Visualization and Analysis of Large-Scale Atomistic Simulations of Plasma-Surface Interactions

Widanagamaachchi, Wathsala; Hammond, Karl D.; Lo, Li-Ta; Wirth, Brian D.; Samsel, Francesca; Sewell, Christopher; Ahrens, James; Pascucci, Valerio

doi:10.2312/eurovisshort.20151117

Cited by 3 publications

(1 citation statement)

References 23 publications

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“…Another example is the coupling of interactive visualization with the analysis of plasma-surface interactions. 164 The analysis of the action sequences of the user interacting with the simulations, which would serve to correlate the effect of some external forces with some dynamics of the system, implies an open problem of recording all the interactive inputs of the user during the simulation: the problem of reproducibility is crucial to confirm the scientific results. This includes synchronizing the timing of the inputs with the simulation time step, considering and selecting the interactive user inputs that allow robust reproducibility (e.g., convergence of several different trajectories to a common stability state).…”

Section: Interactive Visual Analysismentioning

confidence: 99%

Wielding the power of interactive molecular simulations

Lanrezac

Férey

Baaden

2021

WIREs Comput Mol Sci

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Since the dawn of the computer age, scientists have designed devices to represent molecular structures and developed tools to simulate their dynamic behavior in silico. To this day, these tools remain central to our understanding of biomolecular phenomena. In contrast to other fields such as fluid mechanics or meteorology, the observation of molecular motions at the atomic level remains a major experimental challenge. Continuous advances in computer graphics and numerical computation, combined with the emergence of humancomputer interaction approaches, led to the methodology of so-called "interactive molecular simulations", characterized by two main features. First, the possibility to visualize a running simulation in interactive time, that is, compatible with human perception. Second, the possibility to manipulate the simulation interactively by imposing a force, changing a biophysical property, or editing runtime parameters on the fly. Such simulations are still little used in computational biology, where it is more common to run a series of offline simulations and then visualize and analyze the results. However, interactive molecular simulation tools promise to handle time-consuming tasks such as the modeling of particularly complex biomolecular structures more efficiently or to support approaches such as Rational Drug Design with regard to pharmaceutical applications.

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Section: Interactive Visual Analysismentioning

confidence: 99%

Wielding the power of interactive molecular simulations

Lanrezac

Férey

Baaden

2021

WIREs Comput Mol Sci

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Helium flux effects on bubble growth and surface morphology in plasma-facing tungsten from large-scale molecular dynamics simulations

et al. 2019

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We investigate helium flux effects on helium transport and surface evolution in plasma-facing tungsten using molecular dynamics. The simulations span two orders of magnitude, from ITER-relevant levels to those more typical of simulations published to date. Simulation times of up to 2.5 µs (corresponding to actual fluences of m−2) are achieved, revealing concerted bubble-bursting events that are responsible for significant and very sudden changes in surface morphology. The depth distribution of helium depends very strongly on helium flux: helium self-trapping becomes more probable near the surface at high flux, and a layer of near-surface bubbles forms. Helium retention prior to the onset of bubble bursting is also substantially lower at low flux than it is at high flux. Surface features at low fluence are correlated with the positions of bubbles, but at high fluence, bubbles tend to coalesce, venting to the surface at one or more locations and leaving large interconnected cavities below the surface. Ruptured bubbles may serve as pathways deeper into the material, allowing helium to bypass the layer of near-surface bubbles and fill deeper, potentially much larger, bubbles that can produce more substantial surface features. Deeper bubbles also emit prismatic dislocation loops that can fill in cavities closer to the surface. Our results suggest that nearly all molecular dynamics simulations published to date are hampered by finite-size effects, and that helium flux is a very important parameter in determining the behavior of helium in plasma-facing components.

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Helium, hydrogen, and fuzz in plasma-facing materials

Hammond

2017

Mater. Res. Express

118

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Visualization and Analysis of Large-Scale Atomistic Simulations of Plasma-Surface Interactions

Cited by 3 publications

References 23 publications

Wielding the power of interactive molecular simulations

Wielding the power of interactive molecular simulations

Helium flux effects on bubble growth and surface morphology in plasma-facing tungsten from large-scale molecular dynamics simulations

Helium, hydrogen, and fuzz in plasma-facing materials

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