GRANAD - Simulating GRAphene nanoflakes with ADatoms

IF 3.4 2区 物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS
David Dams , Miriam Kosik , Marvin Müller , Abhishek Ghosh , Antton Babaze , Julia Szczuczko , Garnett W. Bryant , Andrés Ayuela , Carsten Rockstuhl , Marta Pelc , Karolina Słowik
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Abstract

GRANAD is a program based on the tight-binding approximation to simulate optoelectronic properties of graphene nanoflakes and Su–Schrieffer–Heeger (SSH) chains with possible adatom defects under electromagnetic illumination. Its core feature is the numerical solution of a time-domain master equation for the spin-traced one-particle reduced density matrix. It provides time-resolved evolution of charge distributions, access to induced-field dynamics, and characterization of the plasmonic response. Other computable quantities include energy profiles, electron distribution in real space, and absorption spectra. GRANAD is written in Python and relies on the JAX library for high-performance array computing, just-in-time (JIT) compilation, and differentiability. It is intended to be lightweight, portable, and easy to set up, offering a transparent and efficient way to access the properties of low-dimensional carbon structures from the nanoscale to the mesoscopic regime. GRANAD is open source, with the full code and extensive documentation with usage examples available at https://github.com/GRANADlauncher/granad.git.

Program summary

Program Title: GRANAD
CPC Library link to program files: https://doi.org/10.17632/723d4m4z9x.1
Developer's repository link: https://github.com/GRANADlauncher/granad
Licensing provisions: MIT
Programming language: Python
Supplementary material: Code, documentation and demo files.
Nature of problem: Accessing the dynamical optical properties of graphene nanoflakes and one-dimensional polymer chains up to the mesoscale in the presence of adatoms represents a conceptual and computational challenge. Easily accessible classical methods fail as they do not accommodate relevant quantum effects. At the same time, quantum-mechanical ab initio time-domain approaches are computationally costly, and their implementations are often difficult for the user to set up and extend due to the high complexity of the codebase.
Solution method: A theoretical framework that combines an electronic mean-field approach with a Lindblad-like master equation is implemented to describe these carbon-based systems, where interaction with an external electric field is described semiclassically in the tight-binding approximation. Many-body effects are modeled via a nonlinear interaction term in the Hamiltonian, while dissipative processes are included in the master equation. Simulations are performed in the time domain, providing detailed access to physically relevant quantities. The implementation is lightweight, easily portable, and can be extended to incorporate other materials and nanoflake stacks.
Additional comments including restrictions and unusual features: The program relies on the JAX library, enabling differentiation of its core functions. It is intended to be extendable to, e.g., electric field parameter optimization for desired nanomaterial response and to popularize the differentiable programming technique further.
GRANAD -用ADatoms模拟石墨烯纳米片
GRANAD是一个基于紧密结合近似的程序,用于模拟电磁照明下可能存在adatom缺陷的石墨烯纳米片和Su-Schrieffer-Heeger (SSH)链的光电特性。它的核心特征是自旋跟踪的单粒子约简密度矩阵的时域主方程的数值解。它提供了时间分辨的电荷分布演化,感应场动力学,以及等离子体响应的表征。其他可计算的量包括能量分布、实际空间中的电子分布和吸收光谱。GRANAD是用Python编写的,依靠JAX库实现高性能数组计算、即时(JIT)编译和可微分性。它的目的是轻巧,便携,易于设置,提供一个透明和有效的方式来访问低维碳结构的性质,从纳米尺度到介观制度。GRANAD是开源的,在https://github.com/GRANADlauncher/granad.git.Program summaryProgram标题:GRANADCPC库链接到程序文件:https://doi.org/10.17632/723d4m4z9x.1Developer's存储库链接:https://github.com/GRANADlauncher/granadLicensing条款:mit编程语言:python补充材料:代码、文档和演示文件。问题性质:在adatoms存在的情况下,获取到中尺度的石墨烯纳米片和一维聚合物链的动态光学特性是一个概念和计算上的挑战。容易获得的经典方法失败了,因为它们不能适应相关的量子效应。与此同时,量子力学从头算时域方法的计算成本很高,并且由于代码库的高度复杂性,用户通常难以设置和扩展它们的实现。解决方法:将电子平均场方法与lindblad类主方程相结合的理论框架用于描述这些碳基系统,其中与外电场的相互作用在紧密结合近似中被半经典地描述。多体效应通过哈密顿量中的非线性相互作用项来建模,而耗散过程则包含在主方程中。在时域中进行模拟,提供对物理相关量的详细访问。该实现是轻量级的,易于移植的,并且可以扩展到包含其他材料和纳米片堆栈。附加注释,包括限制和不寻常的功能:该程序依赖于JAX库,使其核心功能得以区分。本文的目的是将可微规划技术进一步推广到纳米材料响应的电场参数优化等领域。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Computer Physics Communications
Computer Physics Communications 物理-计算机:跨学科应用
CiteScore
12.10
自引率
3.20%
发文量
287
审稿时长
5.3 months
期刊介绍: The focus of CPC is on contemporary computational methods and techniques and their implementation, the effectiveness of which will normally be evidenced by the author(s) within the context of a substantive problem in physics. Within this setting CPC publishes two types of paper. Computer Programs in Physics (CPiP) These papers describe significant computer programs to be archived in the CPC Program Library which is held in the Mendeley Data repository. The submitted software must be covered by an approved open source licence. Papers and associated computer programs that address a problem of contemporary interest in physics that cannot be solved by current software are particularly encouraged. Computational Physics Papers (CP) These are research papers in, but are not limited to, the following themes across computational physics and related disciplines. mathematical and numerical methods and algorithms; computational models including those associated with the design, control and analysis of experiments; and algebraic computation. Each will normally include software implementation and performance details. The software implementation should, ideally, be available via GitHub, Zenodo or an institutional repository.In addition, research papers on the impact of advanced computer architecture and special purpose computers on computing in the physical sciences and software topics related to, and of importance in, the physical sciences may be considered.
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