首页 > 最新文献

Computer Physics Communications最新文献

英文 中文
Code for molecular dynamics simulation of two dimensional Mercedes-Benz water model 二维梅赛德斯-奔驰水模型分子动力学模拟代码
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-06-06 DOI: 10.1016/j.cpc.2024.109267
Peter Ogrin , Cristiano L. Dias , Tomaz Urbic

The Mercedes-Benz (MB) water model is a simple two-dimensional toy model of water that can reproduce many of the anomalous properties of water. Within the model, the water particles are represented as Lennard-Jones disks with explicitly added orientation-dependent interactions that mimic the formation of hydrogen bonds. Due to the simple implementation of the MB model in Monte Carlo simulations, it was mainly studied with Monte Carlo simulations in different ensembles. The implementation of the model in molecular dynamics simulations is not trivial. In this paper we present the code for molecular dynamics simulations. The structural and thermodynamic properties of the model were calculated using molecular dynamics and compared with data from Monte Carlo simulations to confirm that the molecular dynamics code works correctly. We also used molecular dynamics to calculate the dynamic properties of the model. The Fortran source code of our molecular dynamics simulation of the MB water model is provided.

梅赛德斯-奔驰(MB)水模型是一个简单的二维水玩具模型,可以再现水的许多异常特性。在该模型中,水粒子被表示为 Lennard-Jones 盘,并明确添加了取向相关的相互作用,以模拟氢键的形成。由于 MB 模型在蒙特卡罗模拟中的实现比较简单,因此主要通过不同集合的蒙特卡罗模拟进行研究。在分子动力学模拟中实现该模型并非易事。本文介绍了分子动力学模拟的代码。我们利用分子动力学计算了该模型的结构和热力学性质,并与蒙特卡罗模拟的数据进行了比较,以确认分子动力学代码工作正常。我们还利用分子动力学计算了模型的动态特性。我们提供了 MB 水模型分子动力学模拟的 Fortran 源代码。
{"title":"Code for molecular dynamics simulation of two dimensional Mercedes-Benz water model","authors":"Peter Ogrin ,&nbsp;Cristiano L. Dias ,&nbsp;Tomaz Urbic","doi":"10.1016/j.cpc.2024.109267","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109267","url":null,"abstract":"<div><p>The Mercedes-Benz (MB) water model is a simple two-dimensional toy model of water that can reproduce many of the anomalous properties of water. Within the model, the water particles are represented as Lennard-Jones disks with explicitly added orientation-dependent interactions that mimic the formation of hydrogen bonds. Due to the simple implementation of the MB model in Monte Carlo simulations, it was mainly studied with Monte Carlo simulations in different ensembles. The implementation of the model in molecular dynamics simulations is not trivial. In this paper we present the code for molecular dynamics simulations. The structural and thermodynamic properties of the model were calculated using molecular dynamics and compared with data from Monte Carlo simulations to confirm that the molecular dynamics code works correctly. We also used molecular dynamics to calculate the dynamic properties of the model. The Fortran source code of our molecular dynamics simulation of the MB water model is provided.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524001905/pdfft?md5=c7faabbec1a5c5bf10101d941faa7630&pid=1-s2.0-S0010465524001905-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141313564","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}
引用次数: 0
MAM-STM: A software for autonomous control of single moieties towards specific surface positions MAM-STM:用于自主控制单个分子朝向特定表面位置的软件
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-06-06 DOI: 10.1016/j.cpc.2024.109264
Bernhard Ramsauer, Johannes J. Cartus, Oliver T. Hofmann

In this publication we introduce MAM-STM, a software to autonomously manipulate arbitrary moieties towards specific positions on a metal surface utilizing the tip of a scanning tunneling microscope (STM). Finding the optimal manipulation parameters for a specific moiety is challenging and time consuming, even for human experts. MAM-STM combines autonomous data acquisition with a sophisticated Q-learning implementation to determine the optimal bias voltage, the z-approach distance, and the tip position relative to the moiety. This then allows to arrange single molecules and atoms at will. In this work, we provide a tutorial based on a simulated response to offer a comprehensive explanation on how to use and customize MAM-STM. Additionally, we assess the performance of the machine learning algorithm by benchmarking it within a simulated stochastic environment.

PROGRAM SUMMARY

Program title: MAM-STM

CPC Library link to program files: (to be added by Technical Editor)

Developer's repository link: https://gitlab.tugraz.at/software_public/mam_stm.git

Code Ocean capsule: (to be added by Technical Editor)

Licensing provisions: GNU General Public License 3 (GPL)

Programming language: Python 3

Nature of problem: Achieving precise control over the arrangement of individual molecules on surfaces is essential for advancing nanofabrication and understanding molecular interaction processes. While self-assembly offers a method for forming nanostructures, achieving arbitrary arrangements of moieties remains difficult. Current approaches, such as scanning probe microscopy (SPM), require extensive manual intervention and precise control is difficult to achieve consistently due to the stochastic nature of quantum mechanical systems at the nanoscale. Thus, learning to manipulate several moieties in order to build even relatively small structures is challenging and time consuming and the automation through conventional expert systems is hindered by the lack of prior knowledge about the surface-moiety interaction processes.

Solution method: This scenario is ideal for machine learning algorithms, like reinforcement learning (RL), which do not require an underlying model but are able to autonomously learn the optimal manipulation parameters by performing manipulations directly at the machine. Introducing MAM-STM, which stands for Molecular and Atomic Manipulation via Scanning Tunneling Microscopy. MAM-STM allows to control molecules and atoms by learning the manipulation parameters for either vertical or lateral manipulations. However, the vast number of manipulation parameter combinations and the inefficient learning procedure of RL agents exhibit several challenges. MAM-STM overcomes these challenges with an autonomous masking routine that eliminates manipulation parameters that induce structural changes to the moiety or lift it off the surface. Additionally, a sophisticated Q-learning approach

在这篇论文中,我们介绍了 MAM-STM,这是一款利用扫描隧道显微镜(STM)的尖端自主操纵任意分子在金属表面特定位置的软件。为特定分子寻找最佳操作参数既具有挑战性又耗费时间,即使是人类专家也不例外。MAM-STM 将自主数据采集与复杂的 Q-learning 实现相结合,以确定最佳偏置电压、z-接近距离和针尖相对于分子的位置。这样就可以随意排列单个分子和原子。在这项工作中,我们提供了一个基于模拟响应的教程,全面解释了如何使用和定制 MAM-STM。此外,我们还在模拟随机环境中通过基准测试评估了机器学习算法的性能:MAM-STMCPC 程序库链接到程序文件:(由技术编辑添加)开发者资源库链接:https://gitlab.tugraz.at/software_public/mam_stm.gitCode 海洋胶囊:(由技术编辑添加)许可条款:GNU General Public License 3 (GPL) 编程语言:Python 3Python 3问题本质:实现对单个分子在表面上排列的精确控制对于推进纳米制造和了解分子相互作用过程至关重要。虽然自组装提供了一种形成纳米结构的方法,但实现分子的任意排列仍然十分困难。目前的方法,如扫描探针显微镜(SPM),需要大量的人工干预,而且由于量子力学系统在纳米尺度上的随机性,精确控制很难持续实现。因此,学习如何操作多个分子以构建即使是相对较小的结构,既具有挑战性又耗费时间,而且由于缺乏有关表面-分子相互作用过程的先验知识,通过传统专家系统实现自动化也会受到阻碍:这种情况非常适合机器学习算法,如强化学习(RL),它不需要底层模型,而是能够通过直接在机器上执行操作来自主学习最佳操作参数。MAM-STM 是通过扫描隧道显微镜进行分子和原子操作的缩写。MAM-STM 可以通过学习垂直或横向操作参数来控制分子和原子。然而,大量的操纵参数组合和低效的 RL 代理学习程序带来了一些挑战。MAM-STM 通过自主屏蔽程序克服了这些挑战,该程序可消除引起分子结构变化或使其脱离表面的操作参数。此外,还开发了一种复杂的 Q-learning 方法,可加快学习过程,从而在一天的训练时间内完成分子操作。
{"title":"MAM-STM: A software for autonomous control of single moieties towards specific surface positions","authors":"Bernhard Ramsauer,&nbsp;Johannes J. Cartus,&nbsp;Oliver T. Hofmann","doi":"10.1016/j.cpc.2024.109264","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109264","url":null,"abstract":"<div><p>In this publication we introduce MAM-STM, a software to autonomously manipulate arbitrary moieties towards specific positions on a metal surface utilizing the tip of a scanning tunneling microscope (STM). Finding the optimal manipulation parameters for a specific moiety is challenging and time consuming, even for human experts. MAM-STM combines autonomous data acquisition with a sophisticated Q-learning implementation to determine the optimal bias voltage, the z-approach distance, and the tip position relative to the moiety. This then allows to arrange single molecules and atoms at will. In this work, we provide a tutorial based on a simulated response to offer a comprehensive explanation on how to use and customize MAM-STM. Additionally, we assess the performance of the machine learning algorithm by benchmarking it within a simulated stochastic environment.</p></div><div><h3>PROGRAM SUMMARY</h3><p>Program title: MAM-STM</p><p>CPC Library link to program files: (to be added by Technical Editor)</p><p>Developer's repository link: https://gitlab.tugraz.at/software_public/mam_stm.git</p><p>Code Ocean capsule: (to be added by Technical Editor)</p><p>Licensing provisions: GNU General Public License 3 (GPL)</p><p>Programming language: Python 3</p><p>Nature of problem: Achieving precise control over the arrangement of individual molecules on surfaces is essential for advancing nanofabrication and understanding molecular interaction processes. While self-assembly offers a method for forming nanostructures, achieving arbitrary arrangements of moieties remains difficult. Current approaches, such as scanning probe microscopy (SPM), require extensive manual intervention and precise control is difficult to achieve consistently due to the stochastic nature of quantum mechanical systems at the nanoscale. Thus, learning to manipulate several moieties in order to build even relatively small structures is challenging and time consuming and the automation through conventional expert systems is hindered by the lack of prior knowledge about the surface-moiety interaction processes.</p><p>Solution method: This scenario is ideal for machine learning algorithms, like reinforcement learning (RL), which do not require an underlying model but are able to autonomously learn the optimal manipulation parameters by performing manipulations directly at the machine. Introducing MAM-STM, which stands for Molecular and Atomic Manipulation via Scanning Tunneling Microscopy. MAM-STM allows to control molecules and atoms by learning the manipulation parameters for either vertical or lateral manipulations. However, the vast number of manipulation parameter combinations and the inefficient learning procedure of RL agents exhibit several challenges. MAM-STM overcomes these challenges with an autonomous masking routine that eliminates manipulation parameters that induce structural changes to the moiety or lift it off the surface. Additionally, a sophisticated Q-learning approach ","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524001875/pdfft?md5=74c3002522a3586528e738564a9ff30d&pid=1-s2.0-S0010465524001875-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141429351","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}
引用次数: 0
FENNECS: A novel particle-in-cell code for simulating the formation of magnetized non-neutral plasmas trapped by electrodes of complex geometries FENNECS:用于模拟被复杂几何形状电极困住的磁化非中性等离子体形成的新型粒子池代码
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-06-06 DOI: 10.1016/j.cpc.2024.109268
G. Le Bars , J. Loizu , S. Guinchard , J.-Ph. Hogge , A. Cerfon , S. Alberti , F. Romano , J. Genoud , P. Kamiński

This paper presents the new 2D electrostatic particle-in-cell code FENNECS developed to study the formation of magnetized non-neutral plasmas in geometries with azimuthal symmetry. This code has been developed in the domain of gyrotron electron gun design, but solves general equations and can be applied in other domains of plasma physics. FENNECS is capable of simulating electron-neutral collisions using a Monte Carlo approach and considers both elastic and inelastic (ionization) processes. It is also capable of solving the Poisson equation on domains with arbitrary geometries with either Dirichlet or natural boundary conditions. The Poisson solver is based on a meshless Finite Element Method, called web-splines, based on b-splines of any order, and used for the first time in the domain of plasma physics. In addition, the effect of fast ions colliding with the electrodes and causing ion induced electron emission at the electrode surfaces has been implemented in the code. In this paper, the governing equations solved by FENNECS and the numerical methods used to solve them are presented. A number of verification cases are then reported. Finally, the parallelization scheme used in FENNECS and its parallel scalability are presented.

本文介绍了为研究具有方位对称性的几何结构中磁化非中性等离子体的形成而开发的新型二维静电粒子池内代码 FENNECS。该代码是在陀螺仪电子枪设计领域开发的,但可求解一般方程,并可应用于等离子体物理的其他领域。FENNECS 能够使用蒙特卡罗方法模拟电子-中性碰撞,并考虑弹性和非弹性(电离)过程。它还能在具有任意几何形状的域上求解泊松方程,并采用迪里希勒或自然边界条件。泊松求解器基于一种无网格有限元方法,称为网状样条,基于任意阶的 b 样条,首次用于等离子体物理领域。此外,代码中还实现了快速离子与电极碰撞并在电极表面引起离子诱导电子发射的效应。本文介绍了 FENNECS 所求解的支配方程以及用于求解这些方程的数值方法。然后报告了一些验证案例。最后,介绍了 FENNECS 中使用的并行化方案及其并行可扩展性。
{"title":"FENNECS: A novel particle-in-cell code for simulating the formation of magnetized non-neutral plasmas trapped by electrodes of complex geometries","authors":"G. Le Bars ,&nbsp;J. Loizu ,&nbsp;S. Guinchard ,&nbsp;J.-Ph. Hogge ,&nbsp;A. Cerfon ,&nbsp;S. Alberti ,&nbsp;F. Romano ,&nbsp;J. Genoud ,&nbsp;P. Kamiński","doi":"10.1016/j.cpc.2024.109268","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109268","url":null,"abstract":"<div><p>This paper presents the new 2D electrostatic particle-in-cell code FENNECS developed to study the formation of magnetized non-neutral plasmas in geometries with azimuthal symmetry. This code has been developed in the domain of gyrotron electron gun design, but solves general equations and can be applied in other domains of plasma physics. FENNECS is capable of simulating electron-neutral collisions using a Monte Carlo approach and considers both elastic and inelastic (ionization) processes. It is also capable of solving the Poisson equation on domains with arbitrary geometries with either Dirichlet or natural boundary conditions. The Poisson solver is based on a meshless Finite Element Method, called web-splines, based on b-splines of any order, and used for the first time in the domain of plasma physics. In addition, the effect of fast ions colliding with the electrodes and causing ion induced electron emission at the electrode surfaces has been implemented in the code. In this paper, the governing equations solved by FENNECS and the numerical methods used to solve them are presented. A number of verification cases are then reported. Finally, the parallelization scheme used in FENNECS and its parallel scalability are presented.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524001917/pdfft?md5=d12b899e7ef4cc6503231cb81213f8f2&pid=1-s2.0-S0010465524001917-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141313565","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}
引用次数: 0
Corrigendum to “Fast Exact Algorithm for Neutrino Oscillation in Constant Matter Density” [Computer Physics Communications volume 300 (2024) 109200] 恒定物质密度下中微子振荡的快速精确算法"[《计算机物理通讯》第 300 卷 (2024) 109200] 更正
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-06-04 DOI: 10.1016/j.cpc.2024.109262
James Page
{"title":"Corrigendum to “Fast Exact Algorithm for Neutrino Oscillation in Constant Matter Density” [Computer Physics Communications volume 300 (2024) 109200]","authors":"James Page","doi":"10.1016/j.cpc.2024.109262","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109262","url":null,"abstract":"","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524001851/pdfft?md5=dbffac2285cea4454d6759b98a9b4a7c&pid=1-s2.0-S0010465524001851-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141250838","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}
引用次数: 0
A particle-resolved direct numerical simulation method for the compressible gas flow and arbitrary shape solid moving with a uniform framework 均匀框架下可压缩气体流动和任意形状固体运动的粒子分辨直接数值模拟方法
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-06-01 DOI: 10.1016/j.cpc.2024.109266
Baoqing Meng , Junsheng Zeng , Shuai Li , Baolin Tian , Jinhong Liu

Compressible particle-resolved direct numerical simulations (PR-DNS) are widely used in explosion-driven dispersion of particles simulations, multiphase turbulence modelling, and stage separation for two-stage-to-orbit vehicles. The direct forcing immersed boundary method (IBM) is a promising method and widely applied in low speed flow while there is few research regarding compressible flows. We developed a novel IBM to resolve supersonic and hypersonic gas flows interacting with irregularly shaped multi-body particle. The main innovation is that current method can solve the interaction of particles and high-speed fluids, particle translation and rotation, and collision among complex-shaped particles within a uniform framework. Specially, high conservation and computation consumption are strictly satisfied, which is critical for resolving the high speed compressible flow feature. To avoid the non-physical flow penetration around particle surface, an special iterative algorithm is specially derived to handle the coupling force between the gas and particles. The magnitude of the velocity difference error could be reduced by 6–8 orders compared to that of a previous method. Additionally, aerodynamic force integration was achieved using the momentum equation to ensure momentum conservation for two-phase coupling. A high-efficiency cell-type identification method for each step was proposed, and mapping among LPs and cells was used again to select the immersed cells. As for the collision force calculation, the complex shape of a particle was represented by a cloud of LPs and the mapping of LPs and cells was used to reduce the complexity of the algorithm for contact searching. The repetitive use of the mapping relationship could reduce the internal memory and improve the efficiency of the proposed algorithm. Moreover, various verification cases were conducted to evaluate the simulation performance of the proposed algorithm, including two- and three-dimensional moving and motionless particles with regular and complex shapes interacting with high-speed flow. Specifically, an experiment involving a shock passing through a sphere was designed and conducted to provide high-precision data. The corresponding results of the large-scale numerical simulation agree well with those obtained experimentally. The current method supports flow simulations at a particle-resolved scale in engineering.

可压缩颗粒分辨直接数值模拟(PR-DNS)广泛应用于爆炸驱动的颗粒扩散模拟、多相湍流建模和两级入轨飞行器的级间分离。直接强迫沉浸边界法(IBM)是一种很有前途的方法,被广泛应用于低速流,但有关可压缩流的研究却很少。我们开发了一种新型 IBM,用于解决超音速和高超声速气体流与不规则形状的多体粒子相互作用的问题。其主要创新点在于,目前的方法可以在统一框架内解决粒子与高速流体的相互作用、粒子的平移和旋转以及复杂形状粒子之间的碰撞。特别是严格满足了高守恒和计算消耗的要求,这对于解决高速可压缩流特性至关重要。为了避免粒子表面的非物理流动渗透,特别推导出一种特殊的迭代算法来处理气体和粒子之间的耦合力。与之前的方法相比,速度差误差的幅度可减少 6-8 个数量级。此外,利用动量方程实现了空气动力积分,以确保两相耦合的动量守恒。提出了每一步的高效单元型识别方法,并再次使用 LP 和单元之间的映射来选择沉浸单元。至于碰撞力计算,粒子的复杂形状由 LP 云表示,LP 与单元之间的映射用于降低接触搜索算法的复杂性。映射关系的重复使用可以减少内部内存,提高拟议算法的效率。此外,为了评估所提算法的仿真性能,还进行了各种验证案例,包括形状规则和复杂的二维和三维运动和静止粒子与高速流动的相互作用。具体而言,设计并进行了一次冲击通过球体的实验,以提供高精度数据。大规模数值模拟的相应结果与实验结果非常吻合。目前的方法支持在工程中进行颗粒分辨尺度的流动模拟。
{"title":"A particle-resolved direct numerical simulation method for the compressible gas flow and arbitrary shape solid moving with a uniform framework","authors":"Baoqing Meng ,&nbsp;Junsheng Zeng ,&nbsp;Shuai Li ,&nbsp;Baolin Tian ,&nbsp;Jinhong Liu","doi":"10.1016/j.cpc.2024.109266","DOIUrl":"10.1016/j.cpc.2024.109266","url":null,"abstract":"<div><p>Compressible particle-resolved direct numerical simulations (PR-DNS) are widely used in explosion-driven dispersion of particles simulations, multiphase turbulence modelling, and stage separation for two-stage-to-orbit vehicles. The direct forcing immersed boundary method (IBM) is a promising method and widely applied in low speed flow while there is few research regarding compressible flows. We developed a novel IBM to resolve supersonic and hypersonic gas flows interacting with irregularly shaped multi-body particle. The main innovation is that current method can solve the interaction of particles and high-speed fluids, particle translation and rotation, and collision among complex-shaped particles within a uniform framework. Specially, high conservation and computation consumption are strictly satisfied, which is critical for resolving the high speed compressible flow feature. To avoid the non-physical flow penetration around particle surface, an special iterative algorithm is specially derived to handle the coupling force between the gas and particles. The magnitude of the velocity difference error could be reduced by 6–8 orders compared to that of a previous method. Additionally, aerodynamic force integration was achieved using the momentum equation to ensure momentum conservation for two-phase coupling. A high-efficiency cell-type identification method for each step was proposed, and mapping among LPs and cells was used again to select the immersed cells. As for the collision force calculation, the complex shape of a particle was represented by a cloud of LPs and the mapping of LPs and cells was used to reduce the complexity of the algorithm for contact searching. The repetitive use of the mapping relationship could reduce the internal memory and improve the efficiency of the proposed algorithm. Moreover, various verification cases were conducted to evaluate the simulation performance of the proposed algorithm, including two- and three-dimensional moving and motionless particles with regular and complex shapes interacting with high-speed flow. Specifically, an experiment involving a shock passing through a sphere was designed and conducted to provide high-precision data. The corresponding results of the large-scale numerical simulation agree well with those obtained experimentally. The current method supports flow simulations at a particle-resolved scale in engineering.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141233316","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}
引用次数: 0
ENDFtk: A robust tool for reading and writing ENDF-formatted nuclear data ENDFtk:读写ENDF格式核数据的强大工具
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-05-31 DOI: 10.1016/j.cpc.2024.109245
W. Haeck, N. Gibson, P. Talou

ENDFtk is a recently developed C++ and Python interface to interact with ENDF-6 formatted nuclear data files. It provides a robust and complete interface, allowing the reading and writing of all formats currently part of the ENDF-6 formats manual, as well as some non-ENDF formats used by the NJOY processing code. It provides an interface that mimics the names in the ENDF-6 formats manual as well as an equivalent interface using human-readable attribute names. It is robust and powerful enogh for nuclear data experts to develop complex applications, while also simple enough to be used non-experts to retrieve and manipulate evaluated nuclear data. ENDFtk offers the ability to easily interrogate and manipulate data either in large-scale code projects or in simple Python scripts. In this paper, a brief overview of the interface is given, as well as more substantial examples demonstrating plotting simple data, interacting with more complex data, and writing new data to files. ENDFtk is open source and available for download via GitHub (https://github.com/njoy/ENDFtk).

Program summary

Program title: ENDFtk 1.0

CPC Library link to program files: https://doi.org/10.17632/9p4kxc2cvd.1

Developer's repository link: https://github.com/njoy/ENDFtk

Licensing provisions: BSD-3 clause

Programming language: C++ and Python

External routines/libraries: pybind11, ranges-v3, spdlog

Nature of problem: Provide an interface to read, write and manipulate nuclear data files using the ENDF-6 format. This interface can be integrated into other libraries requiring access to nuclear data, or be used directly using the Python interface.

Solution method: Library of C++ routines, with their Python bindings, to be integrated in higher-level codes and scripts

ENDFtk是最近开发的C++和Python界面,用于与ENDF-6格式的核数据文件交互。它提供了一个强大而完整的界面,允许读写目前属于ENDF-6 格式手册一部分的所有格式,以及 NJOY 处理代码使用的一些非 ENDF 格式。它提供了一个模仿ENDF-6 格式手册中名称的界面,以及一个使用人类可读属性名称的等效界面。ENDFtk功能强大,适合核数据专家开发复杂的应用程序,同时也足够简单,可供非专业人员检索和处理已评估的核数据。无论是在大型代码项目中还是在简单的 Python 脚本中,ENDFtk 都能提供轻松查询和操作数据的能力。本文简要介绍了ENDFtk的界面,并通过大量实例演示了如何绘制简单数据、与更复杂的数据交互以及向文件中写入新数据。ENDFtk是开源软件,可通过GitHub下载(https://github.com/njoy/ENDFtk)。程序摘要程序标题:ENDFtk 1.0CPC 库与程序文件的链接:https://doi.org/10.17632/9p4kxc2cvd.1Developer's repository 链接:https://github.com/njoy/ENDFtkLicensing 规定:BSD-3 条款编程语言:C++ 和 PythonC++ 和 Python外部例程/库:pybind11, ranges-v3, spdlog问题性质:提供使用ENDF-6格式读写和操作核数据文件的接口。该接口可集成到其他需要访问核数据的库中,或直接使用 Python 接口:C++ 例程库及其 Python 绑定,可集成到高级代码和脚本中
{"title":"ENDFtk: A robust tool for reading and writing ENDF-formatted nuclear data","authors":"W. Haeck,&nbsp;N. Gibson,&nbsp;P. Talou","doi":"10.1016/j.cpc.2024.109245","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109245","url":null,"abstract":"<div><p><span>ENDFtk</span> is a recently developed C++ and Python interface to interact with ENDF-6 formatted nuclear data files. It provides a robust and complete interface, allowing the reading and writing of all formats currently part of the ENDF-6 formats manual, as well as some non-ENDF formats used by the NJOY processing code. It provides an interface that mimics the names in the ENDF-6 formats manual as well as an equivalent interface using human-readable attribute names. It is robust and powerful enogh for nuclear data experts to develop complex applications, while also simple enough to be used non-experts to retrieve and manipulate evaluated nuclear data. <span>ENDFtk</span> offers the ability to easily interrogate and manipulate data either in large-scale code projects or in simple Python scripts. In this paper, a brief overview of the interface is given, as well as more substantial examples demonstrating plotting simple data, interacting with more complex data, and writing new data to files. <span>ENDFtk</span> is open source and available for download via GitHub (<span>https://github.com/njoy/ENDFtk</span><svg><path></path></svg>).</p></div><div><h3>Program summary</h3><p><em>Program title:</em> <span>ENDFtk</span> 1.0</p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/9p4kxc2cvd.1</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://github.com/njoy/ENDFtk</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> BSD-3 clause</p><p><em>Programming language:</em> C++ and Python</p><p><em>External routines/libraries:</em> pybind11, ranges-v3, spdlog</p><p><em>Nature of problem:</em> Provide an interface to read, write and manipulate nuclear data files using the ENDF-6 format. This interface can be integrated into other libraries requiring access to nuclear data, or be used directly using the Python interface.</p><p><em>Solution method:</em> Library of C++ routines, with their Python bindings, to be integrated in higher-level codes and scripts</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141291808","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}
引用次数: 0
An unconditionally-stable well-posed relativistic particle pusher 无条件稳定的好假设相对论粒子推动器
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-05-28 DOI: 10.1016/j.cpc.2024.109263
Xiang-Ren Zhou, Li Zhang

Particle pushers widely used in Particle-in-Cell(PIC) simulations are commonly required to be unconditionally stable and meet the basic physical laws. In this work, basing on central difference, we propose an unconditionally stable and well posed particle pusher. By mathematical deduction, the high-dimensional non-linear problem for solving tensor-form relativistic Lorentz force law equation is transformed to a quartic scalar problem and a following linear problem. Some practical suggestions for programming and some numerical results are also given.

粒子在胞(PIC)模拟中广泛使用的粒子推动器通常要求无条件稳定并符合基本物理定律。在这项工作中,我们基于中心差分,提出了一种无条件稳定且姿态良好的粒子推动器。通过数学推导,将求解张量形式相对论洛伦兹力定律方程的高维非线性问题转化为四元标量问题和下面的线性问题。此外,还给出了一些实用的编程建议和一些数值结果。
{"title":"An unconditionally-stable well-posed relativistic particle pusher","authors":"Xiang-Ren Zhou,&nbsp;Li Zhang","doi":"10.1016/j.cpc.2024.109263","DOIUrl":"10.1016/j.cpc.2024.109263","url":null,"abstract":"<div><p>Particle pushers widely used in Particle-in-Cell(PIC) simulations are commonly required to be unconditionally stable and meet the basic physical laws. In this work, basing on central difference, we propose an unconditionally stable and well posed particle pusher. By mathematical deduction, the high-dimensional non-linear problem for solving tensor-form relativistic Lorentz force law equation is transformed to a quartic scalar problem and a following linear problem. Some practical suggestions for programming and some numerical results are also given.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141190942","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}
引用次数: 0
FIRE 6.5: Feynman integral reduction with new simplification library FIRE 6.5:使用新简化库的费曼积分还原法
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-05-24 DOI: 10.1016/j.cpc.2024.109261
Alexander V. Smirnov , Mao Zeng

FIRE is a program which performs integration-by-parts (IBP) reductions of Feynman integrals. Originally, the C++ version of FIRE relies on the computer algebra system Fermat by Robert Lewis to simplify rational functions. We present an upgrade of FIRE which incorporates a new library FUEL initially described in a separate publication, which enables a flexible choice of third-party computer algebra systems as simplifiers, as well as efficient communications with some of the simplifiers as C++ libraries rather than through Unix pipes. We achieve significant speedups for IBP reductions of Feynman integrals involving many kinematic variables, when using an open source backend based on FLINT newly added in this work, or the Symbolica backend developed by Ben Ruijl as a potential successor of FORM.

Program summary

Program title: FIRE, version 6.5 (FIRE 6.5)

CPC Library link to program files: https://doi.org/10.17632/cy6k69pb3y.2

Developer's repository link: https://gitlab.com/feynmanintegrals/fire.git

Licensing provisions: GPLv2

Programming language: Wolfram Mathematica 8.0 or higher, C++17

Supplementary material: See linked repository for installation instructions.

Journal reference of previous version: Comput. Phys. Commun. 247 (2020) 106877

Does the new version supersede the previous version?: Yes.

Reasons for the new version: The new version no longer relies on a single computer algebra system, Fermat [1], but instead allows a flexible choice of several systems, some of which offer higher performance, especially when the number of variables is large.

Summary of revisions: A new library FUEL [2] is used as a core component of the new version of FIRE to access different computer algebra systems as simplifiers of rational function expressions. Since the first release of FUEL described elsewhere, FUEL version 1.0 here has been enhanced with a new backend based on the open source library FLINT [3] that provides highly performant simplification of rational functions.

Nature of problem: Feynman integrals of a given family are reduced to a finite set of master integrals, by solving linear equations arising from integration by parts, using Gaussian elimination. The coefficients of the linear equations are generally rational functions in kinematic variables and the spacetime dimension, and the simplification of such rational functions during Gaussian elimination is a key task that is improved in this upgrade of FIRE.

Solution method: Computer algebra systems with state-of-the-art capabilities for polynomial GCD computations are used as simplification backends, or simp

FIRE 是一个对费曼积分进行逐部积分(IBP)还原的程序。最初,FIRE 的 C++ 版本依赖于罗伯特-刘易斯(Robert Lewis)的计算机代数系统费马(Fermat)来简化有理函数。我们介绍了 FIRE 的升级版,它集成了一个新库 FUEL(最初在另一出版物中介绍),可以灵活选择第三方计算机代数系统作为简化器,并以 C++ 库的形式而不是通过 Unix 管道与某些简化器进行高效通信。在使用本研究中新添加的基于 FLINT 的开源后端,或 Ben Ruijl 开发的作为 FORM 潜在后继者的 Symbolica 后端时,我们在涉及许多运动学变量的费曼积分的 IBP 简化方面取得了显著的加速:FIRE, version 6.5 (FIRE 6.5)CPC Library program files link: https://doi.org/10.17632/cy6k69pb3y.2Developer's repository link: https://gitlab.com/feynmanintegrals/fire.gitLicensing provisions:GPLv2 编程语言Wolfram Mathematica 8.0 或更高版本,C++17补充材料:有关安装说明,请参见链接的资源库:Comput.Phys.247 (2020) 106877新版本是否取代旧版本?是:新版本不再依赖于单一的计算机代数系统费马[1],而是允许灵活选择多个系统,其中一些系统性能更高,尤其是当变量数量较多时:新版 FIRE 的核心组件是一个新库 FUEL [2],用于访问不同的计算机代数系统,作为有理函数表达式的简化器。问题的性质:通过使用高斯消元法求解分部积分所产生的线性方程组,将给定族的费曼积分简化为一组有限的主积分。线性方程的系数通常是运动变量和时空维度的有理函数,在高斯消元过程中简化这些有理函数是 FIRE 升级版改进的一项关键任务:解决方法:计算机代数系统具有最先进的多项式 GCD 计算能力,可用作简化后端,简称简化器。由于 FIRE 的设计,文本字符串被用作有理函数简化前后的交换格式。我们编写了一个快速 C++ 解析器,用于将字符串解析为外部化简器 FLINT [3] 的内部格式,该化简器在多变量多项式计算方面性能一流。同样,简化器 Symbolica [4] 在 GCD 计算和解析方面也有很高的性能,并已集成到 FIRE 中。参考文献[1]https://home.bway.net/lewis/,免费软件,有一些限制。[2]https://doi.org/10.26089/NumMet.v24r425,开源软件。[3]https://flintlib.org/,开源软件。[4]https://symbolica.io/,商业软件,有免费许可证,供学生和业余爱好者使用。
{"title":"FIRE 6.5: Feynman integral reduction with new simplification library","authors":"Alexander V. Smirnov ,&nbsp;Mao Zeng","doi":"10.1016/j.cpc.2024.109261","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109261","url":null,"abstract":"<div><p>FIRE is a program which performs integration-by-parts (IBP) reductions of Feynman integrals. Originally, the C++ version of FIRE relies on the computer algebra system Fermat by Robert Lewis to simplify rational functions. We present an upgrade of FIRE which incorporates a new library FUEL initially described in a separate publication, which enables a flexible choice of third-party computer algebra systems as simplifiers, as well as efficient communications with some of the simplifiers as C++ libraries rather than through Unix pipes. We achieve significant speedups for IBP reductions of Feynman integrals involving many kinematic variables, when using an open source backend based on FLINT newly added in this work, or the Symbolica backend developed by Ben Ruijl as a potential successor of FORM.</p></div><div><h3>Program summary</h3><p><em>Program title:</em> FIRE, version 6.5 (FIRE 6.5)</p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/cy6k69pb3y.2</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://gitlab.com/feynmanintegrals/fire.git</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> GPLv2</p><p><em>Programming language:</em> <span>Wolfram Mathematica</span> 8.0 or higher, <span>C++17</span></p><p><em>Supplementary material:</em> See linked repository for installation instructions.</p><p><em>Journal reference of previous version:</em> Comput. Phys. Commun. 247 (2020) 106877</p><p><em>Does the new version supersede the previous version?:</em> Yes.</p><p><em>Reasons for the new version:</em> The new version no longer relies on a single computer algebra system, <span>Fermat</span> [1], but instead allows a flexible choice of several systems, some of which offer higher performance, especially when the number of variables is large.</p><p><em>Summary of revisions:</em> A new library <span>FUEL</span> [2] is used as a core component of the new version of <span>FIRE</span> to access different computer algebra systems as simplifiers of rational function expressions. Since the first release of <span>FUEL</span> described elsewhere, <span>FUEL</span> version 1.0 here has been enhanced with a new backend based on the open source library <span>FLINT</span> [3] that provides highly performant simplification of rational functions.</p><p><em>Nature of problem:</em> Feynman integrals of a given family are reduced to a finite set of master integrals, by solving linear equations arising from integration by parts, using Gaussian elimination. The coefficients of the linear equations are generally rational functions in kinematic variables and the spacetime dimension, and the simplification of such rational functions during Gaussian elimination is a key task that is improved in this upgrade of <span>FIRE</span>.</p><p><em>Solution method:</em> Computer algebra systems with state-of-the-art capabilities for polynomial GCD computations are used as simplification backends, or simp","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141163503","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}
引用次数: 0
CNUCTRAN: A program for computing final nuclide concentrations using a direct simulation approach CNUCTRAN:使用直接模拟方法计算最终核素浓度的程序
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-05-22 DOI: 10.1016/j.cpc.2024.109258
K.A. Bala, M.R. Omar, John Y.H. Soo, W.M.H. Wan Mokhtar

It is essential to precisely determine the evolving concentrations of radioactive nuclides within transmutation problems. It is also a crucial aspect of nuclear physics with widespread applications in nuclear waste management and energy production. This paper introduces CNUCTRAN, a novel computer program that employs a probabilistic approach to estimate nuclide concentrations in transmutation problems. CNUCTRAN directly simulates nuclei transformations arising from various nuclear reactions, diverging from the traditional deterministic methods that solve the Bateman equation using matrix exponential approximation. This approach effectively addresses numerical challenges associated with solving the Bateman equations, therefore, circumventing the need for matrix exponential approximations that risk producing nonphysical concentrations. Our sample calculations using CNUCTRAN shows that the concentration predictions of CNUCTRAN have a relative error of less than 0.001% compared to the state-of-the-art method, CRAM, in different test cases. This makes CNUCTRAN a valuable alternative tool for transmutation analysis.

Program summary

Program Title: CNUCTRAN

CPC Library link to program files: https://doi.org/10.17632/b484w2vx52.1

Developer's repository link: https://github.com/rabieomar92/cnuctran/releases

Licensing provisions: MIT

Programming language: C++

Nature of problem: CNUCTRAN simulates the transmutation of various nuclides such as decays, fissions, and neutron induced reactions using a direct simulation approach. It has the capability of predicting the final concentration of a large system of nuclides altogether after a specified time step, tf.

Solution method: CNUCTRAN works based on the novel probabilistic method such that it does not compute the final nuclide concentrations by solving Bateman equations. Instead, it statistically tracks nuclide transformations into one another in a transmutation problem. The technique encapsulates various possible nuclide transformations into a sparse transfer matrix, T, whose elements are made up of various nuclear reaction probabilities. Next, T serves as a matrix operator acting on the initial nuclide concentrations, y(0), producing the final nuclide concentrations, y.

在嬗变问题中,精确确定放射性核素的演变浓度至关重要。这也是核物理的一个重要方面,在核废料管理和能源生产中有着广泛的应用。本文介绍的 CNUCTRAN 是一种新型计算机程序,它采用概率方法来估算嬗变问题中的核素浓度。CNUCTRAN 直接模拟各种核反应产生的核素转化,有别于使用矩阵指数近似法求解贝特曼方程的传统确定性方法。这种方法有效地解决了与求解贝特曼方程相关的数值难题,从而避免了矩阵指数近似可能产生非物理浓度的风险。我们使用 CNUCTRAN 进行的样本计算显示,在不同的测试案例中,CNUCTRAN 预测的浓度与最先进的 CRAM 方法相比,相对误差小于 0.001%。这使得 CNUCTRAN 成为嬗变分析的重要替代工具:CNUCTRANCPC 程序库链接到程序文件的链接:https://doi.org/10.17632/b484w2vx52.1Developer's repository 链接:https://github.com/rabieomar92/cnuctran/releasesLicensing provisions:MIT编程语言:问题性质:CNUCTRAN 使用直接模拟方法模拟各种核素的嬗变,如衰变、裂变和中子诱发反应。它能够预测指定时间步长 tf 之后大型核素系统的最终浓度:CNUCTRAN 基于新颖的概率方法工作,它不通过求解贝特曼方程来计算最终的核素浓度。相反,它在嬗变问题中对核素的相互转化进行统计跟踪。该技术将各种可能的核素转化囊括到一个稀疏的转移矩阵 T 中,其元素由各种核反应概率组成。然后,T 作为矩阵算子作用于初始核素浓度 y(0),产生最终核素浓度 y。
{"title":"CNUCTRAN: A program for computing final nuclide concentrations using a direct simulation approach","authors":"K.A. Bala,&nbsp;M.R. Omar,&nbsp;John Y.H. Soo,&nbsp;W.M.H. Wan Mokhtar","doi":"10.1016/j.cpc.2024.109258","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109258","url":null,"abstract":"<div><p>It is essential to precisely determine the evolving concentrations of radioactive nuclides within transmutation problems. It is also a crucial aspect of nuclear physics with widespread applications in nuclear waste management and energy production. This paper introduces <span>CNUCTRAN</span>, a novel computer program that employs a probabilistic approach to estimate nuclide concentrations in transmutation problems. <span>CNUCTRAN</span> directly simulates nuclei transformations arising from various nuclear reactions, diverging from the traditional deterministic methods that solve the Bateman equation using matrix exponential approximation. This approach effectively addresses numerical challenges associated with solving the Bateman equations, therefore, circumventing the need for matrix exponential approximations that risk producing nonphysical concentrations. Our sample calculations using <span>CNUCTRAN</span> shows that the concentration predictions of <span>CNUCTRAN</span> have a relative error of less than 0.001% compared to the state-of-the-art method, CRAM, in different test cases. This makes <span>CNUCTRAN</span> a valuable alternative tool for transmutation analysis.</p></div><div><h3>Program summary</h3><p><em>Program Title:</em> <span>CNUCTRAN</span></p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/b484w2vx52.1</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://github.com/rabieomar92/cnuctran/releases</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> MIT</p><p><em>Programming language:</em> C++</p><p><em>Nature of problem:</em> <span>CNUCTRAN</span> simulates the transmutation of various nuclides such as decays, fissions, and neutron induced reactions using a direct simulation approach. It has the capability of predicting the final concentration of a large system of nuclides altogether after a specified time step, <span><math><msub><mrow><mi>t</mi></mrow><mrow><mi>f</mi></mrow></msub></math></span>.</p><p><em>Solution method:</em> <span>CNUCTRAN</span> works based on the novel probabilistic method such that it does not compute the final nuclide concentrations by solving Bateman equations. Instead, it statistically tracks nuclide transformations into one another in a transmutation problem. The technique encapsulates various possible nuclide transformations into a sparse transfer matrix, <span><math><mi>T</mi></math></span>, whose elements are made up of various nuclear reaction probabilities. Next, <span><math><mi>T</mi></math></span> serves as a matrix operator acting on the initial nuclide concentrations, <span><math><mi>y</mi><mo>(</mo><mn>0</mn><mo>)</mo></math></span>, producing the final nuclide concentrations, <strong>y</strong>.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141089732","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}
引用次数: 0
Jiezi: an open-source Python software for simulating quantum transport based on non-equilibrium Green's function formalism 杰子:基于非平衡格林函数形式主义模拟量子输运的开源 Python 软件
IF 6.3 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2024-05-21 DOI: 10.1016/j.cpc.2024.109251
Junyan Zhu , Jiang Cao , Chen Song , Bo Li , Zhengsheng Han

We present a Python-based open-source library named Jiezi, which provides the means of simulating the electronic transport properties of nanoscaled devices on the atomistic level. The key feature of Jiezi lies in its core algorithm, i.e., self-consistent orchestration between the non-equilibrium Green's function (NEGF) method and a Poisson's equation solver. Beyond the construction of the tight-binding (TB) Hamiltonian with empirical parameters for conventional materials, the package offers a comprehensive framework for constructing the Wannier-based Hamiltonian matrix, enabling the investigation of novel materials and their heterostructures. To expedite the solution of NEGF systems, a methodology based on renormalization theory is proposed for reducing the dimension of the Hamiltonian matrix. Additionally, we adopt a non-linear Poisson equation solver with no analytical approximation in this software. The software facilitates seamless integration with external tools for geometry and mesh generation and post-processing. In this paper, we present the main capabilities and workflow by demonstrating with a simulation for the carbon nanotube field-effect transistor (CNTFET).

Program summary

Program Title: Jiezi

CPC Library link to program files: https://doi.org/10.17632/nk79kbtww4.1

Developer's repository link: https://github.com/Jiezi-negf/Jiezi

Licensing provisions: GPLv3

Programming language: Python

Nature of problem: Simulates the quantum transport property of nano-scaled transistors based on the predefined device structure and the material composition.

Solution method: Solves the coupled Schrödinger equation and Poisson equation by NEGF and finite element method.

我们介绍了一个基于 Python 的开源库,名为 Jiezi,它提供了在原子水平上模拟纳米级器件电子传输特性的方法。Jiezi 的主要特点在于其核心算法,即非平衡态格林函数(NEGF)方法与泊松方程求解器之间的自洽协调。除了利用传统材料的经验参数构建紧密结合(TB)哈密顿之外,该软件包还为构建基于万尼尔的哈密顿矩阵提供了一个全面的框架,使新型材料及其异质结构的研究成为可能。为了加快 NEGF 系统的求解速度,我们提出了一种基于重正化理论的方法来降低哈密顿矩阵的维度。此外,我们还在该软件中采用了非线性泊松方程求解器,不使用分析近似值。该软件可与外部工具无缝集成,用于几何和网格生成及后处理。在本文中,我们将通过对碳纳米管场效应晶体管(CNTFET)的仿真演示,介绍该软件的主要功能和工作流程:JieziCPC Library 程序文件链接:https://doi.org/10.17632/nk79kbtww4.1Developer's repository 链接:https://github.com/Jiezi-negf/JieziLicensing 规定:GPLv3 编程语言:Python问题性质:根据预定义的器件结构和材料成分,模拟纳米级晶体管的量子输运特性:通过 NEGF 和有限元法求解耦合薛定谔方程和泊松方程。
{"title":"Jiezi: an open-source Python software for simulating quantum transport based on non-equilibrium Green's function formalism","authors":"Junyan Zhu ,&nbsp;Jiang Cao ,&nbsp;Chen Song ,&nbsp;Bo Li ,&nbsp;Zhengsheng Han","doi":"10.1016/j.cpc.2024.109251","DOIUrl":"https://doi.org/10.1016/j.cpc.2024.109251","url":null,"abstract":"<div><p>We present a Python-based open-source library named <span>Jiezi</span>, which provides the means of simulating the electronic transport properties of nanoscaled devices on the atomistic level. The key feature of <span>Jiezi</span> lies in its core algorithm, i.e., self-consistent orchestration between the non-equilibrium Green's function (NEGF) method and a Poisson's equation solver. Beyond the construction of the tight-binding (TB) Hamiltonian with empirical parameters for conventional materials, the package offers a comprehensive framework for constructing the Wannier-based Hamiltonian matrix, enabling the investigation of novel materials and their heterostructures. To expedite the solution of NEGF systems, a methodology based on renormalization theory is proposed for reducing the dimension of the Hamiltonian matrix. Additionally, we adopt a non-linear Poisson equation solver with no analytical approximation in this software. The software facilitates seamless integration with external tools for geometry and mesh generation and post-processing. In this paper, we present the main capabilities and workflow by demonstrating with a simulation for the carbon nanotube field-effect transistor (CNTFET).</p></div><div><h3>Program summary</h3><p><em>Program Title:</em> Jiezi</p><p><em>CPC Library link to program files:</em> <span>https://doi.org/10.17632/nk79kbtww4.1</span><svg><path></path></svg></p><p><em>Developer's repository link:</em> <span>https://github.com/Jiezi-negf/Jiezi</span><svg><path></path></svg></p><p><em>Licensing provisions:</em> GPLv3</p><p><em>Programming language:</em> Python</p><p><em>Nature of problem:</em> Simulates the quantum transport property of nano-scaled transistors based on the predefined device structure and the material composition.</p><p><em>Solution method:</em> Solves the coupled Schrödinger equation and Poisson equation by NEGF and finite element method.</p></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":null,"pages":null},"PeriodicalIF":6.3,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0010465524001747/pdfft?md5=ab8916061cc89c6369f91c496a5a9fcc&pid=1-s2.0-S0010465524001747-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141084302","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}
引用次数: 0
期刊
Computer Physics Communications
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1