsp;Guang-Yu Sun ,&nbsp;Yue-Lin Liu ,&nbsp;Shu Zhang ,&nbsp;Chang-Chun Qi ,&nbsp;Sheng Zhou ,&nbsp;Wen-Rui Li ,&nbsp;Guan-Jun Zhang","doi":"10.1016/j.cpc.2025.109625","DOIUrl":"10.1016/j.cpc.2025.109625","url":null,"abstract":"<div><div>In vacuum-dielectric insulation systems, surface flashover is commonly considered as an interfacial breakdown induced by high electric field, posing a significant threat to the stable and safe operation of numerous vacuum equipment. To clarify its development mechanism and propose relevant suppression strategies, a novel Particle-in-Cell (PIC) vacuum surface flashover simulation model, FlashSim, based on finite element method (FEM), is introduced. The model computes the real-time electric field at cathode triple junction (CTJ) where seed electrons are generated. Electron collisions with the dielectric surface, including elastic backscattering, inelastic backscattering, and true secondary electron emission, are considered. Firstly, the flashover simulation with flat dielectric surface and parallel-plate electrodes shows that electric field at CTJ is enhanced due to surface charge accumulation, leading to an increase in field electron emission (FEE). Low-energy (&lt;53 eV) electrons concentrate near the dielectric surface due to positive charging in the dielectric layer, while high-energy (53eV-1.9 keV) electrons can escape into higher vertical positions. Furthermore, the model employs adaptive mesh, enabling high simulation accuracy without compromising the computational time. Notably, the adopted FEM mesh generator can handle complex boundary geometries, which is validated by simulations with surface grooving for promoting the flashover capability. The performance of grooves is evaluated through electron distribution, anode current density, average surface charge density and electron flux, demonstrating higher flashover strength. The proposed FlashSim simulation model is expected to assist in further revealing the flashover mechanism and developing novel strategies for flashover suppression, and will be further upgraded to include outgassing and plasma discharge.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109625"},"PeriodicalIF":7.2,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143868632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure-preserving parametric finite element methods for anisotropic surface diffusion flow with minimal deformation formulation","authors":"Yihang Guo,&nbsp;Meng Li","doi":"10.1016/j.cpc.2025.109620","DOIUrl":"10.1016/j.cpc.2025.109620","url":null,"abstract":"<div><div>High mesh quality plays a crucial role in maintaining the stability of solutions in geometric flow problems. Duan and Li (2024) <span><span>[20]</span></span> applied the minimal deformation (MD) formulation to propose an artificial tangential velocity determined by harmonic mapping to improve mesh quality. In this work, we extend the method to anisotropic surface diffusion flows, which, similar to isotropic curvature flow, also preserves excellent mesh quality. Furthermore, developing a numerical algorithm for the flow with MD formulation that guarantees volume conservation and energy stability remains a challenging task. We, in this paper, successfully construct several structure-preserving algorithms, including first-order and high-order temporal discretization methods. Extensive numerical experiments show that our methods effectively preserve mesh quality for anisotropic surface diffusion flows, ensuring high-order temporal accuracy, volume conservation or/and energy stability.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"313 ","pages":"Article 109620"},"PeriodicalIF":7.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143843995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}