Computer Physics Communications最新文献

{"title":"TNSP: A framework supporting symmetry and fermion tensors for tensor network state methods","authors":"Hao Zhang ,&nbsp;Shaojun Dong ,&nbsp;Chao Wang ,&nbsp;Meng Zhang ,&nbsp;Lixin He","doi":"10.1016/j.cpc.2024.109355","DOIUrl":"10.1016/j.cpc.2024.109355","url":null,"abstract":"<div><p>Recent advancements have established tensor network states (TNS) as formidable tools for exploring the complex realm of strongly-correlated many-particle systems in both one and two dimensions. To tackle the challenges presented by strongly-correlated fermion systems, various fermion tensor network states (f-TNS) methodologies have been developed. However, implementing f-TNS methods poses substantial challenges due to their particularly complex nature, making development efforts significantly difficult. This complexity is further exacerbated by the lack of underlying software packages that facilitate the development of f-TNS. Previously, we developed <span>TNSPackage</span>, a software package designed for TNS methods <span><span>[1]</span></span>. Initially, this package was only capable of handling spin and boson models. To confront the challenges presented by f-TNS, <span>TNSPackage</span> has undergone significant enhancements in its latest version, incorporating support for both symmetry and fermion tensors. This updated version provides a uniform interface for the consistent management of tensors across boson, fermion, and various symmetry types, maintaining its user-friendly and versatile nature. This greatly facilitates the development of programs based on f-TNS. The new <span>TNSP</span> framework consists of two principal components: a low-level tensor package named <span>TAT</span>, which supports sophisticated tensor operations, and a high-level interface package called <span>tetragono</span> that is built upon <span>TAT</span>. The <span>tetragono</span> package is designed to significantly simplify the development of complex physical models on square lattices. The <span>TNSPackage</span> framework enables users to implement a wide range of physical models with greater ease, without the need to pay close attention to the underlying implementation details.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109355"},"PeriodicalIF":7.2,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142083139","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":"Parallel and bias-free RSA algorithm for maximal Poisson-sphere sampling","authors":"Marc Josien,&nbsp;Raphaël Prat","doi":"10.1016/j.cpc.2024.109354","DOIUrl":"10.1016/j.cpc.2024.109354","url":null,"abstract":"<div><p>In this paper we propose and benchmark an innovative implementation of the Random Sequential Addition (or adsorption) (<span>Rsa</span>) algorithm. It provides <span>Mpi</span> parallelization and is designed to generate a high number of spheres aiming for maximal compactness, without introducing any bias. Although parallelization of such an algorithm has been successfully undertaken with shared memory (and in particular with <span>Gpu</span>), this is seemingly the first available implementation with distributed memory (<span>Mpi</span>). Our implementation successfully generated more than 12 billions of spheres over 131,072 <span>Mpi</span> processes in 16 seconds in dimension <span><math><mi>d</mi><mo>=</mo><mn>3</mn></math></span>.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109354"},"PeriodicalIF":7.2,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142088754","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":"Jupyter widgets and extensions for education and research in computational physics and chemistry","authors":"Dou Du ,&nbsp;Taylor J. Baird ,&nbsp;Kristjan Eimre ,&nbsp;Sara Bonella ,&nbsp;Giovanni Pizzi","doi":"10.1016/j.cpc.2024.109353","DOIUrl":"10.1016/j.cpc.2024.109353","url":null,"abstract":"<div><p>Interactive notebooks are a precious tool for creating graphical user interfaces and teaching materials. Python and Jupyter are becoming increasingly popular in this context, with Jupyter widgets at the core of the interactive functionalities. However, while packages and libraries which offer a broad range of general-purpose widgets exist, there is limited development of specialized widgets for computational physics, chemistry and materials science. This deficiency implies significant time investments for the development of effective Jupyter notebooks for research and education in these domains. Here, we present custom Jupyter widgets that we have developed to target the needs of these communities. These widgets constitute high-quality interactive graphical components and can be employed, for example, to visualize and manipulate data, or to explore different visual representations of concepts, clarifying the relationships existing between them. In addition, we discuss with one example how similar functionality can be exposed in the form of JupyterLab extensions, modifying the JupyterLab interface for an enhanced user experience when working with applications within the targeted scientific domains.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109353"},"PeriodicalIF":7.2,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524002765/pdfft?md5=eeba4d91253b8bb749a818b2ceb7abe3&pid=1-s2.0-S0010465524002765-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142098479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An efficient eigenvalue bounding method: CFL condition revisited","authors":"F.X. Trias ,&nbsp;X. Álvarez-Farré ,&nbsp;A. Alsalti-Baldellou ,&nbsp;A. Gorobets ,&nbsp;A. Oliva","doi":"10.1016/j.cpc.2024.109351","DOIUrl":"10.1016/j.cpc.2024.109351","url":null,"abstract":"<div><p>Direct and large-eddy simulations of turbulence are often solved using explicit temporal schemes. However, this imposes very small time-steps because the eigenvalues of the (linearized) dynamical system, re-scaled by the time-step, must lie inside the stability region. In practice, fast and accurate estimations of the spectral radii of both the discrete convective and diffusive terms are therefore needed. This is virtually always done using the so-called CFL condition. On the other hand, the large heterogeneity and complexity of modern supercomputing systems are nowadays hindering the efficient cross-platform portability of CFD codes. In this regard, our <em>leitmotiv</em> reads: <em>relying on a minimal set of (algebraic) kernels is crucial for code portability and maintenance!</em> In this context, this work focuses on the computation of eigenbounds for the above-mentioned convective and diffusive matrices which are needed to determine the time-step <em>à la</em> CFL. To do so, a new inexpensive method, that does not require to re-construct these time-dependent matrices, is proposed and tested. It just relies on a sparse-matrix vector product where only vectors change on time. Hence, both implementation in existing codes and cross-platform portability are straightforward. The effectiveness and robustness of the method are demonstrated for different test cases on both structured Cartesian and unstructured meshes. Finally, the method is combined with a self-adaptive temporal scheme, leading to significantly larger time-steps compared with other more conventional CFL-based approaches.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109351"},"PeriodicalIF":7.2,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524002741/pdfft?md5=d575278901cf7df2ab7422a24272b156&pid=1-s2.0-S0010465524002741-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142083136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring hidden signal: Fine-tuning ResNet-50 for dark matter detection","authors":"Ali Celik","doi":"10.1016/j.cpc.2024.109348","DOIUrl":"10.1016/j.cpc.2024.109348","url":null,"abstract":"<div><p>In pursuit of detecting dark matter signals, the Large Hadron Collider (LHC) at CERN has conducted proton-proton collisions to probe for these elusive particles, whose existence has been supported by astronomical observations. Despite extensive efforts by the CMS and ATLAS experiments, the direct detection of dark matter signals remains elusive. The current approaches employed for analyzing dark matter signatures utilize the cut-and-count method based on conventional techniques. This study introduces an alternative method for exploring dark matter signatures by utilizing fine-tuning of pre-trained models, such as ResNet-50, on 2D histograms generated from a combination of signal + background samples and background-only samples. By utilizing various signal-to-background ratios as benchmarks, an accuracy of about 90% for a signal-to-background ratio of 0.008 is achieved. This approach not only offers a more refined search for dark matter signals but also presents an efficient and effective means of analysis using machine learning techniques.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109348"},"PeriodicalIF":7.2,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142083137","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":"libepa — A C++/Python library for calculations of cross sections of ultraperipheral collisions","authors":"E.V. Zhemchugov ,&nbsp;S.I. Godunov ,&nbsp;E.K. Karkaryan ,&nbsp;V.A. Novikov ,&nbsp;A.N. Rozanov ,&nbsp;M.I. Vysotsky","doi":"10.1016/j.cpc.2024.109347","DOIUrl":"10.1016/j.cpc.2024.109347","url":null,"abstract":"<div><p>The library provides a set of C++/Python functions for computing cross sections of ultraperipheral collisions of high energy particles under the equivalent photons approximation. Cross sections are represented through multiple integrals over the phase space. The integrals are calculated through recurrent application of algorithms for one dimensional integration. The paper contains an introduction to the theory of ultraperipheral collisions, discusses the library approach and provides a few examples of calculations.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109347"},"PeriodicalIF":7.2,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142083138","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":"PyArc: A python package for computing absorption and radiative coefficients from first principles","authors":"Siyuan Xu ,&nbsp;Zheng Liu ,&nbsp;Xun Xu ,&nbsp;Yuzheng Guo ,&nbsp;Su-Huai Wei ,&nbsp;Xie Zhang","doi":"10.1016/j.cpc.2024.109352","DOIUrl":"10.1016/j.cpc.2024.109352","url":null,"abstract":"<div><p>Light absorption and radiative recombination are two critical processes in optoelectronic materials that characterize the energy conversion efficiency. The absorption and radiative coefficients are thus key properties for device optimization and design. Here, we develop a python package named pyArc that allows rigorous computation of absorption and radiative coefficients from first principles. By integrating several interpolation strategies to augment <strong>k</strong>-point sampling in reciprocal space, our code is accurate yet highly efficient. In addition to evaluation of the coefficients, our code is capable of intuitive analysis of carrier distribution, facilitating a deeper understanding of the microscopic mechanisms underlying the radiative coefficients. Utilizing GaAs as a prototypical example, we demonstrate how to employ our package to compute absorption and radiative coefficients and to investigate the key features in the electronic structure that give rise to these coefficients.</p><p><strong>Program summary</strong></p><p>Program Title: PyArc</p><p>CPC Library link to program files: <span><span>https://doi.org/10.17632/5</span><svg><path></path></svg></span> × 9g9bvhcv.1</p><p>Licensing provisions: MIT license</p><p>Programming language: Python 3</p><p>Nature of problem: Light absorption and radiative recombination processes in semiconductors critically impact the energy conversion efficiency of optoelectronic devices. Developing a method to calculate coefficients of the two processes based on first-principles theory is essential, which not only can help to obtain the key properties of those semiconductor materials and guide the device design, but also can unveil the underlying microscopic mechanisms.</p><p>Solution method: PyArc, written in the Python language, implements first-principles methodologies for the computation of absorption and radiative coefficients of semiconductors based on Fermi's golden rule. This package takes the electronic eigenvalues and dipole matrix elements of a material computed from first-principles codes such as VASP as input. Dense <strong>k</strong>-point sampling for the Brillouin zone is achieved through efficient interpolation schemes implemented in our code to acquire well converged results. The functionality of cross-sectional visualization of carrier distribution in our code provides intuitive insights into the fundamental mechanism beneath the charge-carrier radiative recombination process.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109352"},"PeriodicalIF":7.2,"publicationDate":"2024-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047858","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":"Computer modeling of a new type galactic cosmic rays simulator","authors":"I.S. Gordeev ,&nbsp;A.N. Bugay","doi":"10.1016/j.cpc.2024.109346","DOIUrl":"10.1016/j.cpc.2024.109346","url":null,"abstract":"<div><p>A new type of a galactic cosmic rays (GCR) simulator, provided at the JINR Laboratory of Radiation Biology, is potentially capable of generating a complex radiation field with inclusions of a variety of ions with a wide energy range and with required abundance at the charged particle accelerators. This complex multicomponent radiation field simulates radiation environment inside a spacecraft during an interplanetary flight, for example, to Mars. The article provides an analytical description of the GCR simulator as well as a description of a specially developed software that enables selection of necessary parameters of a simulator model for creating relevant mixed radiation conditions. The software implements processing of data obtained with Monte Carlo-based FLUKA and PHITS programs, fitting and optimization of model parameters as well as data visualization tools.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109346"},"PeriodicalIF":7.2,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142006817","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":"QRCODE: Massively parallelized real-time time-dependent density functional theory for periodic systems","authors":"Min Choi ,&nbsp;Mahmut Sait Okyay ,&nbsp;Adrian Perez Dieguez ,&nbsp;Mauro Del Ben ,&nbsp;Khaled Z. Ibrahim ,&nbsp;Bryan M. Wong","doi":"10.1016/j.cpc.2024.109349","DOIUrl":"10.1016/j.cpc.2024.109349","url":null,"abstract":"<div><p>We present a new software module, QRCODE (Quantum Research for Calculating Optically Driven Excitations), for massively parallelized real-time time-dependent density functional theory (RT-TDDFT) calculations of periodic systems in the open-source Qbox software package. Our approach utilizes a custom implementation of a fast Fourier transformation scheme that significantly reduces inter-node message passing interface (MPI) communication of the major computational kernel and shows impressive scaling up to 16,344 CPU cores. In addition to improving computational performance, QRCODE contains a suite of various time propagators for accurate RT-TDDFT calculations. As benchmark applications of QRCODE, we calculate the current density and optical absorption spectra of hexagonal boron nitride (h-BN) and photo-driven reaction dynamics of the ozone-oxygen reaction. We also calculate the second and higher harmonic generation of monolayer and multi-layer boron nitride structures as examples of large material systems. Our optimized implementation of RT-TDDFT in QRCODE enables large-scale calculations of real-time electron dynamics of chemical and material systems with enhanced computational performance and impressive scaling across several thousand CPU cores.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109349"},"PeriodicalIF":7.2,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524002728/pdfft?md5=a5f7076a1b55e6e220016f622443470d&pid=1-s2.0-S0010465524002728-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142098480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Massively parallel axisymmetric fluid model for streamer discharges","authors":"A. Fierro ,&nbsp;A. Alibalazadeh ,&nbsp;J. Stephens ,&nbsp;C. Moore","doi":"10.1016/j.cpc.2024.109345","DOIUrl":"10.1016/j.cpc.2024.109345","url":null,"abstract":"<div><p>A highly parallelizable fluid plasma simulation tool based upon the first-order drift-diffusion equations is discussed. Atmospheric pressure plasmas have densities and gradients that require small element sizes in order to accurately simulate the plasm resulting in computational meshes on the order of millions to tens of millions of elements for realistic size plasma reactors. To enable simulations of this nature, parallel computing is required and must be optimized for the particular problem. Here, a finite-volume, electrostatic drift-diffusion implementation for low-temperature plasma is discussed. The implementation is built upon the Message Passing Interface (MPI) library in C++ using Object Oriented Programming. The underlying numerical method is outlined in detail and benchmarked against simple streamer formation from other streamer codes. Electron densities, electric field, and propagation speeds are compared with the reference case and show good agreement. Convergence studies are also performed showing a minimal space step of approximately 4 μm required to reduce relative error to below 1% during early streamer simulation times and even finer space steps are required for longer times. Additionally, strong and weak scaling of the implementation are studied and demonstrate the excellent performance behavior of the implementation up to 100 million elements on 1024 processors. Finally, different advection schemes are compared for the simple streamer problem to analyze the influence of numerical diffusion on the resulting quantities of interest.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"305 ","pages":"Article 109345"},"PeriodicalIF":7.2,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142006816","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}