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Danny Perez

Publications and source records attributed to Danny Perez.

At least 37 records · Page 2Linked to original sources

Best of Both Worlds: Enforcing Detailed Balance in Machine Learning Models of Transition Rates

The slow microstructural evolution of materials often plays a key role in determining material properties. When the unit steps of the evolution process are slow, direct simulation approaches such as molecular dynamics become prohibitive and Kinetic Monte-Carlo (kMC) algorithms, where the state-to-state evolution of the system is represented in terms of a continuous-time Markov chain, are instead frequently relied upon to efficiently predict long-time evolution. The accuracy of kMC simulations however relies on the complete and accurate knowledge of reaction pathways and corresponding kinetics. This requirement becomes extremely stringent in complex systems such as concentrated alloys where the astronomical number of local atomic configurations makes the a priori tabulation of all possible transitions impractical. Machine learning models of transition kinetics have been used to mitigate this problem by enabling the efficient on-the-fly prediction of kinetic parameters. In this study, we show how physics-informed ML architectures can exactly enforce the detailed balance condition, by construction. Using the diffusion of a vacancy in a concentrated alloy as an example, we show that such ML architectures also exhibit superior performance in terms of prediction accuracy, demonstrating that the imposition of physical constraints can facilitate the accurate learning of barriers at no increase in computational cost.

cond-mat.mtrl-sci↗

Changes in Dislocation Punching Behavior Due to Hydrogen-Seeded Helium Bubble Growth in Tungsten

The accumulation of gas atoms in tungsten is a topic of long-standing interest to the plasma-facing materials community due the metal's use as a divertor material in some tokamak fusion reactors. The nucleation and growth of He/H gas bubbles (along with their isotopes) can result from impinging fluxes of these gases which give rise to damage at the W divertor surface. The inclusion of He or H in W has been studied extensively by the community, finding that He bubbles modify the surface through periodic dislocation punching and bursting mechanisms while H bubbles impact the metal through plastic-strain induced material failure. However, the mechanisms which are present during the combined flux of both He and H is not well-studied atomistically. Motivated by this, an atomistic modeling study is conducted using molecular dynamics to assess the behavior of mixed concentration He:H bubbles in W. We find that the introduction of H into a growing He bubble results in a dramatic change in the nature and presence of dislocation loops which are typically generated via dislocation punching in over-pressurized He bubbles. Most notably, at high H concentrations, there is a switchover in energetic favorability from glissile 1/2$<$111$>$ dislocations to sessile $<$100$>$ dislocations. This thermodynamic crossover could imply a significant reduction in W surface morphology changes than with pure He bubbles and, additionally, we show this to have implications on the trapping of H in the bubbles and their associated dislocations.

cond-mat.mtrl-sci↗

Breaking the Molecular Dynamics Timescale Barrier Using a Wafer-Scale System

Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale supercomputers, however, runtimes are excessive for systems and timescales of scientific interest. Here, we demonstrate strong scaling of MD simulations on the Cerebras Wafer-Scale Engine. By dedicating a processor core for each simulated atom, we demonstrate a 179-fold improvement in timesteps per second versus the Frontier GPU-based Exascale platform, along with a large improvement in timesteps per unit energy. Reducing every year of runtime to two days unlocks currently inaccessible timescales of slow microstructure transformation processes that are critical for understanding material behavior and function. Our dataflow algorithm runs Embedded Atom Method (EAM) simulations at rates over 270,000 timesteps per second for problems with up to 800k atoms. This demonstrated performance is unprecedented for general-purpose processing cores.

physics.comp-ph↗

Data-Driven Modeling of Dislocation Mobility from Atomistics using Physics-Informed Machine Learning

Dislocation mobility, which dictates the response of dislocations to an applied stress, is a fundamental property of crystalline materials that governs the evolution of plastic deformation. Traditional approaches for deriving mobility laws rely on phenomenological models of the underlying physics, whose free parameters are in turn fitted to a small number of intuition-driven atomic scale simulations under varying conditions of temperature and stress. This tedious and time-consuming approach becomes particularly cumbersome for materials with complex dependencies on stress, temperature, and local environment, such as body-centered cubic crystals (BCC) metals and alloys. In this paper, we present a novel, uncertainty quantification-driven active learning paradigm for learning dislocation mobility laws from automated high-throughput large-scale molecular dynamics simulations, using Graph Neural Networks (GNN) with a physics-informed architecture. We demonstrate that this Physics-informed Graph Neural Network (PI-GNN) framework captures the underlying physics more accurately compared to existing phenomenological mobility laws in BCC metals.

cond-mat.mtrl-sci↗

From anti-Arrhenius to Arrhenius behavior in a dislocation-obstacle bypass: Atomistic Simulations and Theoretical Investigation

Dislocations are the primary carriers of plasticity in metallic material. Understanding the basic mechanisms for dislocation movement is paramount to predicting the material mechanical response. Relying on atomistic simulations, we observe a transition from non-Arrhenius to Arrhenius behavior in the rate for an edge dislocation to overcome the elastic interaction with a prismatic loop in tungsten. Beyond the critical resolved shear stress, the process shows a non-Arrhenius behavior at low temperatures. However, as the temperature increases, the activation entropy starts to dominate, leading to a traditional Arrhenius behavior. We have computed the activation entropy analytically along the minimum energy path following Schoeck's methods [1], which capture the cross-over between anti-Arrhenius and Arrhenius domains. Also, the Projected Average Force Integrator (PAFI) [2], another simulation method to compute free energies along an initial transition path, exhibits considerable concurrence with Schoeck's formalism. We conclude that entropic effects need to be considered to understand processes involving dislocations bypassing elastic barriers close to the critical resolved shear stress. More work needs to be performed to fully understand the discrepancies between Schoeck's and PAFI results compared to molecular dynamics.

cond-mat.mtrl-sci↗

Acceleration of Solvation Free Energy Calculation via Thermodynamic Integration Coupled with Gaussian Process Regression and Improved Gelman-Rubin Convergence Diagnostics

The determination of the solvation free energy of ions and molecules holds profound importance across a spectrum of applications spanning chemistry, biology, energy storage, and the environment. Molecular dynamics simulations are a powerful tool for computing this critical parameter. Nevertheless, the accurate and efficient calculation of solvation free energy becomes a formidable endeavor when dealing with complex systems characterized by potent Coulombic interactions and sluggish ion dynamics and, consequently, slow transition across various metastable states. In the present study, we expose limitations stemming from the conventional calculation of the statistical inefficiency g in the thermodynamic integration method, a factor that can hinder the determination of convergence of the solvation free energy and its associated uncertainty. Instead, we propose a robust scheme based on Gelman-Rubin convergence diagnostics. We leverage this improved estimation of uncertainties to introduce an innovative accelerated thermodynamic integration method based on Gaussian Process regression. This methodology is applied to the calculation of the solvation free energy of trivalent rare earth elements immersed in ionic liquids, a scenario where the aforementioned challenges render standard approaches ineffective. The proposed method proves effective in computing solvation free energy in situations where traditional thermodynamic integration methods fall short.

cond-mat.mes-hall↗

Formation of field-induced breakdown precursors on metallic electrode surfaces

Understanding the underlying factors responsible for higher-than-anticipated local field enhancements that trigger vacuum breakdown on pristine metal surfaces is crucial for the development of devices capable of withstanding intense operational fields. In this study, we investigate the behavior of nominally flat copper electrode surfaces exposed to electric fields of hundreds of MV/m. Our novel approach considers curvature-driven diffusion processes to elucidate the formation of sharp breakdown precursors. To do so, we develop a mesoscale finite element model that accounts for driving forces arising from both electrostatic and surface-tension-induced contributions to the free energy. Our findings reveal a dual influence: surface tension tends to mitigate local curvature, while the electric field drives mass transport toward regions of high local field density. This phenomenon triggers the growth of sharper protrusions, ultimately leading to a rapid enhancement of local fields and, consequently, system instability. Furthermore, we delineate supercritical and subcritical regimes across a range of initial surface roughness. Our numerical results align closely with experimentally reported data, predicting critical precursor formation fields in the range of 200 MV/m to 500 MV/m.

cond-mat.mes-hall↗

Thermal and electric field driven breakdown precursor formation on metal surfaces

The phenomenon of electric breakdown poses serious challenge to the design of devices that operate under high gradient environments. Experimental evidence often points towards breakdown events that are accompanied by elevated temperatures and dark current spikes, presumably due to high-asperity nano-structure formation that enhances the local electric field and triggers a runaway process. However, the exact mechanistic origin of such nano-structures under typical macroscopic operational conditions of electric gradient and magnetic-field-mediated heating remains poorly understood. In this work, a model is presented that describes the evolution of a typical copper surface under the combined action of the electric fields and elevated temperatures. Using a mesoscale curvature-driven growth model, we show how the copper surface can undergo a type of dynamical instability that naturally leads to the formation of sharp asperities in realistic experimental conditions. Exploring the combined effect of fields and temperature rise, we identify critical regimes that allow for the formation of breakdown precursors. These regimes strongly resonate with previous experimental findings on breakdown of copper electrodes, hence suggesting surface diffusion to be a crucial breakdown precursor mechanism.

physics.app-ph↗

Stand-off runaway electron beam termination by tungsten particulates for tokamak disruption mitigation

Stand-off runaway electron termination by injected tungsten particulates offers a plausible option in the toolbox of disruption mitigation. Tungsten is an attractive material choice for this application due to large electron stopping power and high melting point. To assess the feasibility of this scheme, we simulate runaway collisions with tungsten particulates using the MCNP program for incident runaway energies ranging from 1 to 10 MeV. We assess runaway termination from energetics and collisional kinematics perspectives. Energetically, the simulations show that 99% of runaway beam energy is removed by tungsten particulates on a timescale of 4-9 $μ$s. Kinematically, the simulations show that 99% of runaways are terminated by absorption or backscattering on a timescale of 3-4 $μ$s. By either metric, the runaway beam is effectively terminated before the onset of particulate melting. Furthermore, the simulations show that secondary radiation emission by tungsten particulates does not significantly impact the runaway termination efficacy of this scheme. Secondary radiation is emitted at lower particle energies than the incident runaways and with a broad angular distribution such that the majority of secondary electrons emitted will not experience efficient runaway re-acceleration. Overall, the stand-off runaway termination scheme is a promising concept for last-ditch runaway mitigation in ITER, SPARC, and other future burning-plasma tokamaks.

physics.plasm-ph↗

Arbitrarily accurate, nonparametric coarse graining with Markov renewal processes and the Mori-Zwanzig formulation

Stochastic dynamics, such as molecular dynamics, are important in many scientific applications. However, summarizing and analyzing the results of such simulations is often challenging, due to the high dimension in which simulations are carried out, and consequently to the very large amount of data that is typically generated. Coarse graining is a popular technique for addressing this problem by providing compact and expressive representations. Coarse graining, however, potentially comes at the cost of accuracy, as dynamical information is in general lost when projecting the problem in a lower dimensional space. This article shows how to eliminate coarse-graining error using two key ideas. First, we represent coarse-grained dynamics as a Markov renewal process. Second, we outline a data-driven, non-parametric Mori-Zwanzig approach for computing jump times of the renewal process. Numerical tests on a small protein illustrate the method.

math.DS↗

MolSieve: A Progressive Visual Analytics System for Molecular Dynamics Simulations

Molecular Dynamics (MD) simulations are ubiquitous in cutting-edge physio-chemical research. They provide critical insights into how a physical system evolves over time given a model of interatomic interactions. Understanding a system's evolution is key to selecting the best candidates for new drugs, materials for manufacturing, and countless other practical applications. With today's technology, these simulations can encompass millions of unit transitions between discrete molecular structures, spanning up to several milliseconds of real time. Attempting to perform a brute-force analysis with data-sets of this size is not only computationally impractical, but would not shed light on the physically-relevant features of the data. Moreover, there is a need to analyze simulation ensembles in order to compare similar processes in differing environments. These problems call for an approach that is analytically transparent, computationally efficient, and flexible enough to handle the variety found in materials based research. In order to address these problems, we introduce MolSieve, a progressive visual analytics system that enables the comparison of multiple long-duration simulations. Using MolSieve, analysts are able to quickly identify and compare regions of interest within immense simulations through its combination of control charts, data-reduction techniques, and highly informative visual components. A simple programming interface is provided which allows experts to fit MolSieve to their needs. To demonstrate the efficacy of our approach, we present two case studies of MolSieve and report on findings from domain collaborators.

physics.comp-ph↗

Improving Estimation of the Koopman Operator with Kolmogorov-Smirnov Indicator Functions

It has become common to perform kinetic analysis using approximate Koopman operators that transforms high-dimensional time series of observables into ranked dynamical modes. Key to a practical success of the approach is the identification of a set of observables which form a good basis in which to expand the slow relaxation modes. Good observables are, however, difficult to identify {\em a priori} and sub-optimal choices can lead to significant underestimations of characteristic timescales. Leveraging the representation of slow dynamics in terms of Hidden Markov Model (HMM), we propose a simple and computationally efficient clustering procedure to infer surrogate observables that form a good basis for slow modes. We apply the approach to an analytically solvable model system, as well as on three protein systems of different complexities. We consistently demonstrate that the inferred indicator functions can significantly improve the estimation of the leading eigenvalues of the Koopman operators and correctly identify key states and transition timescales of stochastic systems, even when good observables are not known {\em a priori}.

physics.data-an↗

Regression-based projection for learning Mori-Zwanzig operators

We propose to adopt statistical regression as the projection operator to enable data-driven learning of the operators in the Mori--Zwanzig formalism. We present a principled method to extract the Markov and memory operators for any regression models. We show that the choice of linear regression results in a recently proposed data-driven learning algorithm based on Mori's projection operator, which is a higher-order approximate Koopman learning method. We show that more expressive nonlinear regression models naturally fill in the gap between the highly idealized and computationally efficient Mori's projection operator and the most optimal yet computationally infeasible Zwanzig's projection operator. We performed numerical experiments and extracted the operators for an array of regression-based projections, including linear, polynomial, spline, and neural-network-based regressions, showing a progressive improvement as the complexity of the regression model increased. Our proposition provides a general framework to extract memory-dependent corrections and can be readily applied to an array of data-driven learning methods for stationary dynamical systems in the literature.

math.DS↗

Combining machine-learned and empirical force fields with the parareal algorithm: application to the diffusion of atomistic defects

We numerically investigate an adaptive version of the parareal algorithm in the context of molecular dynamics. This adaptive variant has been originally introduced in [F. Legoll, T. Lelievre and U. Sharma, SISC 2022]. We focus here on test cases of physical interest where the dynamics of the system is modelled by the Langevin equation and is simulated using the molecular dynamics software LAMMPS. In this work, the parareal algorithm uses a family of machine-learning spectral neighbor analysis potentials (SNAP) as fine, reference, potentials and embedded-atom method potentials (EAM) as coarse potentials. We consider a self-interstitial atom in a tungsten lattice and compute the average residence time of the system in metastable states. Our numerical results demonstrate significant computational gains using the adaptive parareal algorithm in comparison to a sequential integration of the Langevin dynamics. We also identify a large regime of numerical parameters for which statistical accuracy is reached without being a consequence of trajectorial accuracy.

math.NA↗

Roadmap on Electronic Structure Codes in the Exascale Era

Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing.

cond-mat.mtrl-sci↗

Training Data Selection for Accuracy and Transferability of Interatomic Potentials

Advances in machine learning (ML) techniques have enabled the development of interatomic potentials that promise both the accuracy of first principles methods and the low-cost, linear scaling, and parallel efficiency of empirical potentials. Despite rapid progress in the last few years, ML-based potentials often struggle to achieve transferability, that is, to provide consistent accuracy across configurations that significantly differ from those used to train the model. In order to truly realize the promise of ML-based interatomic potentials, it is therefore imperative to develop systematic and scalable approaches for the generation of diverse training sets that ensure broad coverage of the space of atomic environments. This work explores a diverse-by-construction approach that leverages the optimization of the entropy of atomic descriptors to create a very large ($>2\cdot10^{5}$ configurations, $>7\cdot10^{6}$ atomic environments) training set for tungsten in an automated manner, i.e., without any human intervention. This dataset is used to train polynomial as well as multiple neural network potentials with different architectures. For comparison, a corresponding family of potentials were also trained on an expert-curated dataset for tungsten. The models trained to entropy-optimized data exhibited vastly superior transferability compared to the expert-curated models. Furthermore, while the models trained with heavy user input (i.e., domain expertise) yield the lowest errors when tested on similar configurations, out-sample predictions are dramatically more robust when the models are trained on a deliberately diverse set of training data. Herein we demonstrate the development of both accurate and transferable ML potentials using automated and data-driven approaches for generating large and diverse training sets.

physics.comp-ph↗

Reaction-drift-diffusion models from master equations: application to material defects

We present a general method to produce well-conditioned continuum reaction-drift-diffusion equations directly from master equations on a discrete, periodic state space. We assume the underlying data to be kinetic Monte Carlo models (i.e., continuous-time Markov chains) produced from atomic sampling of point defects in locally periodic environments, such as perfect lattices, ordered surface structures or dislocation cores, possibly under the influence of a slowly varying external field. Our approach also applies to any discrete, periodic Markov chain. The analysis identifies a previously omitted non-equilibrium drift term, present even in the absence of external forces, which can compete in magnitude with the reaction rates, thus being essential to correctly capture the kinetics. To remove fast modes which hinder time integration, we use a generalized Bloch relation to efficiently calculate the eigenspectrum of the master equation. A well conditioned continuum equation then emerges by searching for spectral gaps in the long wavelength limit, using an established kinetic clustering algorithm (e.g., PCCA+) to define a proper reduced state space.

cond-mat.stat-mech↗

Atomistic mechanisms of binary alloy surface segregation from nanoseconds to seconds using accelerated dynamics

Although the equilibrium composition of many alloy surfaces is well understood, the rate of transient surface segregation during annealing is not known, despite its crucial effect on alloy corrosion and catalytic reactions occurring on overlapping timescales. In this work, CuNi bimetallic alloys representing (100) surface facets are annealed in vacuum using atomistic simulations to observe the effect of vacancy diffusion on surface separation. We employ multi-timescale methods to sample the early transient, intermediate, and equilibrium states of slab surfaces during the separation process, including standard MD as well as three methods to perform atomistic, long-time dynamics: parallel trajectory splicing (ParSplice), adaptive kinetic Monte Carlo (AKMC), and kinetic Monte Carlo (KMC). From nanosecond (ns) to second timescales, our multiscale computational methodology can observe rare stochastic events not typically seen with standard MD, closing the gap between computational and experimental timescales for surface segregation. Rapid diffusion of a vacancy to the slab is resolved by all four methods in tens of ns. Stochastic re-entry of vacancies into the subsurface, however, is only seen on the microsecond timescale in the two KMC methods. Kinetic vacancy trapping on the surface and its effect on the segregation rate are discussed. The equilibrium composition profile of CuNi after segregation during annealing is estimated to occur on a timescale of seconds as determined by KMC, a result directly comparable to nanoscale experiments.

cond-mat.mtrl-sci↗