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Reproducible validation and replication studies in nanoscale physics
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences ( IF 4.3 ) Pub Date : 2021-03-29 , DOI: 10.1098/rsta.2020.0068
N. C. Clementi 1 , L. A. Barba 1
Affiliation  

Credibility building activities in computational research include verification and validation, reproducibility and replication, and uncertainty quantification. Though orthogonal to each other, they are related. This paper presents validation and replication studies in electromagnetic excitations on nanoscale structures, where the quantity of interest is the wavelength at which resonance peaks occur. The study uses the open-source software PyGBe: a boundary element solver with treecode acceleration and GPU capability. We replicate a result by Rockstuhl et al. (2005, doi:10/dsxw9d) with a two-dimensional boundary element method on silicon carbide (SiC) particles, despite differences in our method. The second replication case from Ellis et al. (2016, doi:10/f83zcb) looks at aspect ratio effects on high-order modes of localized surface phonon-polariton nanostructures. The results partially replicate: the wavenumber position of some modes match, but for other modes they differ. With virtually no information about the original simulations, explaining the discrepancies is not possible. A comparison with experiments that measured polarized reflectance of SiC nano pillars provides a validation case. The wavenumber of the dominant mode and two more do match, but differences remain in other minor modes. Results in this paper were produced with strict reproducibility practices, and we share reproducibility packages for all, including input files, execution scripts, secondary data, post-processing code and plotting scripts, and the figures (deposited in Zenodo). In view of the many challenges faced, we propose that reproducible practices make replication and validation more feasible.

This article is part of the theme issue ‘Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico’.



中文翻译:

纳米级物理学中的可重复验证和复制研究

计算研究中的可信度建设活动包括验证和确认,可再现性和复制以及不确定性量化。尽管彼此正交,但它们是相关的。本文介绍了在纳米结构上的电磁激发中的验证和复制研究,其中感兴趣的数量是发生共振峰的波长。该研究使用开源软件y:具有树码加速和GPU功能的边界元素求解器。我们复制了Rockstuhl等人的结果(2005,doi:10 / dsxw9d),尽管我们的方法有所不同,但使用二维边界元方法对碳化硅(SiC)颗粒进行了分析。Ellis等人的第二个复制案例(2016,doi:10 / f83zcb)研究了纵横比对局部表面声子-极化子纳米结构的高阶模态的影响。结果部分重复:某些模式的波数位置匹配,但对于其他模式,它们不同。由于几乎没有有关原始模拟的信息,因此不可能解释差异。与测量SiC纳米柱的偏振反射率的实验的比较提供了一个验证案例。主导模式的波数与另外两个模式确实匹配,但其他次要模式仍存在差异。本文的结果均采用严格的可重复性做法制作,我们共享所有文件的可重复性软件包,包括输入文件,执行脚本,辅助数据,后处理代码和绘图脚本以及图形(保存在Zenodo中)。

这篇文章是主题问题的一部分“计算科学可靠性和可重复性:实施验证,确认和量化的不确定性,在硅片”。

更新日期:2021-03-29
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