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DOE OSTI2020

Parallel algorithms for hyperdynamics and local hyperdynamics

Hyperdynamics (HD) is a method for accelerating the timescale of standard molecular dynamics (MD). It can be used for simulations of systems with an energy potential landscape that is a collection of basins, separated by barriers, where transitions between basins are infrequent. HD enables the system to escape from a basin more quickly while enabling a statistically accurate renormalization of the simulation time, thus effectively boosting the timescale of the simulation. In [Kim, Perez, Voter, J Chem Phys, 139:144110, 2013)1, a local version of HD was formulated, which exploits the intrinsic locality characteristic typical of most systems to mitigate the poor scaling properties of standard HD as the system size is increased. In this paper, we discuss how both HD and local HD can be formulated to run efficiently in parallel. We have implemented these ideas in the LAMMPS MD code, which means HD can be used with any interatomic potential LAMMPS supports. Together, these parallel methods allow simulations of any size to achieve the time acceleration offered by HD (which can be orders of magnitude), at a cost 3-5x that of standard MD. As examples, we performed two simulations of a million-atom system to model the diffusion and clustering of Pt adatoms on a large patch of Pt(100) surface for 80 and 160 μs.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Evolution of dislocation loops in irradiated α-Uranium: An atomistically-informed cluster dynamics investigation

An atomistically-informed mean field cluster dynamics model has been developed to investigate the nucleation and growth of prismatic loops in irradiated a-Uranium. TEM analysis of neutron irradiated a-Uranium shows the evolution of self-interstitial atom and vacancy loops on (010) and (100) crystallographic planes, respectively, resulting in an anisotropic lattice swelling of its face-centered orthorhombic crystal. To provide model parameters, the crystallography of loops and the binding energy of point defects to these loops were studied using an angular dependent EAM potential and classical molecular dynamics (MD) simulations. Furthermore, using the bond-boost hyperdynamics method, the anisotropic diffusion of interstitials and vacancies in a-Uranium was investigated. Here, the mechanisms of point defect diffusion and the associated migration energies were reported and compared with previous DFT studies. The energetics and kinetic quantities mentioned above were used in the cluster dynamics model to predict the cluster density as a function of dose rate, dose and temperature and the results were compared to the reported neutron irradiation experiments. The model predictions reveal an accumulation of small sized vacancy loops along with a population of large and growing self-interstitial loops, which closely corresponds to the TEM observations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

A Joint Modeling/Experimental Approach to Characterize Ionization and Fragmentation of SOA Molecules with CIMS

The Molecular Dynamics technique Collective variable hyperdynamics (CVHD) interfaced with density functional tight-binding at the GFN1-xTB and GFN2-xTB levels of electronic structure theory has been applied to the H + GAG positively charged peptide system to explore the fragmentation of this simple tripeptide under relatively low temperature/energy conditions. Unlike conventional chemical dynamics simulations which can only be performed up to hundreds of picoseconds when coupled with semi-empirical Hamiltonians, CVHD is able to capture the long-time dynamics of multiple proton hopping, the formation of reversible ring structures, and ester rearrangement of the H + GAG system prior to fragmentation. The CVHD method applied to H + GAG is also able to uncover alternative fragmentation pathways not considered previously such as glycine fragmentation on the N-terminal side of the charged peptide and new cyclic cationic species. These findings in the H + GAG case have implications for other peptide systems.

74 ATOMIC AND MOLECULAR PHYSICS↗