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Register a new userAccelerated Molecular Dynamics through stochastic iterations to strengthen yield of path hopping over upper states (SISYPHUS)
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We present a new method, called SISYPHUS (Stochastic Iterations to Strengthen Yield of Path Hopping over Upper States), for extending accessible time-scales in atomistic simulations. The method proceeds by separating phase space into basins, and transition regions between the basins based on a general collective variable (CV) criterion. The transition regions are treated via traditional molecular dynamics (MD) while Monte Carlo (MC) methods are used to (i) estimate the expected time spent in each basin and (ii) thermalize the system between two MD episodes. In particular, an efficient adiabatic switching based scheme is used to estimate the time spent inside the basins. The method offers various advantages over existing approaches in terms of (i) providing an accurate real time scale, (ii) avoiding reliance on harmonic transition state theory and (iii) avoiding the need to enumerate all possible transition events. Applications of SISYPHUS to low temperature vacancy diffusion in BCC Ta and adatom island ripening in FCC Al are presented. A new CV appropriate for such condensed phases, especially for transitions involving collective motions of several atoms, is also introduced.
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In the previous paper of this series [JCTC 2020, 16, 3757], we presented a theoretical and algorithmic framework based on a localized representation of the occupied space that exploits the inherent sparsity in the real-space evaluation of the EXX interaction in finite-gap systems. This was accompanied by a detailed description of exx, a massively parallel hybrid MPI/OpenMP implementation of this approach in Quantum ESPRESSO that enables linear-scaling hybrid DFT based AIMD in the NVE/NVT ensembles of condensed-phase systems containing 500--1000 atoms (in fixed orthorhombic cells) with a wall time cost comparable to semi-local DFT. In this work, we extend exx to enable hybrid DFT based AIMD of large-scale condensed-phase systems with general and fluctuating cells in the NpH/NpT ensembles. Our theoretical extension includes an analytical derivation of the EXX contribution to the stress tensor for systems in general cells with a computational complexity that scales linearly with system size. The corresponding algorithmic extensions to exx include optimized routines that: (i) handle static/fluctuating cells with non-orthogonal lattice symmetries, (ii) solve Poissons equation in general cells via an automated selection of the auxiliary grid directions in the Natan-Kronik representation of the discrete Laplacian operator, and (iii) evaluate the EXX contribution to the stress tensor. We also critically assess the computational performance of the extended exx module across several different HPC architectures via case studies on ice Ih, II, and III as well as ambient liquid water. We find that the extended exx can evaluate the EXX contribution to the stress tensor with negligible cost (< 1%) and remains highly scalable, thereby bringing us another step closer to routinely performing hybrid DFT based AIMD for large-scale condensed-phase systems across a wide range of thermodynamic conditions.
We perform nonadiabatic simulations of warm dense aluminum based on the electron-force field (EFF) variant of wave-packet molecular dynamics. Comparison of the static ion-ion structure factor with density functional theory (DFT) is used to validate the technique across a range of temperatures and densities spanning the warm dense matter regime. Focusing on a specific temperature and density (3.5 eV, 5.2 g/cm3), we report on differences in the dynamic structure factor and dispersion relation across a variety of adiabatic and nonadiabatic techniques. We find the dispersion relation produced with EFF is in close agreement with the more robust and adiabatic Kohn-Sham DFT.
We propose a rigorous construction of a 1D path collective variable to sample structural phase transformations in condensed matter. The path collective variable is defined in a space spanned by global collective variables that serve as classifiers derived from local structural units. A reliable identification of local structural environments is achieved by employing a neural network based classification. The 1D path collective variable is subsequently used together with enhanced sampling techniques to explore the complex migration of a phase boundary during a solid-solid phase transformation in molybdenum.
The equations of the temperature-accelerated molecular dynamics (TAMD) method for the calculations of free energies and partition functions are analyzed. Specifically, the exponential convergence of the law of these stochastic processes is established, with a convergence rate close to the one of the limiting, effective dynamics at higher temperature obtained with infinite acceleration. It is also shown that the invariant measures of TAMD are close to a known reference measure, with an error that can be quantified precisely. Finally, a Central Limit Theorem is proven, which allows the estimation of errors on properties calculated by ergodic time averages. These results not only demonstrate the usefulness and validity range of the TAMD equations, but they also permit in principle to adjust the parameter in these equations to optimize their efficiency.
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
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