Development of a machine learning interatomic potential for exploring pressure-dependent kinetics of phase transitions in germanium.

We introduce a data-driven potential aimed at the investigation of pressure-dependent phase transitions in bulk germanium, including the estimate of kinetic barriers. This is achieved by suitably building a database including several configurations along minimum energy paths, as computed using the solid-state nudged elastic band method. After training the model based on density functional theory (DFT)-computed energies, forces, and stresses, we provide validation and rigorously test the potential on unexplored paths. The resulting agreement with the DFT calculations is remarkable in a wide range of pressures. The potential is exploited in large-scale isothermal-isobaric simulations, displaying local nucleation in the R8 to ß-Sn pressure-induced phase transformation, taken here as an illustrative example.

Solving the Structure and Dynamics of Metal Nanoparticles by Combining X-Ray Absorption Fine Structure Spectroscopy and Atomistic Structure Simulations.

Extended X-ray absorption fine structure (EXAFS) spectroscopy is a premiere method for analysis of the structure and structural transformation of nanoparticles. Extraction of analytical information about the three-dimensional structure and dynamics of metal-metal bonds from EXAFS spectra requires special care due to their markedly non-bulk-like character. In recent decades, significant progress has been made in the first-principles modeling of structure and properties of nanoparticles. In this review, we summarize new approaches for EXAFS data analysis that incorporate particle structure modeling into the process of structural refinement.

Mechanistic insights on ethanol dehydrogenation on Pd-Au model catalysts: a combined experimental and DFT study.

In this study, we have combined ultra-high vacuum (UHV) experiments and density functional theory (DFT) calculations to investigate ethanol (EtOH) dehydrogenation on Pd-Au model catalysts. Using EtOH reactive molecular beam scattering (RMBS), EtOH temperature-programmed desorption (TPD), and DFT calculations, we show how different Pd ensemble sizes on Au(111) can affect the mechanism for EtOH dehydrogenation and H2 production. The Au(111) surface with an initial coverage of 2 monolayers of Pd (2 ML Pd-Au) had the highest H2 yield. However, the 1 ML Pd-Au catalyst showed the highest selectivity and stability, yielding appreciable amounts of only H2 and acetaldehyde. Arrhenius plots of H2 production confirm that the mechanisms for EtOH dehydrogenation differed between 1 and 2 ML Pd-Au, supporting the perceived difference in selectivity between the two surfaces. DFT calculations support this difference in mechanism, showing a dependence of the initial dehydrogenation selectivity of EtOH on the size of Pd ensemble. DFT binding energies and EtOH TPD confirm that EtOH has increasing surface affinity with increasing Pd ensemble size and Pd coverage, indicating that surfaces with more Pd are more likely to induce an EtOH reaction instead of desorb. Our theoretical results show that the synergistic influence of atomic ensemble and electronic effects on Pd/Au(111) can lead to different H2 association energies and EtOH dehydrogenation capacities at different Pd ensembles. These results provide mechanistic insights into ethanol's dehydrogenation interactions with different sites on the Pd-Au surface and can potentially aid in bimetallic catalyst design for applications such as fuel cells.

A grid-based Bader analysis algorithm without lattice bias.

A computational method for partitioning a charge density grid into Bader volumes is presented which is efficient, robust, and scales linearly with the number of grid points. The partitioning algorithm follows the steepest ascent paths along the charge density gradient from grid point to grid point until a charge density maximum is reached. In this paper, we describe how accurate off-lattice ascent paths can be represented with respect to the grid points. This improvement maintains the efficient linear scaling of an earlier version of the algorithm, and eliminates a tendency for the Bader surfaces to be aligned along the grid directions. As the algorithm assigns grid points to charge density maxima, subsequent paths are terminated when they reach previously assigned grid points. It is this grid-based approach which gives the algorithm its efficiency, and allows for the analysis of the large grids generated from plane-wave-based density functional theory calculations.

Comparison of methods for finding saddle points without knowledge of the final states.

Within the harmonic approximation to transition state theory, the biggest challenge involved in finding the mechanism or rate of transitions is the location of the relevant saddle points on the multidimensional potential energy surface. The saddle point search is particularly challenging when the final state of the transition is not specified. In this article we report on a comparison of several methods for locating saddle points under these conditions and compare, in particular, the well-established rational function optimization (RFO) methods using either exact or approximate Hessians with the more recently proposed minimum mode following methods where only the minimum eigenvalue mode is found, either by the dimer or the Lanczos method. A test problem involving transitions in a seven-atom Pt island on a Pt(111) surface using a simple Morse pairwise potential function is used and the number of degrees of freedom varied by varying the number of movable atoms. In the full system, 175 atoms can move so 525 degrees of freedom need to be optimized to find the saddle points. For testing purposes, we have also restricted the number of movable atoms to 7 and 1. Our results indicate that if attempting to make a map of all relevant saddle points for a large system (as would be necessary when simulating the long time scale evolution of a thermal system) the minimum mode following methods are preferred. The minimum mode following methods are also more efficient when searching for the lowest saddle points in a large system, and if the force can be obtained cheaply. However, if only the lowest saddle points are sought and the calculation of the force is expensive but a good approximation for the Hessian at the starting position of the search can be obtained at low cost, then the RFO approaches employing an approximate Hessian represent the preferred choice. For small and medium sized systems where the force is expensive to calculate, the RFO approaches employing an approximate Hessian is also the more efficient, but when the force and Hessian can be obtained cheaply and only the lowest saddle points are sought the RFO approach using an exact Hessian is the better choice. These conclusions have been reached based on a comparison of the total computational effort needed to find the saddle points and the number of saddle points found for each of the methods. The RFO methods do not perform very well with respect to the latter aspect, but starting the searches further away from the initial minimum or using the hybrid RFO version presented here improves this behavior considerably in most cases.

Structure and mobility of defects formed from collision cascades in MgO.

We study radiation-damage events in MgO on experimental time scales by augmenting molecular dynamics cascade simulations with temperature accelerated dynamics, molecular statics, and density functional theory. At 400 eV, vacancies and mono- and di-interstitials form, but often annihilate within milliseconds. At 2 and 5 keV, larger clusters can form and persist. While vacancies are immobile, interstitials aggregate into clusters (In) with surprising properties; e.g., an I4 is immobile, but an impinging I2 can create a metastable I6 that diffuses on the nanosecond time scale but is stable for years.

Theoretical calculations of dissociative adsorption of CH4 on an Ir(111) surface.

The activation energy for chemisorption of CH(4) at an Ir(111) surface is determined using density functional theory combined with an estimate of the long range dispersion interaction. The results are found to be in good agreement with published results of bulb and beam experiments analyzed with a precursor model. A surprisingly large surface relaxation is found where an Ir surface atom is displaced outwards by as much as 0.6 A. A strongly bound molecular state at kinks and adatoms involving eta(2)-H,H bonding was also found.