[go: up one dir, main page]
More Web Proxy on the site http://driver.im/ Skip to main content
Springer Nature Link
Log in

Visual analysis of defect clustering in 3D irradiation damage simulation data

  • Regular Paper
  • Published:
Journal of Visualization Aims and scope Submit manuscript

Abstract

Molecular dynamics simulation has become a powerful tool to deepen the understanding of the radiation damage mechanism of nuclear materials. Extracting point defects, analyzing their diffusion, and visualizing the defect dynamics in atomic simulation data are important, but challenging tasks to understand irradiation behavior. In the past, irradiation defects have been detected using the so-called Wigner–Seitz cell method and analyzed by the statistics of Frenkel pairs. However, traditional analysis modes blur the fine details of defect dynamics. In this paper, we present a visual analysis pipeline for domain scientists to comfortably explore radiation damage simulation data. We couple defect identification, defect clustering, molecule visualization, and tracking graph to form an integrated visual exploration approach. We describe the application of our approach in practice to study defect clustering in Ni–Fe alloy. With our proposed pipeline, defects can be extracted in a robust way, clusters can be visualized with a favorable representation, in-depth data analysis can be setup, and defect dynamics can be demonstrated in greater detail than previously possible.

Graphic Abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
£29.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (United Kingdom)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12

Similar content being viewed by others

References

  • Alam A, Khan SN, Wilson BG, Johnson DD (2011) Efficient isoparametric integration over arbitrary space-filling voronoi polyhedra for electronic structure calculations. Phys Rev B 84(4):045105

    Article  Google Scholar 

  • Bhardwaj U, Sand AE, Warrier M (2020) Classification of clusters in collision cascades. Comput Mater Sci 172:109364

    Article  Google Scholar 

  • Bonny G, Castin N, Terentyev D (2013) Interatomic potential for studying aging under irradiation in stainless steels: the fe ni cr model alloy. Modell Simul Maters Sci Eng 21(8):5897–5909

    Google Scholar 

  • Bremer P, Bringa E, Duchaineau M et al (2007) Topological feature extraction and tracking. J Phys Conf Series 78:012007

    Article  Google Scholar 

  • Bremer P, Weber G, Pascucci V, Day M, Bell J (2010) Analyzing and tracking buring structures in lean premixed hydrogen flames. IEEE Trans Visual Comput Graph 16:248–260

    Article  Google Scholar 

  • Bremer PT, Weber GH, Tierny J, Pascucci V, Day MS, BBell J (2011) Interactive exploration and analysis of large scale simulations using topology-based data segmentations. IEEE Trans Visual Comput Graph 17(9):1307–1324

  • Davis M, Efstathiou G, CSF, White SDM (1985) The evolution of large-scale structure in a universe dominated by code dark matter. Astrophys J 292:371–394

  • Duclos G, Adkins R, Banerjee D, Peterson MS, Varghese M et al (2020) Topological structure and dynamics of three dimensional active nematics. Science 367:1120–1124

    Article  Google Scholar 

  • Ester M, Kriegel H, Sander J, Xu X (1996) A density-based algorithm for discovering clusters in large spatial databases with noise. In: Proceedings of the 2nd international conference on knowledge discovery and data mining, pp 226–231

  • Gasparotto P, Bochicchio D, Ceriotti M, Pavan GM (2020) Identifying and tracking defects in dynamic supramolecular polymers. J Phys Chem B 124:589–599. https://doi.org/10.1021/acs.jpcb.9b11015

    Article  Google Scholar 

  • Gonen RR, Gelbard R (2017) Cluster evolution analysis: identification and detection of similar clusters and migration patterns. Exp Syst Appl 83:363–373. https://doi.org/10.1016/j.eswa.2017.04.007

    Article  Google Scholar 

  • Grottel S, Reina G, Vrabec J, Ertl T (2007) Visual verification and analysis of cluster detection for molecular dynamics. IEEE Trans Visual Comput Graph 13(6):1624–1631. https://doi.org/10.1109/TVCG.2007.70614

    Article  Google Scholar 

  • Grottel S, Dietrich CA, Comba JLD, Ertl T (2009) Topological extraction and tracking of defects in crystal structures. In: Proceedings of the 3rd workshop on topological methods in data analysis and visualization, Snowbird, UT, pp 167–178, https://doi.org/10.1007/978-3-642-15014-2_14

  • Guo HQ, Phillips CL, Peterka T, Karpeyev D, Glatz A (2016) Extracting, tracking, and visualizing magnetic flux vortices in 3d complex-valued superconductor simulation data. IEEE Trans Visual Comput Graph 22:827–836. https://doi.org/10.1109/TVCG.2015.2466838

    Article  Google Scholar 

  • Keys AS, Iacovella CR, Glotzer SC (2011) Characterizing complex particle morphologies through shape matching: descriptors, applications, and algorithms. J Comput Phys 230:6438–6463. https://doi.org/10.1016/j.jcp.2011.04.017

    Article  MATH  Google Scholar 

  • Koch L, Granberg F, Brink T et al (2017) Local segregation versus irradiation effects in high-entropy alloys: steady-state conditions in a driven system. J Appl Phys 122:105106

    Article  Google Scholar 

  • Kozlíková B, Krone M, Lindow N, Falk M, Baaden M, Baum D, Viola I, Parulek J, Hege HC (2015) Visualization of biomolecular structure: The state of the art. In: EuroVis, https://doi.org/10.2312/eurovisstar.20151112

  • Laney D, Bremer PT, Mascarenhas A, Miller P, Pascucci V (2006) Understanding the structure of the turbulent mixing layer in hydrodynamic instabilities. IEEE Trans Visual Comput Graph 12:1053–1060. https://doi.org/10.1109/TVCG.2006.186

    Article  Google Scholar 

  • Liu YN, Ahlgren T, Bukonte L, Nordlund K, Shu X, Yu Y, Li X, Lu G (2013) Mechanism of vacancy formation induced by hydrogen in tungsten. AIP Adv 3:122111

    Article  Google Scholar 

  • Lorensen WE, Cline HE (1987) Marching cubes: A high resolution 3d surface construction algorithm. In: ACM SIGGRAPH Computer Graphics, New York, NY, pp 163–169, https://doi.org/10.1145/37401.37422

  • Lukasczyk J, Aldrich G, Steptoe M, Favelier G, Gueunet C, Tierny J, Maciejewski R, Hamann B, Leitte H (2017a) Viscous fingering: a topological visual analytic approach. Appl Mech Mater 869:9–19

    Article  Google Scholar 

  • Lukasczyk J, Weber G, Maciejewski R, Garth C, Leitte H (2017b) Nested tracking graphs. Comput Graph Forum 36(3):12–22. https://doi.org/10.1111/cgf.13164

    Article  Google Scholar 

  • Lümmen N, Kraska T (2007) Common neighbour analysis for binary atomic systems. Model Simul Mater Sci Eng 15:319–334. https://doi.org/10.1088/0965-0393/15/3/010

    Article  Google Scholar 

  • Palla G, Barabasi AL, Vicsek T (2007) Quantifying social group evolution. Nature 446:664. https://doi.org/10.1038/nature05670

    Article  Google Scholar 

  • Partner HL, Nigmatullin R, Burgermeister T, Pyka K, Keller J, Retzker A, Plenio MB, Mehlstaubler TE (2013) Dynamics of topological defects in ion coulomb crystals. New J Phys 15(10):103013

    Article  Google Scholar 

  • Patwary MMA, Palsetia D, Agrawal A, et al. (2012) A new scalable parallel dbscan algorithm using the disjoint-set data structure. In: Proc. SC, IEEE, Salt Lake City, UT, https://doi.org/10.1109/SC.2012.9

  • Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput Phys 117:1–19. https://doi.org/10.1006/jcph.1995.1039

    Article  MATH  Google Scholar 

  • Reina G, Ertl T (2005) Hardware-accelerated glyphs for mono- and dipoles in molecular dynamics visualization. In: Eurovis, Eurographics Assoc., pp 177–182, https://doi.org/10.2312/VisSym/EuroVis05/177-182

  • Rycroft CH (2009) Voro++: a three-dimensional Voronoi cell library in C++. Chaos 19:041111

    Article  Google Scholar 

  • Sauer F, Yu HF, liu Ma K, (2014) Trajectory-based flow feature tracking in joint particle/volume datasets. IEEE Trans Visual Comput Graph 20:2565–2574. https://doi.org/10.1109/TVCG.2014.2346423

  • Soneda N (2014) Irradiation Embrittlement of Reactor Pressure Vessels (RPVs) in Nuclear Power Plants, first ed. edn. Woodhead Publishing Series in Energy, https://doi.org/10.1016/C2013-0-17428-4

  • Stukowski A (2010) Visualization and analysis of atomistic simulation data with ovito-the open visualization tool. Model Simul Mater Sci Eng 18(1):015012

    Article  Google Scholar 

  • Tierny J, Favelier G, Levine JA, Gueunet C, Michaux M (2018) The topology toolkit. IEEE Trans Visual Comput Graph 24(1):832–842. https://doi.org/10.1109/TVCG.2017.2743938

    Article  Google Scholar 

  • Wei JS, Yu HF, Grout RW, Chen JH, liu Ma K, (2011) Visual analysis of particle behaviors to understand combustion simulations. IEEE Comput Graph Appl 32:22–33. https://doi.org/10.1109/mcg.2011.108

  • Wigner E, Seitz F (1933) On the constitution of metallic sodium. Physl Rev 43(10):804–810. https://doi.org/10.1103/PhysRev.43.804

    Article  MATH  Google Scholar 

  • Zhu Y, Bridson R (2005) Animating sand as a fluid. ACM Trans Graph 24(3):965–972. https://doi.org/10.1145/1073204.1073298

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by National Key R&D Program of China [2017YFB0701502] and National Natural Science Fund of China [61403036, 11871109, and 61672003].

Author information

Authors and Affiliations

  1. Institute of Applied Physics and Computational Mathematics, Beijing, China

    Guoqing Wu & Huawei Wang

  2. CAEP Software Center for High Performance Numerical Simulation, Beijing, China

    Deye Lin

  3. Beijing Advanced Innovation Center for Material Genome Engineering, State Key Laboratory for Advanced Mentals and Materials, University of Science and Technology Beijing, Beijing, China

    Leqing Liu

Authors
  1. Guoqing Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Deye Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Huawei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Leqing Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Guoqing Wu.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wu, G., Lin, D., Wang, H. et al. Visual analysis of defect clustering in 3D irradiation damage simulation data. J Vis 25, 31–45 (2022). https://doi.org/10.1007/s12650-021-00769-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12650-021-00769-9

Keywords

Search

Navigation