arXiv - PHYS - Computational Physics最新文献

Influence of dislocations in multilayer graphene stacks: A phase field crystal study 多层石墨烯堆栈中位错的影响：相场晶体研究

arXiv - PHYS - Computational Physics Pub Date : 2024-09-18 DOI: arxiv-2409.12073

K. R. Elder, Zhi-Feng Huang, T. Ala-Nissila

{"title":"Influence of dislocations in multilayer graphene stacks: A phase field crystal study","authors":"K. R. Elder, Zhi-Feng Huang, T. Ala-Nissila","doi":"arxiv-2409.12073","DOIUrl":"https://doi.org/arxiv-2409.12073","url":null,"abstract":"In this work the influence of $5|7$ dislocations in multiplayer graphene\u0000stacks (up to six layers) is examined. The study is conducted through a\u0000recently developed Phase Field Crystal (PFC) model for multilayer systems\u0000incorporating out-of-plane deformations and parameterized to match to density\u0000functional theory calculations for graphene bilayers and other systems. The\u0000specific configuration considered consists of one monolayer containing four\u0000$5|7$ dislocations (i.e., two dislocation dipoles) sandwiched in between\u0000perfect graphene layers. The study reveals how the strain field from the\u0000dislocations in the defected layer leads to out-of-plane deformations that in\u0000turn cause deformations of neighboring layers. Quantitative predictions are\u0000made for the defect free energy of the multilayer stacks as compared to a\u0000defect-free system, which is shown to increase with the number of layers and\u0000system size. Furthermore it is predicted that system defect energy saturates by\u0000roughly ten sheets in the stack, indicating the range of defect influence\u0000across the multilayer. Variations of stress field distribution and layer height\u0000profiles in different layer of the stack are also quantitatively identified.","PeriodicalId":501369,"journal":{"name":"arXiv - PHYS - Computational Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AHKASH: a new Hybrid particle-in-cell code for simulations of astrophysical collisionless plasma AHKASH：用于模拟天体物理无碰撞等离子体的新型混合粒子-单元代码

arXiv - PHYS - Computational Physics Pub Date : 2024-09-18 DOI: arxiv-2409.12151

Radhika Achikanath Chirakkara, Christoph Federrath, Amit Seta

{"title":"AHKASH: a new Hybrid particle-in-cell code for simulations of astrophysical collisionless plasma","authors":"Radhika Achikanath Chirakkara, Christoph Federrath, Amit Seta","doi":"arxiv-2409.12151","DOIUrl":"https://doi.org/arxiv-2409.12151","url":null,"abstract":"We introduce $texttt{A}$strophysical $texttt{H}$ybrid-$texttt{K}$inetic\u0000simulations with the $texttt{flASH}$ code ($texttt{AHKASH}$) -- a new Hybrid\u0000particle-in-cell (PIC) code developed within the framework of the multi-physics\u0000code $texttt{FLASH}$. The new code uses a second-order accurate Boris\u0000integrator and a predictor-predictor-corrector algorithm for advancing the\u0000Hybrid-kinetic equations, using the constraint transport method to ensure that\u0000magnetic fields are divergence-free. The code supports various interpolation\u0000schemes between the particles and grid cells, with post-interpolation smoothing\u0000to reduce finite particle noise. We further implement a $delta f$ method to\u0000study instabilities in weakly collisional plasmas. The new code is tested on\u0000standard physical problems such as the motion of charged particles in uniform\u0000and spatially varying magnetic fields, the propagation of Alfv'en and whistler\u0000waves, and Landau damping of ion acoustic waves. We test different\u0000interpolation kernels and demonstrate the necessity of performing\u0000post-interpolation smoothing. We couple the $texttt{TurbGen}$ turbulence\u0000driving module to the new Hybrid PIC code, allowing us to test the code on the\u0000highly complex physical problem of the turbulent dynamo. To investigate\u0000steady-state turbulence with a fixed sonic Mach number, it is important to\u0000maintain isothermal plasma conditions. Therefore, we introduce a novel cooling\u0000method for Hybrid PIC codes and provide tests and calibrations of this method\u0000to keep the plasma isothermal. We describe and test the `hybrid precision'\u0000method, which significantly reduces (by a factor $sim1.5$) the computational\u0000cost, without compromising the accuracy of the numerical solutions. Finally, we\u0000test the parallel scalability of the new code, showing excellent scaling up to\u000010,000~cores.","PeriodicalId":501369,"journal":{"name":"arXiv - PHYS - Computational Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exascale Quantum Mechanical Simulations: Navigating the Shifting Sands of Hardware and Software 超大规模量子力学模拟：驾驭硬件和软件的风云变幻

arXiv - PHYS - Computational Physics Pub Date : 2024-09-18 DOI: arxiv-2409.11881

Ravindra Shinde, Claudia Filippi, Anthony Scemama, William Jalby

引用次数: 0

Designing a minimal Landau theory to stabilize desired quasicrystals 设计最小朗道理论以稳定所需的准晶体

arXiv - PHYS - Computational Physics Pub Date : 2024-09-18 DOI: arxiv-2409.11830

Wei Si, Shifeng Li, Pingwen Zhang, An-Chang Shi, Kai Jiang

{"title":"Designing a minimal Landau theory to stabilize desired quasicrystals","authors":"Wei Si, Shifeng Li, Pingwen Zhang, An-Chang Shi, Kai Jiang","doi":"arxiv-2409.11830","DOIUrl":"https://doi.org/arxiv-2409.11830","url":null,"abstract":"Interparticle interactions with multiple length scales play a pivotal role in\u0000the formation and stability of quasicrystals. Choosing a minimal set of length\u0000scales to stabilize a given quasicrystal is a challenging problem. To address\u0000this challenge, we propose an intelligent screening method (ISM) to design a\u0000Landau theory with a minimal number of length scales -- referred to as the\u0000minimal Landau theory -- that includes only the essential length scales\u0000necessary to stabilize quasicrystals. Based on a generalized\u0000multiple-length-scale Landau theory, ISM first evaluates various spectral\u0000configurations of candidate structures under a hard constraint. It then\u0000identifies the configuration with the lowest free energy. Using this optimal\u0000configuration, ISM calculates phase diagrams to explore the thermodynamic\u0000stability of desired quasicrystals. ISM can design a minimal Landau theory\u0000capable of stabilizing the desired quasicrystals by incrementally increasing\u0000the number of length scales. Our application of ISM has not only confirmed\u0000known behaviors in 10- and 12-fold quasicrystals but also led to a significant\u0000prediction that quasicrystals with 8-, 14-, 16-, and 18-fold symmetry could be\u0000stable within three-length-scale Landau models.","PeriodicalId":501369,"journal":{"name":"arXiv - PHYS - Computational Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Uncovering liquid-substrate fluctuation effects on crystal growth and disordered hyperuniformity of two-dimensional materials 揭示液体-基底波动对晶体生长和二维材料无序超均匀性的影响

arXiv - PHYS - Computational Physics Pub Date : 2024-09-18 DOI: arxiv-2409.12090

S. K. Mkhonta, Zhi-Feng Huang, K. R. Elder

引用次数: 0

Thermolectricity in irradiated bilayer graphene flakes 辐照双层石墨烯薄片的热电性

arXiv - PHYS - Computational Physics Pub Date : 2024-09-16 DOI: arxiv-2409.10380

Cynthia Ihuoma Osuala, Tanu Choudhary, Raju K. Biswas, Sudin Ganguly, Chunlei Qu, Santanu K. Maiti

{"title":"Thermolectricity in irradiated bilayer graphene flakes","authors":"Cynthia Ihuoma Osuala, Tanu Choudhary, Raju K. Biswas, Sudin Ganguly, Chunlei Qu, Santanu K. Maiti","doi":"arxiv-2409.10380","DOIUrl":"https://doi.org/arxiv-2409.10380","url":null,"abstract":"We present a comprehensive study on enhancing the thermoelectric (TE)\u0000performance of bilayer graphene (BLG) through irradiation with arbitrarily\u0000polarized light, focusing on $AA$- and $AB$-stacked configurations with zigzag\u0000edges. Utilizing a combination of tight-binding theory and density functional\u0000theory (DFT), we systematically analyze the impact of light irradiation on\u0000electronic and phononic transport properties. Light irradiation alters the\u0000electronic hopping parameters, creating an asymmetric transmission function,\u0000which significantly increases the Seebeck coefficient, thereby boosting the\u0000overall {it figure of merit} (FOM). For the phononic contribution, DFT\u0000calculations reveal that $AB$-stacked BLG exhibits lower lattice thermal\u0000conductivity compared to $AA$-stacked, attributed to enhanced anharmonic\u0000scattering and phonon group velocity. The combined analysis shows that FOM\u0000exceeds unity in both stacking types, with notable improvements near the\u0000irradiation-induced gap. Additionally, we explore the dependence of FOM on the\u0000system dimensions and temperature, demonstrating that light-irradiated BLG\u0000holds great promise for efficient thermoelectric energy conversion and waste\u0000heat recovery. Our results show favorable responses over a wide range of\u0000irradiation parameters. These findings provide crucial insights into optimizing\u0000BLG for advanced TE applications through light-induced modifications.","PeriodicalId":501369,"journal":{"name":"arXiv - PHYS - Computational Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Accelerating Molecular Dynamics through Informed Resetting 通过知情重置加速分子动力学发展

arXiv - PHYS - Computational Physics Pub Date : 2024-09-16 DOI: arxiv-2409.10115

Jonathan R. Church, Ofir Blumer, Tommer D. Keidar, Leo Ploutno, Shlomi Reuveni, Barak Hirshberg

{"title":"Accelerating Molecular Dynamics through Informed Resetting","authors":"Jonathan R. Church, Ofir Blumer, Tommer D. Keidar, Leo Ploutno, Shlomi Reuveni, Barak Hirshberg","doi":"arxiv-2409.10115","DOIUrl":"https://doi.org/arxiv-2409.10115","url":null,"abstract":"We present a procedure for enhanced sampling of molecular dynamics\u0000simulations through informed stochastic resetting. Many phenomena, such as\u0000protein folding and crystal nucleation, occur over time scales that are\u0000inaccessible using standard simulation methods. We recently showed that\u0000stochastic resetting can accelerate molecular simulations that exhibit broad\u0000transition time distributions. However, standard stochastic resetting does not\u0000exploit any information about the reaction progress. Here, we demonstrate that\u0000an informed resetting protocol leads to greater accelerations than standard\u0000stochastic resetting, both for molecular dynamics and Metadynamics simulations.\u0000This is achieved by resetting only when a certain condition is met, e.g., when\u0000the distance from the target along the reaction coordinate is larger than some\u0000threshold. We then employ recently obtained theoretical results to identify the\u0000condition that leads to the greatest acceleration and to infer the unbiased\u0000mean transition time from accelerated simulations. Our work significantly\u0000extends the applicability of stochastic resetting for enhanced sampling of\u0000molecular simulations.","PeriodicalId":501369,"journal":{"name":"arXiv - PHYS - Computational Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The shape of convection in 2D and 3D global simulations of stellar interiors 恒星内部二维和三维全局模拟中的对流形状

arXiv - PHYS - Computational Physics Pub Date : 2024-09-15 DOI: arxiv-2409.09815

M. -G. Dethero, J. Pratt, D. G. Vlaykov, I. Baraffe, T. Guillet, T. Goffrey, A. Le Saux, A. Morison

{"title":"The shape of convection in 2D and 3D global simulations of stellar interiors","authors":"M. -G. Dethero, J. Pratt, D. G. Vlaykov, I. Baraffe, T. Guillet, T. Goffrey, A. Le Saux, A. Morison","doi":"arxiv-2409.09815","DOIUrl":"https://doi.org/arxiv-2409.09815","url":null,"abstract":"Theoretical descriptions of convective overshooting often rely on a\u0000one-dimensional parameterization of the flow called the filling factor for\u0000convection. Several definitions of the filling factor have been developed,\u0000based on: (1) the percentage of the volume, (2) the mass flux, and (3) the\u0000convective flux that moves through the boundary. We examine these definitions\u0000of the filling factor with the goal of establishing their ability to explain\u0000differences between 2D and 3D global simulations of stellar interiors that\u0000include fully compressible hydrodynamics and realistic microphysics for stars.\u0000We study pairs of identical two- and three-dimensional global simulations of\u0000stars produced with MUSIC, a fully compressible, time-implicit hydrodynamics\u0000code. We examine (1) a $3 M_odot$ red giant star near the first dredge-up\u0000point, (2) a $1 M_odot$ pre-main-sequence star with a large convection zone,\u0000(3) the current sun, and (4) a $20 M_odot$ main-sequence star with a large\u0000convective core. Our calculations of the filling factor based on the volume\u0000percentage and the mass flux indicate asymmetrical convection near the surface\u0000for each star with an outer convection zone. However, near the convective\u0000boundary, convective flows achieve inward-outward symmetry; for 2D and 3D\u0000simulations, these filling factors are indistinguishable. A filling factor\u0000based on the convective flux is contaminated by boundary-layer-like flows,\u0000making theoretical interpretation difficult. We present two new alternatives to\u0000these standard definitions, which compare flows at two different radial points.\u0000The first is the penetration parameter of Anders et al. (2022). The second is a\u0000new statistic, the plume interaction parameter. We demonstrate that both of\u0000these parameters capture systematic differences between 2D and 3D simulations\u0000around the convective boundary.","PeriodicalId":501369,"journal":{"name":"arXiv - PHYS - Computational Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GPU acceleration of LCAO basis set first-principle calculations GPU 加速 LCAO 基集第一原理计算

arXiv - PHYS - Computational Physics Pub Date : 2024-09-14 DOI: arxiv-2409.09399

Haochong Zhang, Shi Yin, Lixin He

引用次数: 0

PiNNAcLe: Adaptive Learn-On-The-Fly Algorithm for Machine-Learning Potential PiNNAcLe：机器学习潜能的自适应即时学习算法

arXiv - PHYS - Computational Physics Pub Date : 2024-09-13 DOI: arxiv-2409.08886

Yunqi Shao, Chao Zhang

{"title":"PiNNAcLe: Adaptive Learn-On-The-Fly Algorithm for Machine-Learning Potential","authors":"Yunqi Shao, Chao Zhang","doi":"arxiv-2409.08886","DOIUrl":"https://doi.org/arxiv-2409.08886","url":null,"abstract":"PiNNAcLe is an implementation of our adaptive learn-on-the-fly algorithm for\u0000running machine-learning potential (MLP)-based molecular dynamics (MD)\u0000simulations -- an emerging approach to simulate the large-scale and long-time\u0000dynamics of systems where empirical forms of the PES are difficult to obtain. The algorithm aims to solve the challenge of parameterizing MLPs for\u0000large-time-scale MD simulations, by validating simulation results at adaptive\u0000time intervals. This approach eliminates the need of uncertainty quantification\u0000methods for labelling new data, and thus avoids the additional computational\u0000cost and arbitrariness thereof. The algorithm is implemented in the NextFlow workflow language (Di Tommaso et\u0000al., 2017). Components such as MD simulation and MLP engines are designed in a\u0000modular fashion, and the workflows are agnostic to the implementation of such\u0000modules. This makes it easy to apply the same algorithm to different\u0000references, as well as scaling the workflow to a variety of computational\u0000resources. The code is published under BSD 3-Clause License, the source code and\u0000documentation are hosted on Github. It currently supports MLP generation with\u0000the atomistic machine learning package PiNN (Shao et al., 2020), electronic\u0000structure calculations with CP2K (K\"uhne et al., 2020) and DFTB+ (Hourahine et\u0000al., 2020), and MD simulation with ASE (Larsen et al., 2017).","PeriodicalId":501369,"journal":{"name":"arXiv - PHYS - Computational Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0