A Path to the Exascale for Atomistic Simulations with Improved Accuracy Length and Time Scales.
Abstract not provided.
Wood, Mitchell↗
Engineering topics
Perez, Danny
Publications and source records attributed to Perez, Danny.
Exascale applications: skin in the game
As noted in Wikipedia, skin in the game refers to having ‘incurred risk by being involved in achieving a goal’, where ‘ skin is a synecdoche for the person involved, and game is the metaphor for actions on the field of play under discussion’. For exascale applications under development in the US Department of Energy Exascale Computing Project, nothing could be more apt, with the skin being exascale applications and the game being delivering comprehensive science-based computational applications that effectively exploit exascale high-performance computing technologies to provide breakthrough modelling and simulation and data science solutions. These solutions will yield high-confidence insights and answers to the most critical problems and challenges for the USA in scientific discovery, national security, energy assurance, economic competitiveness and advanced healthcare. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.
97 MATHEMATICS AND COMPUTING↗
Mobility of tungsten clusters on tungsten surfaces
It is reported on an accelerated molecular dynamics investigation of surface transport mechanisms on W surfaces. These mechanisms likely influence the formation of nano-fuzz in fusion plasma-facing conditions. The simulations use an embedded-atom potential to investigate the diffusion mechanisms of W clusters (W n , n = 2–9) on W(1 1 0) and W(1 0 0) surfaces at 1000 K, reaching timescales beyond 10 microseconds. A number of fast moving adatom species, W n (n = 2–6), were observed. In contrast, slightly larger clusters W n (n = 7–9), especially W 8 , exhibit significantly lower diffusivities. The diffusion mechanisms of W n clusters on the W(1 1 0) surface are complex, with the most common elementary steps involving hops of monomers and dimers. Moreover, we observe tetramer hopping in the diffusion processes of W n (n = 4–7), trimer hopping in W n (n = 5, 6, 8), and pentamer hopping in W 5 on the W(1 1 0) surface. W n (n ≤ 3) and metastable W n (n > 3) clusters on the W(1 0 0) surface diffuse predominantly through monomer exchange with surface atoms. However, W clusters containing square tetramers are essentially immobile on the W(1 0 0) surface at 1000 K.
Instruments & Instrumentation↗
An Overview of Recent Standard and Accelerated Molecular Dynamics Simulations of Helium Behavior in Tungsten
One of the most critical challenges for the successful adoption of nuclear fusion power corresponds to plasma-facing materials. Due to its favorable properties in this context (low sputtering yield, high thermal conductivity, high melting point, among others), tungsten is a leading candidate material. Nevertheless, tungsten is affected by the plasma and fusion byproducts. Irradiation by helium nuclei, in particular, strongly modifies the surface structure by a synergy of processes, whose origin is the nucleation and growth of helium bubbles. In this review, we present recent advances in the understanding of helium effects in tungsten from a simulational approach based on accelerated molecular dynamics, which emphasizes the use of realistic parameters, as are expected in experimental and operational fusion power conditions.
36 MATERIALS SCIENCE↗
Direct observations of shape fluctuation in long-time atomistic simulations of metallic nanoclusters
Metallic nanoclusters are functional materials whose unique physical and chemical properties are sensitively controlled by their shapes and structures. An in-depth understanding of their morphological stability is therefore of crucial importance. It has been well documented by transmission electron microscopy (TEM) studies that metallic nanoclusters can interconvert between different isomers. However, the relevant mechanisms remain elusive because the timescales of such shape fluctuations are too short to be resolved experimentally and yet too long for conventional atomistic simulations. By employing massively parallel accelerated molecular dynamics (AMD) simulations reaching timescales of milliseconds, here we provide a clear description of the dynamical processes leading to shape fluctuation in metallic nanoclusters of platinum, silver, copper, and gold at different sizes and temperatures. In all these materials, direct transformations between face-centered-cubic and fivefold symmetric structures (decahedron or icosahedron) are observed away from the melting point. These transitions occur following either a slip-mediated twinning mechanism or a surface-reconstruction driven process. The identified pathways are shown to be reversible, allowing for genuine shape fluctuation processes that do not involve melting or other external factors.
36 MATERIALS SCIENCE↗
Formation of helium-bubble networks in tungsten
The nucleation and subsequent growth of helium bubbles in bulk tungsten is investigated using molecular dynamics simulations. By considering a setting that includes the diffusion process of helium clusters, we study their attachment to existing bubbles and their interaction with tungsten crowdion structures generated in the bubble growth process. Here, we find that incoming helium atoms, and especially small helium clusters, can become trapped in the crowdion structures, providing nucleation sites for new helium bubbles, and leading to a distributed network of bubbles rather than a single, growing bubble. The nature of this network depends on both the temperature and the implantation flux of helium. Our results indicate that the kinetic interaction of He with generated dislocations is a key factor dictating the evolution of bubble distributions in plasma-exposed tungsten.
36 MATERIALS SCIENCE↗
Atomistic simulation methods for long-time dynamics in materials for nuclear energy systems
Many important processes in materials systems are intrinsically atomistic in nature but involve time scales that span many orders of magnitude, thus exceeding what can be directly simulated using molecular dynamics. This is especially true for materials in nuclear energy applications, in which defects created by collision cascades on the femtosecond-picosecond time scale cause microstructural changes that continue to evolve for years, in many cases leading to failure of the material. In this chapter, we review atomistic methods for reaching long time scales in systems like these. These accelerated molecular dynamics and adaptive kinetic Monte Carlo methods exploit the infrequent-event nature of the diffusive events that comprise this long-time evolution. In favorable cases, these methods can predict state-to-state evolution that approximates what would result from an extremely long molecular dynamics simulation, and the most accurate of the methods can do this to arbitrary accuracy. We present some examples of applications of these methods to problems relevant to nuclear energy materials, the subject of this volume. We then discuss situations that are difficult for the methods, causing them to be less efficient, and we conclude with a short list of the most pressing issues in the further development of these approaches to make them as powerful and predictive as possible for realistic problems.
36 MATERIALS SCIENCE↗
Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification
Here, a massively parallel method to build large transition rate matrices from temperature-accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state space, providing crucial uncertainty quantification for higher-scale simulation schemes such as kinetic Monte Carlo or cluster dynamics. The estimators are additionally used to optimize where exploration is performed and the degree of temperature acceleration on the fly, giving an autonomous, optimal procedure to explore the state space of complex systems. The method is tested against exactly solvable models and used to explore the dynamics of C15 interstitial defects in iron. Our uncertainty quantification scheme allows for accurate modeling of the evolution of these defects over timescales of several seconds.
36 MATERIALS SCIENCE↗
Discovering mechanisms relevant for radiation damage evolution
he response of a material to irradiation is a consequence of the kinetic evolution of defects produced during energetic damage events. Thus, accurate predictions of radiation damage evolution require knowing the atomic scale mechanisms associated with those defects. Atomistic simulations are a key tool in providing insight into the types of mechanisms possible. Further, by extending the time scale beyond what is achievable with conventional molecular dynamics, even greater insight can be obtained. Here, we provide examples in which such simulations have revealed new kinetic mechanisms that were not obvious before performing the simulations. We also demonstrate, through the coupling with higher level models, how those mechanisms impact experimental observables in irradiated materials. Lastly, we discuss the importance of these types of simulations in the context of predicting material behavior.
36 MATERIALS SCIENCE↗
Speculation and replication in temperature accelerated dynamics
Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time scale simulation of atomistic systems that are characterized by rare-event transitions. Temperature-Accelerated Dynamics (TAD), a traditional AMD approach, hastens state-to-state transitions by performing MD at an elevated temperature. Recently, Speculatively-Parallel TAD (SpecTAD) was introduced, allowing the TAD procedure to exploit parallel computing systems by concurrently executing in a dynamically generated list of speculative future states. Although speculation can be very powerful, it is not always the most efficient use of parallel resources. In this paper, we compare the performance of speculative parallelism with a replica-based technique, similar to the Parallel Replica Dynamics method. A hybrid SpecTAD approach is also presented, in which each speculation process is further accelerated by a local set of replicas. Finally and overall, this work motivates the use of hybrid parallelism whenever possible, as some combination of speculation and replication is typically most efficient.
36 MATERIALS SCIENCE↗
Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing
Molecular dynamics (MD) is one of the most widely used techniques in computational materials science. By providing fully resolved trajectories, it allows for a natural description of static, thermodynamic, and kinetic properties. A major hurdle that has hampered the use of MD is the fact that the timescales that can be directly simulated are very limited, even when using massively parallel computers. We compare two time-parallelization approaches, parallel replica dynamics (ParRep) and parallel trajectory splicing (ParSplice), that were specifically designed to address this issue for rare event systems by leveraging parallel computing resources. Using simulations of the relaxation of small disordered platinum nanoparticles, a comparative performance analysis of the two methods is presented. Finally, the results show that ParSplice can significantly outperform ParRep in the common case where the trajectory remains trapped for a long time within a region of configuration space but makes rapid structural transitions within this region.
36 MATERIALS SCIENCE↗
Parallel Temperature Accelerated Dynamics: Speculation, Replication and Splicing
Explore the source record for details and available documents.
Material Science↗
Evidence for percolation diffusion of cations and reordering in disordered pyrochlore from accelerated molecular dynamics
Diffusion in complex oxides is critical to ionic transport, radiation damage evolution, sintering, and aging. In complex oxides such as pyrochlores, anionic diffusion is dramatically affected by cation disorder. However, little is known about how disorder influences cation transport. Here, we report results from classical and accelerated molecular dynamics simulations of vacancy-mediated cation diffusion in Gd 2 Ti 2 O 7 pyrochlore, on the microsecond timescale. We find that diffusion is slow at low levels of disorder, while higher disorder allows for fast diffusion, which is then accompanied by antisite annihilation and reordering, and thus a slowing of cation transport. Cation diffusivity is therefore not constant, but decreases as the material reorders. We also show that fast cation diffusion is triggered by the formation of a percolation network of antisites. This is in contrast with observations from other complex oxides and disordered media models, suggesting a fundamentally different relation between disorder and mass transport.
74 ATOMIC AND MOLECULAR PHYSICS↗
Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles
Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which has to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex Accelerated Molecular Dynamics trajectories exhibiting shape uctuations in Pt nanoclusters. This analysis provides an easily-interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.
74 ATOMIC AND MOLECULAR PHYSICS↗
Performing density-functional tight-binding calculations with LAMMPS and the LATTE library
Explore the source record for details and available documents.
Computer Science↗
The mobility of small vacancy/helium complexes in tungsten and its impact on retention in fusion-relevant conditions
Tungsten is a promising plasma facing material for fusion reactors. Despite many favorable properties, helium ions incoming from the plasma are known to dramatically affect the microstructure of tungsten, leading to bubble growth, blistering, and/or to the formation of fuzz. In order to develop mitigation strategies, it is essential to understand the atomistic processes that lead to bubble formation and subsequent microstructural changes. In this work, we use large-scale Accelerated Molecular Dynamics simulations to investigate small (N=1,2) V N He M vacancy/helium complexes, which serve as the nuclei for larger helium bubble growth, over timescales reaching into the milliseconds under conditions typical of the operation of fusion reactors. These complexes can interconvert between different I L V N+L He M variants via Frenkel pair nucleation (leading to the creation of a additional vacancy/interstitial pair) and annihilation events; sequences of these events can lead to net migration of these embryonic bubbles. The competition between nucleation and annihilation produces a very complex dependence of the diffusivity on the number of heliums. Finally, through cluster dynamics simulations, we show that diffusion of these complexes provides an efficient pathway for helium release at fluxes expected in fusion reactors, and hence that accounting for the mobility of these complexes is crucial.
36 MATERIALS SCIENCE↗
Fusion Energy Sciences Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and Fusion Energy Sciences, January 27-29, 2016, Gaithersburg, Maryland
The additional computing power offered by the planned exascale facilities could be transformational across the spectrum of plasma and fusion research — provided that the new architectures can be efficiently applied to our problem space. The collaboration that will be required to succeed should be viewed as an opportunity to identify and exploit cross-disciplinary synergies. To assess the opportunities and requirements as part of the development of an overall strategy for computing in the exascale era, the Exascale Requirements Review meeting of the Fusion Energy Sciences (FES) community was convened January 27–29, 2016, with participation from a broad range of fusion and plasma scientists, specialists in applied mathematics and computer science, and representatives from the U.S. Department of Energy (DOE) and its major computing facilities. This report is a summary of that meeting and the preparatory activities for it and includes a wealth of detail to support the findings. Technical opportunities, requirements, and challenges are detailed in this report (and in the recent report on the Workshop on Integrated Simulation). Science applications are described, along with mathematical and computational enabling technologies. Also see http://exascaleage.org/fes/ for more information.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗