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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 ’.
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This content will become publicly available on July 31, 2026
Code Review, Reproducibility, and Improving the Scholarly Record
An ongoing theme in this Reinforcing Reproducibility and Replicability column is the verification of reproducibility packages by institutions, see Butler (2023), Peer (2024), Pérignon (2024), and Jones (2024) for examples. In this present piece, Limor Peer and her co-author, Nicholas Ottone, build on their experience at the Institution for Social and Policy Studies at Yale University to not just provide guidance to authors (a sine-qua-non of any such recommendation), but also for those who will provide constructive comments, including post-publication updates, on efforts to reproduce replication packages. Ottone and Peer’s short piece describes the idea of a “curator note,” which can be added to already published replication packages at, well, “curated” deposits to enhance the future reproducibility for others. It is worth pointing out that many archives provide the ability for authors themselves to provide such notes, see for instance the American Economic Association’s Policy on Revisions of Data and Code Deposits. Students, researchers, and authors themselves should read Ottone’s and Peer’s recommendations.
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- Award ID(s):
- 2217493
- PAR ID:
- 10634642
- Editor(s):
- Vilhuber, Lars
- Publisher / Repository:
- Harvard Data Science Review
- Date Published:
- Journal Name:
- Harvard Data Science Review
- Volume:
- 7
- Issue:
- 3
- ISSN:
- 2644-2353
- Subject(s) / Keyword(s):
- reproducibility, verification, code review, open scholarship
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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